metfrag: metfrag.py annotate

annotate metfrag.py @ 0:fd5c0b39569a draft

"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"

author	computational-metabolomics
date	Wed, 05 Feb 2020 12:30:06 -0500
parents
children	9ee2e2ceb2c9

rev	line source
0 fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	1 from __future__ import absolute_import, print_function
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	2
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	3 import ConfigParser
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	4 import argparse
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	5 import csv
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	6 import glob
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	7 import multiprocessing
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	8 import os
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	9 import re
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	10 import shutil
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	11 import sys
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	12 import tempfile
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	13 from collections import defaultdict
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	14
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	15 import six
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	16
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	17 print(sys.version)
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	18
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	19 parser = argparse.ArgumentParser()
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	20 parser.add_argument('--input_pth')
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	21 parser.add_argument('--result_pth', default='metfrag_result.csv')
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	22
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	23 parser.add_argument('--temp_dir')
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	24 parser.add_argument('--polarity', default='pos')
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	25 parser.add_argument('--minMSMSpeaks', default=1)
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	26
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	27 parser.add_argument('--MetFragDatabaseType', default='PubChem')
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	28 parser.add_argument('--LocalDatabasePath', default='')
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	29 parser.add_argument('--LocalMetChemDatabaseServerIp', default='')
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	30
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	31 parser.add_argument('--DatabaseSearchRelativeMassDeviation', default=5)
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	32 parser.add_argument('--FragmentPeakMatchRelativeMassDeviation', default=10)
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	33 parser.add_argument('--FragmentPeakMatchAbsoluteMassDeviation', default=0.001)
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	34 parser.add_argument('--NumberThreads', default=1)
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	35 parser.add_argument('--UnconnectedCompoundFilter', action='store_true')
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	36 parser.add_argument('--IsotopeFilter', action='store_true')
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	37
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	38 parser.add_argument('--FilterMinimumElements', default='')
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	39 parser.add_argument('--FilterMaximumElements', default='')
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	40 parser.add_argument('--FilterSmartsInclusionList', default='')
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	41 parser.add_argument('--FilterSmartsExclusionList', default='')
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	42 parser.add_argument('--FilterIncludedElements', default='')
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	43 parser.add_argument('--FilterExcludedElements', default='')
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	44 parser.add_argument('--FilterIncludedExclusiveElements', default='')
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	45
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	46 parser.add_argument('--score_thrshld', default=0)
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	47 parser.add_argