metfrag_vis: metfrag-vis.py annotate

author	computational-metabolomics
date	Tue, 14 Jul 2020 07:42:34 -0400
parents
children

rev	line source
0 3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	1 #!/usr/bin/env python
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	2
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	3 # Load modules
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	4 import argparse
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	5 import base64
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	6 import csv
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	7 import os
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	8 import re
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	9 import time
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	10 import urllib.parse
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	11
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	12 import matplotlib.pyplot as plt
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	13
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	14 import pubchempy
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	15
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	16 import requests
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	17
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	18 # Parse arguments
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	19 parser = argparse.ArgumentParser(
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	20 description='Visualise MetFrag results in html.')
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	21 parser.add_argument('-v', '--version', action='version',
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	22 version='MetFrag-vis Version 0.9',
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	23 help='show version')
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	24 parser.add_argument('-i', '--input', metavar='metfrag_results.tsv',
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	25 dest="input_tsv", required=True,
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	26 help='MetFrag results as input')
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	27 parser.add_argument('-o', '--output', metavar='metfrag_results.html',
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	28 dest="output_html", required=True,
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	29 help='Write MetFrag results into this output file')
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	30 parser.add_argument('-m', '--max-candidates', metavar='10',
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	31 dest="max_candidates", default=10, type=int,
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	32 required=False,
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	33 help='Maximum number of candidates per compound [1-1000]')
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	34 parser.add_argument('-s', '--synonyms', dest='synonyms', action='store_true',
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	35 required=False,
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	36 help='Fetch synonyms from PubChem [disabled by default]')
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	37 parser.add_argument('-c', '--classyfire', dest='classyfire',
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	38 action='store_true', required=False,
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	39 help='Fetch compound classes from ClassyFire'
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	40 ' [disabled by default]')
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	41
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	42 args = parser.parse_args()
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	43
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	44 # Input CSV with MetFrag results
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	45 input_tsv = args.input_tsv
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	46
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	47 # Output html of MetFrag results
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	48 output_html = args.output_html
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	49
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	50 # Max number of candidates per compound
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	51 max_candidates = args.max_candidates
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	52
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	53 # PubChem synonyms
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	54 pubchem_synonyms_enabled = args.synonyms
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	55
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	56 # ClassyFire classes
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	57 classyfire_classes_enabled = args.classyfire
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	58
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	59
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	60 # ---------- cdk_inchi_to_svg ----------
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	61 def cdk_inchi_to_svg(inchi):
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	62 if "cdk-inchi-to-svg" in os.environ:
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	63 JAVA_CMD = 'cdk-inchi-to-svg' + ' ' + str(
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	64 '\'' + inchi + '\'') + ' ' + 'cdk-inchi-to-svg-output.svg'
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	65 else:
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	66 JAVA_BINARY = '/usr/local/bin/java'
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	67 CDK_INCHI_TO_SVG_JAR = '/usr/local/bin/' \
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	68 'cdk-inchi-to-svg-0.0.1-' \
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	69 'SNAPSHOT-jar-with-dependencies.jar'
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	70 JAVA_CMD = str(
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	71 JAVA_BINARY + ' ' + '-jar' + ' ' + CDK_INCHI_TO_SVG_JAR + ' '
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	72 + str('\'' + inchi + '\'') + ' ' + 'cdk-inchi-to-svg-output.svg')
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	73
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	74 # Exec cdk-inchi-to-svg JAVA binary
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	75 exitcode = os.system(JAVA_CMD)
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	76
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	77 # Check whether binary has successfully been run
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	78 if (exitcode == 0):
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	79 with open("cdk-inchi-to-svg-output.svg", "r") as svg_file:
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	80 svg_string = []
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	81 for line in svg_file:
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	82 if not ('<?xml' in line) and not ('<!DOCTYPE' in line):
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	83 if (' fill=\'#FFFFFF\'' in line):
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	84 line = re.sub(' fill=\'#FFFFFF\'',
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	85 ' fill=\'#FFFFFF\' fill-opacity=\'0.0\'',
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	86 line)
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	87 svg_string.append(line)
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	88 svg_file.close()
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	89 os.remove("cdk-inchi-to-svg-output.svg")
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	90 return (str(''.join(svg_string)))
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	91 else:
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	92 return (' ')
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	93
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	94
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	95 # ---------- pubchem_link ----------
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	96 def pubchem_link(compound_name):
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	97 return (str('https://pubchem.ncbi.nlm.nih.gov/#query=' + compound_name))
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	98
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	99
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	100 # ---------- kegg_link ----------
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	101 def kegg_link(compound_name):
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	102 return (str(
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	103 'https://www.genome.jp/dbget-bin/'
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	104 'www_bfind_sub?mode=bfind&max_hit=1000&dbkey=kegg&keywords=' +
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	105 compound_name))
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	106
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	107
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	108 # ---------- biocyc_link ----------
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	109 def biocyc_link(compound_name):
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	110 biocyc_url = urllib.parse.urlparse(
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	111 str(
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	112 'https://www.biocyc.org/'
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	113 'substring-search?type=NIL&object=' +
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	114 compound_name + '&quickSearch=Quick+Search'))
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	115 return (biocyc_url.geturl())
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	116
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	117
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	118 # ---------- hmdb_link ----------
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	119 def hmdb_link(compound_name):
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	120 hmdb_url = urllib.parse.urlparse(
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	121 str(
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	122 'https://hmdb.ca/unearth/q?utf8=\xe2&query=' +
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	123 compound_name + '&searcher=metabolites&button='))
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	124 return (hmdb_url.geturl())
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	125
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	126
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	127 # ---------- hmdb_link ----------
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	128 def chebi_link(inchi):
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	129 return (str(
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	130 'https://www.ebi.ac.uk/chebi/advancedSearchFT.do?searchString='
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	131 + inchi))
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	132
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	133
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	134 # ---------- PubChem Synonyms ----------
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	135 def fetch_pubchem_synonyms(inchi):
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	136 if not ('InChI=' in inchi):
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	137 return (' ')
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	138
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	139 # Fetch CID from InChI
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	140 print('Retrieving PubChem CID from InChI...')
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	141 compound = pubchempy.get_compounds(identifier=inchi, namespace='inchi')
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	142 compound_cid = re.sub(r'\).', '', re.sub(r'.\(', '', str(compound)))
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	143 if len(compound_cid) <= 1:
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	144 print(str('Warning. No match for InChI \"' + str(inchi) + '\".'))
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	145 return (' ')
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	146
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	147 # Retrieve compound
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	148 print('Retrieving PubChem compound information...')
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	149 compound = pubchempy.Compound.from_cid(compound_cid)
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	150 if ('synonyms' in dir(compound)):
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	151 return ('; '.join(compound.synonyms))
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	152 else:
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	153 print(str('Warning. No synonyms found for CID \"' + str(
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	154 compound_cid) + '\".'))
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	155 return (' ')
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	156
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	157
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	158 # ---------- ClassyFire ----------
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	159 def fetch_classyfire_classes(inchi):
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	160 if not ('InChI=' in inchi):
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	161 return (' ')
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	162
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	163 # Send POST request to ClassyFire
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	164 print('Sending request to ClassyFire...')
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	165 classyfire_url = 'http://classyfire.wishartlab.com/queries.json'
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	166 classyfire_post = str(
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	167 '{\"label\":\"metfrag\",\"query_input\":\"' + inchi +
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	168 '\",\"query_type\":\"STRUCTURE\"}')
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	169 classyfire_headers = {'Content-Type': 'application/json'}
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	170 classyfire_request = requests.post(classyfire_url, data=classyfire_post,
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	171 headers=classyfire_headers)
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	172
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	173 # Only continue when request has been successfully sent
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	174 if (classyfire_request.status_code != 201):
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	175 print('Error! Could not send request to ClassyFire. \"',
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	176 str(classyfire_request.status_code) + ': ' + str(
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	177 classyfire_request.reason), '\". Skipping entry.')
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	178 return (' ')
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	179
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	180 # Get ClassyFire Query ID
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	181 classyfire_request.json()
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	182 classyfire_query_id = classyfire_request.json()['id']
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	183
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	184 # Query ClassyFire in max. 20 attempts
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	185 classyfire_request_loop = 0
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	186 while (classyfire_request_loop < 20):
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	187 print(str(
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	188 'Sending query ' + str(classyfire_query_id) + ' to ClassyFire...'))
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	189 time.sleep(10)
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	190 classyfire_query = requests.get(
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	191 str('http://classyfire.wishartlab.com/queries/' + str(
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	192 classyfire_query_id) + '.json'))
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	193
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	194 if (classyfire_query.status_code == 200) and (
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	195 classyfire_query.json()['classification_status'] == 'Done'):
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	196 classyfire_request_loop = 999
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	197 break
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	198 else:
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	199 classyfire_request_loop += 1
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	200
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	201 if classyfire_request_loop == 999:
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	202 # Direct parent
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	203 direct_parent_name = classyfire_query.json()[
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	204 'entities'][0]['direct_parent']['name']
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	205 direct_parent_url = classyfire_query.json()[
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	206 'entities'][0]['direct_parent']['url']
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	207 direct_parent = str(
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	208 '<a target="_blank" href="' + direct_parent_url + '">' +
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	209 direct_parent_name + '</a>')
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	210
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	211 # Alternative parents
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	212 alt_parents = []
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	213 for i in range(0, len(classyfire_query.json()['entities'][0][
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	214 'alternative_parents'])):
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	215 alt_parent_name = classyfire_query.json()[
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	216 'entities'][0]['alternative_parents'][i]['name']
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	217 alt_parent_url = classyfire_query.json()[
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	218 'entities'][0]['alternative_parents'][i]['url']
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	219 alt_parent = str(
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	220 '<a target="_blank" href="' + alt_parent_url + '">' +
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	221 alt_parent_name + '</a>')
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	222 alt_parents.append(alt_parent)
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	223
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	224 # Concat classes
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	225 classes = str('<b>' + direct_parent + '</b>, <br>' + str(
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	226 ', <br>'.join(alt_parents)))
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	227 else:
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	228 print('Warning. Timout sending query to ClassyFire. Skipping entry.')
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	229 classes = ' '
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	230
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	231 return (classes)
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	232
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	233
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	234 # ---------- Plot Spectrum ----------
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	235 def plot_spectrum(spectrum, spectrum_explained, spectrum_explained_formulas):
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	236 # Plot
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	237 plt.figure(figsize=[5.5, 4.4])
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	238 plt.xlabel('m/z')
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	239 plt.ylabel('intensity')
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	240
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	241 # Plot spectrum
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	242 x = []
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	243 y = []
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	244 for i in spectrum.split(';'):
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	245 t = i.split('_')
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	246 x.append(t[0])
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	247 y.append(t[1])
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	248
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	249 for i in range(0, len(x)):
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	250 plt.plot([float(x[i]), float(x[i])], [0, float(y[i])], linewidth=1,
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	251 color='black')
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	252 plt.plot(float(x[i]), float(y[i]), 'o', color='black', markersize=4)
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	253
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	254 if not (spectrum_explained == 'NA') and not (
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	255 spectrum_explained_formulas == 'NA'):
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	256 # Plot explained peaks
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	257 ex = []
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	258 ey = []
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	259 for i in spectrum_explained.split(';'):
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	260 t = i.split('_')
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	261 ex.append(t[0])
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	262 ey.append(y[x.index(t[0])])
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	263
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	264 for i in range(0, len(ex)):
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	265 plt.plot([float(ex[i]), float(ex[i])], [0, float(ey[i])],
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	266 linewidth=3, color='#2b8126')
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	267 plt.plot(float(ex[i]), float(ey[i]), 'o', color='#2b8126',
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	268 markersize=8)
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	269
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	270 # Plot formulas on explained peaks
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	271 ex = []
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	272 ey = []
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	273 ez = []
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	274 for i in spectrum_explained_formulas.split(';'):
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	275 t = i.split(':')
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	276 ex.append(t[0])
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	277 ey.append(y[x.index(t[0])])
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	278 ez.append(t[1])
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	279
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	280 for i in range(0, len(ex)):
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	281 plt.text(float(ex[i]), float(ey[i]) + 1000, ez[i], color='#2b8126',
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	282 fontsize=8,
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	283 horizontalalignment='center', verticalalignment='bottom')
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	284
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	285 # Save SVG
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	286 plt.savefig("metfrag-vis-spectrum.svg", format="svg", transparent=True)
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	287 plt.close()
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	288
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	289 # Import SVG
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	290 with open("metfrag-vis-spectrum.svg", "r") as svg_file:
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	291 svg_string = []
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	292 for line in svg_file:
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	293 if not ('<?xml' in line) and not ('<!DOCTYPE' in line) and not (
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	294 ' "http://www.w3.org/Graphics' in line):
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	295 svg_string.append(line)
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	296 svg_file.close()
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	297 os.remove("metfrag-vis-spectrum.svg")
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	298 return (str(''.join(svg_string)))
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	299
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	300
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	301 # #################### MAIN ####################
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	302 if pubchem_synonyms_enabled:
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	303 print('Fetching of PubChem Synonyms enabled.')
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	304 if classyfire_classes_enabled:
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	305 print('Fetching of ClassyFire Classes enabled.')
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	306
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	307 # Open output html file
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	308 try:
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	309 metfrag_html = open(output_html, "w")
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	310 except Exception as e:
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	311 print("Error writing output file. {}".format(e))
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	312 exit(1)
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	313
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	314 # Write html header
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	315 metfrag_html.write('<!DOCTYPE html>\n')
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	316 metfrag_html.write('<html>\n')
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	317 metfrag_html.write('<head>\n')
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	318 metfrag_html.write('<title>' + 'msPurity MetFrag results' + '</title>\n')
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	319 metfrag_html.write('<style type="text/css">\n')
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	320 metfrag_html.write('svg { width: 200px; height: 100%; }\n')
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	321 metfrag_html.write(
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	322 'body { font-family: Lucida, Verdana, Arial, Helvetica, sans-serif; '
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	323 'font-size: 13px; text-align: left; '
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	324 'color: #000000; margin: 8px 8px 8px 8px; }\n')
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	325 metfrag_html.write(
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	326 'A { color: #2b8126; text-decoration: none; background: transparent; }\n')
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	327 metfrag_html.write(
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	328 'A:visited { '
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	329 'color: #19681a; text-decoration: none; background: transparent; '
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	330 '}\n')
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	331 metfrag_html.write(
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	332 'A:hover { '
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	333 'color: #8fc180; text-decoration: underline; background: transparent; '
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	334 '}\n')
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	335 metfrag_html.write(
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	336 'h1 { font-size: 32px; font-weight: bold; text-align: center; '
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	337 'padding: 0px 0px 4px 0px; margin: 26px 0px 0px 0px; }\n')
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	338 metfrag_html.write(
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	339 'h2 { font-size: 24px; font-weight: bold; text-align: left; '
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	340 'padding: 0px 0px 4px 0px; margin: 26px 0px 0px 0px; }\n')
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	341 metfrag_html.write(
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	342 'table { font-family: Lucida, Verdana, Arial, Helvetica, sans-serif; '
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	343 'font-size: 10px; text-align: left; '
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	344 'line-height: 10px; border: 1px solid #e3efdf; '
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	345 'background-color: #ecf5ea; margin-bottom: 8px; '
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	346 'min-width: 1600px; max-width: 2400px; }\n')
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	347 metfrag_html.write(
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	348 '#tablediv { width: 100%; min-width: 20px; max-width: 200px; }\n')
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	349 metfrag_html.write('.tdmax { min-width: 200px; max-width: 200px; }\n')
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	350 metfrag_html.write('.tdvar { min-width: 200px; max-width: 600px; }\n')
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	351 metfrag_html.write('tr:nth-child(even) { background-color: #f6faf5; }\n')
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	352 metfrag_html.write('</style>\n')
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	353 metfrag_html.write('</head>\n')
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	354 metfrag_html.write('<body>\n')
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	355
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	356 # Read input csv file
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	357 with open(input_tsv, "r") as metfrag_file:
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	358 metfrag_results = csv.DictReader(metfrag_file, delimiter='\t')
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	359 # Parse each line
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	360 line_count = 0
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	361 compound = ""
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	362 candidates = 0
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	363 for row in metfrag_results:
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	364
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	365 # Start new document
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	366 if (line_count == 0):
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	367 if os.path.join(os.path.dirname(os.path.abspath(__file__)),
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	368 'metfrag_logo.png'):
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	369 logo_pth = os.path.join(
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	370 os.path.dirname(os.path.abspath(__file__)),
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	371 'metfrag_logo.png')
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	372 else:
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	373 logo_pth = '/usr/local/share/metfrag/metfrag_logo.png'
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	374
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	375 with open(logo_pth, "rb") as png_file:
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	376 png_encoded = base64.b64encode(png_file.read())
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	377 metfrag_html.write(str(
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	378 '\n<h1><img style="vertical-align:bottom" '
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	379 'src="data:image/png;base64,' +
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	380 png_encoded.decode('utf-8') +
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	381 '" alt="metfrag-logo" width="150"></img><text '
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	382 'style="line-height:2.0">  results</text></h1>\n'
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	383 ))
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	384 else:
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	385 # Parameter list at beginning of document
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	386 if (line_count == 1):
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	387 metfrag_html.write('\n<h2>Parameter list</h2>\n')
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	388 metfrag_html.write(str('MetFragDatabaseType=' +
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	389 re.sub(' .*', '',
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	390 re.sub('.*MetFragDatabaseType=',
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	391 '',
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	392 row[
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	393 "MetFragCLIString"]))
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	394 + '<br>\n')
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	395 )
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	396 metfrag_html.write(str('PrecursorIonMode=' +
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	397 re.sub(' .*', '',
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	398 re.sub('.*PrecursorIonMode=', '',
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	399 row[
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	400 "MetFragCLIString"]))
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	401 + '<br>\n')
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	402 )
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	403 metfrag_html.write(str('DatabaseSearchRelativeMassDeviation=' +
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	404 re.sub(' .*', '',
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	405 re.sub(
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	406 '.*DatabaseSearchRelative'
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	407 'MassDeviation=',
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	408 '',
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	409 row[
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	410 "MetFragCLIString"])) +
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	411 '<br>\n')
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	412 )
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	413 metfrag_html.write(
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	414 str('FragmentPeakMatchAbsoluteMassDeviation=' +
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	415 re.sub(' .*', '',
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	416 re.sub(
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	417 '.*FragmentPeakMatchAbsoluteMassDeviation=',
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	418 '',
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	419 row["MetFragCLIString"])) + '<br>\n')
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	420 )
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	421 metfrag_html.write(
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	422 str('FragmentPeakMatchRelativeMassDeviation=' +
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	423 re.sub(' .*', '',
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	424 re.sub(
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	425 '.*FragmentPeakMatchRelativeMassDeviation=',
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	426 '',
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	427 row["MetFragCLIString"])) + '<br>\n')
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	428 )
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	429 metfrag_html.write(str('FilterExcludedElements=' +
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	430 re.sub(' .*', '',
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	431 re.sub(
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	432 '.*FilterExcludedElements=',
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	433 '',
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	434 row[
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	435 "MetFragCLIString"])) +
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	436 '<br>\n')
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	437 )
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	438 metfrag_html.write(str('FilterIncludedElements=' +
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	439 re.sub(' .*', '',
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	440 re.sub(
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	441 '.*FilterIncludedElements=',
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	442 '',
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	443 row[
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	444 "MetFragCLIString"])) +
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	445 '<br>\n')
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	446 )
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	447 metfrag_html.write(str('MetFragScoreTypes=' +
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	448 re.sub(' .*', '',
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	449 re.sub('.*MetFragScoreTypes=',
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	450 '',
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	451 row[
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	452 "MetFragCLIString"]))
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	453 + '<br>\n')
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	454 )
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	455 # New compound in list
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	456 if (row["name"] != compound):
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	457 compound = row["name"]
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	458 candidates = 0
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	459 identifier = row["name"]
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	460 monoisotopic_mass = row["MonoisotopicMass"]
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	461 precursor_mz = row["precursor_mz"]
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	462
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	463 if "retention_time" in row:
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	464 precursor_rt = row["retention_time"]
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	465 try:
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	466 precursor_rt = round(float(precursor_rt), 4)
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	467 except ValueError:
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	468 continue
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	469 else:
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	470 precursor_rt = ''
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	471
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	472 if "precursor_type" in row:
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	473 precursor_type = row["precursor_type"]
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	474 elif "adduct" in row:
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	475 precursor_type = row["adduct"]
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	476 else:
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	477 precursor_type = ''
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	478
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	479 if line_count > 1:
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	480 metfrag_html.write(str('</table>\n'))
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	481
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	482 metfrag_html.write(str('\n' + '<h2>' + identifier + '</h2>\n'))
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	483 metfrag_html.write(str('<p><b>Precursor Type:</b> ' + str(
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	484 precursor_type) + '<br>'))
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	485 metfrag_html.write(str('<b>Precursor Mass:</b> ' + str(
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	486 round(float(precursor_mz), 4)) + '<br>'))
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	487 metfrag_html.write(
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	488 str('<b>Precursor Retention Time:</b> ' + str(
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	489 precursor_mz) + '<br></p>'))
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	490 metfrag_html.write(str('\n' + '<table>\n'))
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	491 metfrag_html.write(str(
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	492 '<tr style="vertical-align:bottom; '
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	493 'background-color:#e3efdf;">'
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	494 + '<td class="tdmax">' + '<b>Spectrum</b>' + '</td>'
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	495 + '<td class="tdmax">' + '<b>Structure</b>' + '</td>'
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	496 + '<td>' + '<b>Monoisotopic Mass</b>' + '</td>'
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	497 + '<td>' + '<b>Molecular Formula</b>' + '</td>'
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	498 + '<td>' + '<b>Compound Name</b>' + '</td>'
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	499 + '<td class="tdvar">' + '<b>PubChem Synonyms</b>'+'</td>'
3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: diff changeset	500 + '<td>' + '<b>Compound Classes</b>' + '</td>'

0

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

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diff changeset

1 #!/usr/bin/env python

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

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2

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

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3 # Load modules

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

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4 import argparse

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

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5 import base64

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

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6 import csv

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

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7 import os

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

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8 import re

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

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9 import time

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

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10 import urllib.parse

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

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11

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

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12 import matplotlib.pyplot as plt

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13

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14 import pubchempy

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15

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16 import requests

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17

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

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18 # Parse arguments

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

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19 parser = argparse.ArgumentParser(

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

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20 description='Visualise MetFrag results in html.')

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

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21 parser.add_argument('-v', '--version', action='version',

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

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22 version='MetFrag-vis Version 0.9',

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23 help='show version')

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24 parser.add_argument('-i', '--input', metavar='metfrag_results.tsv',

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

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25 dest="input_tsv", required=True,

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26 help='MetFrag results as input')

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27 parser.add_argument('-o', '--output', metavar='metfrag_results.html',

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

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28 dest="output_html", required=True,

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

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29 help='Write MetFrag results into this output file')

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

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30 parser.add_argument('-m', '--max-candidates', metavar='10',

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

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31 dest="max_candidates", default=10, type=int,

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

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32 required=False,

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33 help='Maximum number of candidates per compound [1-1000]')

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

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34 parser.add_argument('-s', '--synonyms', dest='synonyms', action='store_true',

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

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35 required=False,

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36 help='Fetch synonyms from PubChem [disabled by default]')

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

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37 parser.add_argument('-c', '--classyfire', dest='classyfire',

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

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38 action='store_true', required=False,

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

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39 help='Fetch compound classes from ClassyFire'

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

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40 ' [disabled by default]')

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41

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42 args = parser.parse_args()

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

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43

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

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44 # Input CSV with MetFrag results

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

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45 input_tsv = args.input_tsv

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

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46

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47 # Output html of MetFrag results

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

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48 output_html = args.output_html

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49

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50 # Max number of candidates per compound

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

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51 max_candidates = args.max_candidates

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52

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

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53 # PubChem synonyms

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

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54 pubchem_synonyms_enabled = args.synonyms

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55

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56 # ClassyFire classes

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57 classyfire_classes_enabled = args.classyfire

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58

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59

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60 # ---------- cdk_inchi_to_svg ----------

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61 def cdk_inchi_to_svg(inchi):

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

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62 if "cdk-inchi-to-svg" in os.environ:

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

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63 JAVA_CMD = 'cdk-inchi-to-svg' + ' ' + str(

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

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64 '\'' + inchi + '\'') + ' ' + 'cdk-inchi-to-svg-output.svg'

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

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65 else:

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

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66 JAVA_BINARY = '/usr/local/bin/java'

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

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67 CDK_INCHI_TO_SVG_JAR = '/usr/local/bin/' \

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

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68 'cdk-inchi-to-svg-0.0.1-' \

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

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69 'SNAPSHOT-jar-with-dependencies.jar'

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

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70 JAVA_CMD = str(

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71 JAVA_BINARY + ' ' + '-jar' + ' ' + CDK_INCHI_TO_SVG_JAR + ' '

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

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72 + str('\'' + inchi + '\'') + ' ' + 'cdk-inchi-to-svg-output.svg')

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

73

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

74 # Exec cdk-inchi-to-svg JAVA binary

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

75 exitcode = os.system(JAVA_CMD)

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

76

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

77 # Check whether binary has successfully been run

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

78 if (exitcode == 0):

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

79 with open("cdk-inchi-to-svg-output.svg", "r") as svg_file:

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

80 svg_string = []

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

81 for line in svg_file:

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

82 if not ('<?xml' in line) and not ('<!DOCTYPE' in line):

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

83 if (' fill=\'#FFFFFF\'' in line):

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

84 line = re.sub(' fill=\'#FFFFFF\'',

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

85 ' fill=\'#FFFFFF\' fill-opacity=\'0.0\'',

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

86 line)

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

87 svg_string.append(line)

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

88 svg_file.close()

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

89 os.remove("cdk-inchi-to-svg-output.svg")

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

90 return (str(''.join(svg_string)))

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

91 else:

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

92 return (' ')

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

93

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

94

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

95 # ---------- pubchem_link ----------

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

96 def pubchem_link(compound_name):

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

97 return (str('https://pubchem.ncbi.nlm.nih.gov/#query=' + compound_name))

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

98

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

99

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

100 # ---------- kegg_link ----------

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

101 def kegg_link(compound_name):

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

102 return (str(

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

103 'https://www.genome.jp/dbget-bin/'

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

104 'www_bfind_sub?mode=bfind&max_hit=1000&dbkey=kegg&keywords=' +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

105 compound_name))

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

106

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

107

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

108 # ---------- biocyc_link ----------

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

109 def biocyc_link(compound_name):

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

110 biocyc_url = urllib.parse.urlparse(

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

111 str(

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

112 'https://www.biocyc.org/'

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

113 'substring-search?type=NIL&object=' +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

114 compound_name + '&quickSearch=Quick+Search'))

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

115 return (biocyc_url.geturl())

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

116

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

117

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

118 # ---------- hmdb_link ----------

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

119 def hmdb_link(compound_name):

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

120 hmdb_url = urllib.parse.urlparse(

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

121 str(

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

122 'https://hmdb.ca/unearth/q?utf8=\xe2&query=' +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

123 compound_name + '&searcher=metabolites&button='))

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

124 return (hmdb_url.geturl())

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

125

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

126

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

127 # ---------- hmdb_link ----------

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

128 def chebi_link(inchi):

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

129 return (str(

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

130 'https://www.ebi.ac.uk/chebi/advancedSearchFT.do?searchString='

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

131 + inchi))

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

132

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

133

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

134 # ---------- PubChem Synonyms ----------

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

135 def fetch_pubchem_synonyms(inchi):

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

136 if not ('InChI=' in inchi):

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

137 return (' ')

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

138

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

139 # Fetch CID from InChI

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

140 print('Retrieving PubChem CID from InChI...')

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

141 compound = pubchempy.get_compounds(identifier=inchi, namespace='inchi')

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

142 compound_cid = re.sub(r'\).*', '', re.sub(r'.*\(', '', str(compound)))

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

143 if len(compound_cid) <= 1:

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

144 print(str('Warning. No match for InChI \"' + str(inchi) + '\".'))

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

145 return (' ')

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

146

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

147 # Retrieve compound

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

148 print('Retrieving PubChem compound information...')

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

149 compound = pubchempy.Compound.from_cid(compound_cid)

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

150 if ('synonyms' in dir(compound)):

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

151 return ('; '.join(compound.synonyms))

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

152 else:

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

153 print(str('Warning. No synonyms found for CID \"' + str(

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

154 compound_cid) + '\".'))

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

155 return (' ')

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

156

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

157

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

158 # ---------- ClassyFire ----------

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

159 def fetch_classyfire_classes(inchi):

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

160 if not ('InChI=' in inchi):

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

161 return (' ')

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

162

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

163 # Send POST request to ClassyFire

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

164 print('Sending request to ClassyFire...')

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

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165 classyfire_url = 'http://classyfire.wishartlab.com/queries.json'

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

166 classyfire_post = str(

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

167 '{\"label\":\"metfrag\",\"query_input\":\"' + inchi +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

168 '\",\"query_type\":\"STRUCTURE\"}')

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

169 classyfire_headers = {'Content-Type': 'application/json'}

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

170 classyfire_request = requests.post(classyfire_url, data=classyfire_post,

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

171 headers=classyfire_headers)

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

172

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

173 # Only continue when request has been successfully sent

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

174 if (classyfire_request.status_code != 201):

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

175 print('Error! Could not send request to ClassyFire. \"',

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

176 str(classyfire_request.status_code) + ': ' + str(

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

177 classyfire_request.reason), '\". Skipping entry.')

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

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178 return (' ')

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

179

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

180 # Get ClassyFire Query ID

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

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181 classyfire_request.json()

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

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182 classyfire_query_id = classyfire_request.json()['id']

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

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183

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

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184 # Query ClassyFire in max. 20 attempts

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

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185 classyfire_request_loop = 0

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

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186 while (classyfire_request_loop < 20):

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

187 print(str(

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

188 'Sending query ' + str(classyfire_query_id) + ' to ClassyFire...'))

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

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189 time.sleep(10)

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

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190 classyfire_query = requests.get(

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

191 str('http://classyfire.wishartlab.com/queries/' + str(

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

192 classyfire_query_id) + '.json'))

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

193

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

194 if (classyfire_query.status_code == 200) and (

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

195 classyfire_query.json()['classification_status'] == 'Done'):

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

196 classyfire_request_loop = 999

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

197 break

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

198 else:

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

199 classyfire_request_loop += 1

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

200

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

201 if classyfire_request_loop == 999:

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

202 # Direct parent

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

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203 direct_parent_name = classyfire_query.json()[

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

204 'entities'][0]['direct_parent']['name']

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

205 direct_parent_url = classyfire_query.json()[

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

206 'entities'][0]['direct_parent']['url']

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

207 direct_parent = str(

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

208 '<a target="_blank" href="' + direct_parent_url + '">' +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

209 direct_parent_name + '</a>')

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

210

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

211 # Alternative parents

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

212 alt_parents = []

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

213 for i in range(0, len(classyfire_query.json()['entities'][0][

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

214 'alternative_parents'])):

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

215 alt_parent_name = classyfire_query.json()[

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

216 'entities'][0]['alternative_parents'][i]['name']

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

217 alt_parent_url = classyfire_query.json()[

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

218 'entities'][0]['alternative_parents'][i]['url']

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

219 alt_parent = str(

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

220 '<a target="_blank" href="' + alt_parent_url + '">' +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

221 alt_parent_name + '</a>')

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

222 alt_parents.append(alt_parent)

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

223

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

224 # Concat classes

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

225 classes = str('<b>' + direct_parent + '</b>, <br>' + str(

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

226 ', <br>'.join(alt_parents)))

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

227 else:

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

228 print('Warning. Timout sending query to ClassyFire. Skipping entry.')

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

229 classes = ' '

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

230

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

231 return (classes)

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

232

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

233

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

234 # ---------- Plot Spectrum ----------

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

235 def plot_spectrum(spectrum, spectrum_explained, spectrum_explained_formulas):

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

236 # Plot

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

237 plt.figure(figsize=[5.5, 4.4])

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

238 plt.xlabel('m/z')

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

239 plt.ylabel('intensity')

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

240

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

241 # Plot spectrum

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

242 x = []

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

243 y = []

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

244 for i in spectrum.split(';'):

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

245 t = i.split('_')

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

246 x.append(t[0])

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

247 y.append(t[1])

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

248

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

249 for i in range(0, len(x)):

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

250 plt.plot([float(x[i]), float(x[i])], [0, float(y[i])], linewidth=1,

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

251 color='black')

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

252 plt.plot(float(x[i]), float(y[i]), 'o', color='black', markersize=4)

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

253

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

254 if not (spectrum_explained == 'NA') and not (

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

255 spectrum_explained_formulas == 'NA'):

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

256 # Plot explained peaks

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

257 ex = []

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

258 ey = []

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

259 for i in spectrum_explained.split(';'):

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

260 t = i.split('_')

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

261 ex.append(t[0])

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

262 ey.append(y[x.index(t[0])])

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

263

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

264 for i in range(0, len(ex)):

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

265 plt.plot([float(ex[i]), float(ex[i])], [0, float(ey[i])],

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

266 linewidth=3, color='#2b8126')

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

267 plt.plot(float(ex[i]), float(ey[i]), 'o', color='#2b8126',

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

268 markersize=8)

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

269

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

270 # Plot formulas on explained peaks

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

271 ex = []

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

272 ey = []

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

273 ez = []

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

274 for i in spectrum_explained_formulas.split(';'):

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

275 t = i.split(':')

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

276 ex.append(t[0])

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

277 ey.append(y[x.index(t[0])])

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

278 ez.append(t[1])

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

279

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

280 for i in range(0, len(ex)):

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

281 plt.text(float(ex[i]), float(ey[i]) + 1000, ez[i], color='#2b8126',

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

282 fontsize=8,

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

283 horizontalalignment='center', verticalalignment='bottom')

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

284

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

285 # Save SVG

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

286 plt.savefig("metfrag-vis-spectrum.svg", format="svg", transparent=True)

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

287 plt.close()

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

288

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

289 # Import SVG

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

290 with open("metfrag-vis-spectrum.svg", "r") as svg_file:

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

291 svg_string = []

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

292 for line in svg_file:

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

293 if not ('<?xml' in line) and not ('<!DOCTYPE' in line) and not (

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

294 ' "http://www.w3.org/Graphics' in line):

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

295 svg_string.append(line)

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

296 svg_file.close()

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

297 os.remove("metfrag-vis-spectrum.svg")

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

298 return (str(''.join(svg_string)))

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

299

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

300

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

301 # #################### MAIN ####################

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

302 if pubchem_synonyms_enabled:

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

303 print('Fetching of PubChem Synonyms enabled.')

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

304 if classyfire_classes_enabled:

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

305 print('Fetching of ClassyFire Classes enabled.')

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

306

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

307 # Open output html file

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

308 try:

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

309 metfrag_html = open(output_html, "w")

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

310 except Exception as e:

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

311 print("Error writing output file. {}".format(e))

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

312 exit(1)

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

313

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

314 # Write html header

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

315 metfrag_html.write('<!DOCTYPE html>\n')

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

316 metfrag_html.write('<html>\n')

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

317 metfrag_html.write('<head>\n')

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

318 metfrag_html.write('<title>' + 'msPurity MetFrag results' + '</title>\n')

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

319 metfrag_html.write('<style type="text/css">\n')

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

320 metfrag_html.write('svg { width: 200px; height: 100%; }\n')

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

321 metfrag_html.write(

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

322 'body { font-family: Lucida, Verdana, Arial, Helvetica, sans-serif; '

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

323 'font-size: 13px; text-align: left; '

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

324 'color: #000000; margin: 8px 8px 8px 8px; }\n')

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

325 metfrag_html.write(

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

326 'A { color: #2b8126; text-decoration: none; background: transparent; }\n')

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

327 metfrag_html.write(

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

328 'A:visited { '

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

329 'color: #19681a; text-decoration: none; background: transparent; '

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

330 '}\n')

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

331 metfrag_html.write(

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

332 'A:hover { '

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

333 'color: #8fc180; text-decoration: underline; background: transparent; '

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

334 '}\n')

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

335 metfrag_html.write(

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

336 'h1 { font-size: 32px; font-weight: bold; text-align: center; '

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

337 'padding: 0px 0px 4px 0px; margin: 26px 0px 0px 0px; }\n')

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

338 metfrag_html.write(

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

339 'h2 { font-size: 24px; font-weight: bold; text-align: left; '

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

340 'padding: 0px 0px 4px 0px; margin: 26px 0px 0px 0px; }\n')

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

341 metfrag_html.write(

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

342 'table { font-family: Lucida, Verdana, Arial, Helvetica, sans-serif; '

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

343 'font-size: 10px; text-align: left; '

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

344 'line-height: 10px; border: 1px solid #e3efdf; '

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

345 'background-color: #ecf5ea; margin-bottom: 8px; '

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

346 'min-width: 1600px; max-width: 2400px; }\n')

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

347 metfrag_html.write(

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

348 '#tablediv { width: 100%; min-width: 20px; max-width: 200px; }\n')

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

349 metfrag_html.write('.tdmax { min-width: 200px; max-width: 200px; }\n')

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

350 metfrag_html.write('.tdvar { min-width: 200px; max-width: 600px; }\n')

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

351 metfrag_html.write('tr:nth-child(even) { background-color: #f6faf5; }\n')

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

352 metfrag_html.write('</style>\n')

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

353 metfrag_html.write('</head>\n')

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

354 metfrag_html.write('<body>\n')

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

355

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

356 # Read input csv file

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

357 with open(input_tsv, "r") as metfrag_file:

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

358 metfrag_results = csv.DictReader(metfrag_file, delimiter='\t')

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

359 # Parse each line

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

360 line_count = 0

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

361 compound = ""

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

362 candidates = 0

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

363 for row in metfrag_results:

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

364

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

365 # Start new document

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

366 if (line_count == 0):

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

367 if os.path.join(os.path.dirname(os.path.abspath(__file__)),

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

368 'metfrag_logo.png'):

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

369 logo_pth = os.path.join(

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

370 os.path.dirname(os.path.abspath(__file__)),

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

371 'metfrag_logo.png')

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

372 else:

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

373 logo_pth = '/usr/local/share/metfrag/metfrag_logo.png'

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

374

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

375 with open(logo_pth, "rb") as png_file:

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

376 png_encoded = base64.b64encode(png_file.read())

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

377 metfrag_html.write(str(

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

378 '\n<h1><img style="vertical-align:bottom" '

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

379 'src="data:image/png;base64,' +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

380 png_encoded.decode('utf-8') +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

381 '" alt="metfrag-logo" width="150"></img><text '

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

382 'style="line-height:2.0">  results</text></h1>\n'

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

383 ))

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

384 else:

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

385 # Parameter list at beginning of document

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

386 if (line_count == 1):

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

387 metfrag_html.write('\n<h2>Parameter list</h2>\n')

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

388 metfrag_html.write(str('MetFragDatabaseType=' +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

389 re.sub(' .*', '',

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

390 re.sub('.*MetFragDatabaseType=',

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

391 '',

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

392 row[

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

393 "MetFragCLIString"]))

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

394 + '<br>\n')

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

395 )

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

396 metfrag_html.write(str('PrecursorIonMode=' +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

397 re.sub(' .*', '',

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

398 re.sub('.*PrecursorIonMode=', '',

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

399 row[

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

400 "MetFragCLIString"]))

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

401 + '<br>\n')

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

402 )

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

403 metfrag_html.write(str('DatabaseSearchRelativeMassDeviation=' +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

404 re.sub(' .*', '',

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

405 re.sub(

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

406 '.*DatabaseSearchRelative'

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

407 'MassDeviation=',

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

408 '',

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

409 row[

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

410 "MetFragCLIString"])) +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

411 '<br>\n')

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

412 )

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

413 metfrag_html.write(

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

414 str('FragmentPeakMatchAbsoluteMassDeviation=' +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

415 re.sub(' .*', '',

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

416 re.sub(

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

417 '.*FragmentPeakMatchAbsoluteMassDeviation=',

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

418 '',

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

419 row["MetFragCLIString"])) + '<br>\n')

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

420 )

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

421 metfrag_html.write(

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

422 str('FragmentPeakMatchRelativeMassDeviation=' +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

423 re.sub(' .*', '',

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

424 re.sub(

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

425 '.*FragmentPeakMatchRelativeMassDeviation=',

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

426 '',

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

427 row["MetFragCLIString"])) + '<br>\n')

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

428 )

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

429 metfrag_html.write(str('FilterExcludedElements=' +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

430 re.sub(' .*', '',

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

431 re.sub(

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

432 '.*FilterExcludedElements=',

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

433 '',

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

434 row[

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

435 "MetFragCLIString"])) +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

436 '<br>\n')

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

437 )

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

438 metfrag_html.write(str('FilterIncludedElements=' +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

439 re.sub(' .*', '',

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

440 re.sub(

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

441 '.*FilterIncludedElements=',

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

442 '',

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

443 row[

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

444 "MetFragCLIString"])) +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

445 '<br>\n')

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

446 )

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

447 metfrag_html.write(str('MetFragScoreTypes=' +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

448 re.sub(' .*', '',

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

449 re.sub('.*MetFragScoreTypes=',

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

450 '',

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

451 row[

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

452 "MetFragCLIString"]))

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

453 + '<br>\n')

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

454 )

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

455 # New compound in list

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

456 if (row["name"] != compound):

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

457 compound = row["name"]

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

458 candidates = 0

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

459 identifier = row["name"]

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

460 monoisotopic_mass = row["MonoisotopicMass"]

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

461 precursor_mz = row["precursor_mz"]

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

462

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

463 if "retention_time" in row:

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

464 precursor_rt = row["retention_time"]

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

465 try:

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

466 precursor_rt = round(float(precursor_rt), 4)

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

467 except ValueError:

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

468 continue

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

469 else:

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

470 precursor_rt = ''

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

471

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

472 if "precursor_type" in row:

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

473 precursor_type = row["precursor_type"]

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

474 elif "adduct" in row:

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

475 precursor_type = row["adduct"]

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

476 else:

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

477 precursor_type = ''

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

478

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

479 if line_count > 1:

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

480 metfrag_html.write(str('</table>\n'))

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

481

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

482 metfrag_html.write(str('\n' + '<h2>' + identifier + '</h2>\n'))

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

483 metfrag_html.write(str('<p><b>Precursor Type:</b> ' + str(

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

484 precursor_type) + '<br>'))

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

485 metfrag_html.write(str('<b>Precursor Mass:</b> ' + str(

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

486 round(float(precursor_mz), 4)) + '<br>'))

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

487 metfrag_html.write(

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

488 str('<b>Precursor Retention Time:</b> ' + str(

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

489 precursor_mz) + '<br></p>'))

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

490 metfrag_html.write(str('\n' + '<table>\n'))

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

491 metfrag_html.write(str(

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

492 '<tr style="vertical-align:bottom; '

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

493 'background-color:#e3efdf;">'

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

494 + '<td class="tdmax">' + '<b>Spectrum</b>' + '</td>'

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

495 + '<td class="tdmax">' + '<b>Structure</b>' + '</td>'

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

496 + '<td>' + '<b>Monoisotopic Mass</b>' + '</td>'

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

497 + '<td>' + '<b>Molecular Formula</b>' + '</td>'

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

498 + '<td>' + '<b>Compound Name</b>' + '</td>'

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

499 + '<td class="tdvar">' + '<b>PubChem Synonyms</b>'+'</td>'

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

500 + '<td>' + '<b>Compound Classes</b>' + '</td>'

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

501 + '<td>' + '<b>MetFrag Score</b>' + '</td>'

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

502 + '<td>' + '<b>MetFusion Score</b>' + '</td>'

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

503 + '<td>' + '<b>Fragmenter Score</b>' + '</td>'

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

504 + '<td>' + '<b>Suspectlist Score</b>' + '</td>'

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

505 + '<td>' + '<b>Explained Peaks</b>' + '</td>'

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

506 + '<td>' + '<b>MetFrag Web</b>' + '</td>'

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

507 + '<td>' + '<b>External Links</b>' + '</td>'

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

508 + '<td class="tdmax">' + '<b>InChI</b>' + '</td>'

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

509 + '</tr>\n'))

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

510

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

511 # Compound candidate

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

512 if (candidates < max_candidates):

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

513 # Column variables

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

514 inchi = row["InChI"]

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

515 smiles = row["SMILES"]

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

516 mol_formula = row["MolecularFormula"]

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

517 compound_name = row["IUPACName"]

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

518 frag_score = row["FragmenterScore"]

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

519 metfusion_score = row["OfflineMetFusionScore"]

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

520 score = row["Score"]

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

521 if "SuspectListScore" in row:

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

522 suspectlist_score = row["SuspectListScore"]

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

523 else:

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

524 suspectlist_score = 0

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

525 peaks_explained = row["NoExplPeaks"]

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

526 peaks_used = row["NumberPeaksUsed"]

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

527 spectrum_explained = row["ExplPeaks"]

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

528 spectrum_explained_formulas = row["FormulasOfExplPeaks"]

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

529 identifier = row["Identifier"]

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

530

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

531 # PubChem Synonyms

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

532 if pubchem_synonyms_enabled:

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

533 pubchem_synonyms = fetch_pubchem_synonyms(inchi)

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

534 else:

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

535 pubchem_synonyms = ' '

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

536

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

537 # Compound Classes

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

538 if classyfire_classes_enabled:

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

539 compound_classes = fetch_classyfire_classes(inchi)

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

540 else:

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

541 compound_classes = ' '

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

542

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

543 # Draw Spectrum

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

544 spectrum = re.sub(' .*', '', re.sub('.*PeakListString=', '',

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

545 row["MetFragCLIString"]))

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

546 spectrum_string = plot_spectrum(spectrum, spectrum_explained,

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

547 spectrum_explained_formulas)

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

548

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

549 # Draw SVG

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

550 svg_string = cdk_inchi_to_svg(str(inchi))

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

551

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

552 # External links

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

553 external_links = str(

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

554 '<a target="_blank" href="' + pubchem_link(

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

555 compound_name) + '">PubChem</a>' + ', ' +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

556 '<a target="_blank" href="' + kegg_link(

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

557 compound_name) + '">KEGG</a>' + ', ' +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

558 '<a target="_blank" href="' + hmdb_link(

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

559 compound_name) + '">HMDB</a>' + ', ' +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

560 '<a target="_blank" href="' + biocyc_link(

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

561 compound_name) + '">BioCyc</a>' + ', ' +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

562 '<a target="_blank" href="' + chebi_link(

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

563 inchi) + '">ChEBI</a>')

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

564

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

565 # MetFragWeb

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

566 FragmentPeakMatchAbsoluteMassDeviation = str(

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

567 '' +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

568 re.sub(' .*', '',

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

569 re.sub(

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

570 '.*FragmentPeakMatchAbsoluteMassDeviation=',

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

571 'FragmentPeakMatchAbsoluteMassDeviation=',

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

572 row["MetFragCLIString"]))

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

573 )

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

574 FragmentPeakMatchRelativeMassDeviation = str(

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

575 '' +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

576 re.sub(' .*', '',

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

577 re.sub(

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

578 '.*FragmentPeakMatchRelativeMassDeviation=',

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

579 'FragmentPeakMatchRelativeMassDeviation=',

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

580 row["MetFragCLIString"]))

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

581 )

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

582 DatabaseSearchRelativeMassDeviation = str(

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

583 '' +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

584 re.sub(' .*', '',

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

585 re.sub(

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

586 '.*DatabaseSearchRelativeMassDeviation=',

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

587 'DatabaseSearchRelativeMassDeviation=',

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

588 row["MetFragCLIString"]))

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

589 )

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

590 IonizedPrecursorMass = str(

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

591 'IonizedPrecursorMass=' + str(row["precursor_mz"]))

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

592 NeutralPrecursorMass = str(

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

593 '' + re.sub(' .*', '',

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

594 re.sub(

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

595 '.*NeutralPrecursorMass=',

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

596 'NeutralPrecursorMass=',

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

597 row[

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

598 "MetFragCLIString"]))

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

599 )

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

600 NeutralPrecursorMolecularFormula = str(

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

601 'NeutralPrecursorMolecularFormula=' + str(

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

602 row["MolecularFormula"]))

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

603 PrecursorIonMode = str(

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

604 '' + re.sub(' .*', '', re.sub('.*PrecursorIonMode=',

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

605 'PrecursorIonMode=',

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

606 row["MetFragCLIString"])))

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

607 PeakList = str(

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

608 '' + re.sub(' .*', '',

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

609 re.sub('.*PeakListString=', 'PeakList=',

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

610 row["MetFragCLIString"])))

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

611 MetFragDatabaseType = str(

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

612 '' + re.sub(' .*', '',

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

613 re.sub(

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

614 '.*MetFragDatabaseType=',

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

615 'MetFragDatabaseType=',

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

616 row["MetFragCLIString"])))

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

617

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

618 metfrag_web = str(

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

619 'https://msbi.ipb-halle.de/MetFrag/landing.xhtml?' +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

620 FragmentPeakMatchAbsoluteMassDeviation + '&' +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

621 FragmentPeakMatchRelativeMassDeviation + '&' +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

622 DatabaseSearchRelativeMassDeviation + '&' +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

623 IonizedPrecursorMass + '&' +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

624 NeutralPrecursorMass + '&' +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

625 # NeutralPrecursorMolecularFormula + '&' +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

626 PrecursorIonMode + '&' +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

627 PeakList + '&' +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

628 MetFragDatabaseType)

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

629

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

630 # Write html code

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

631 metfrag_html.write(str('<tr style="vertical-align:center">' +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

632 '<td class="tdmax">' +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

633 spectrum_string +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

634 '</td>' +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

635 '<td class="tdmax">' +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

636 svg_string +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

637 '</td>' +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

638 '<td>' +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

639 monoisotopic_mass +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

640 '</td>' +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

641 '<td>' +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

642 mol_formula +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

643 '</td>' +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

644 '<td>' +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

645 compound_name +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

646 '</td>' +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

647 '<td class="tdvar">' +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

648 pubchem_synonyms +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

649 '</td>' +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

650 '<td>' +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

651 compound_classes + '</td>' +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

652 '<td>' +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

653 str(round(float(score), 3)) +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

654 '</td>' +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

655 '<td>' +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

656 str(round(float(metfusion_score), 3)) +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

657 '</td>' +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

658 '<td>' +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

659 str(round(float(frag_score), 3)) +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

660 '</td>' +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

661 '<td>' +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

662 str(

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

663 round(float(suspectlist_score), 3)

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

664 ) +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

665 '</td>' +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

666 '<td>' +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

667 peaks_explained +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

668 ' / ' +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

669 peaks_used +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

670 '</td>' +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

671 '<td>' +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

672 '<a target="_blank" href="' +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

673 metfrag_web +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

674 '">MetFragWeb</a>' +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

675 '</td>' +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

676 '<td>' +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

677 external_links +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

678 '</td>' +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

679 '<td class="tdmax">' +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

680 inchi +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

681 '</td>' +

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

682 '</tr>\n'))

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

683

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

684 line_count += 1

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

685 candidates += 1

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

686

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

687 # Finish candidate list

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

688 metfrag_html.write(str('</table>\n'))

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

689

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

690 # Write html footer

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

691 metfrag_html.write('\n</body>\n')

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

692 metfrag_html.write('</html>\n')

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

693

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

694 # Close output html file

3dbe79671820 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

computational-metabolomics

parents:

diff changeset

695 metfrag_html.close()

Mercurial > repos > computational-metabolomics > metfrag_vis

annotate metfrag-vis.py @ 0:3dbe79671820 draft default tip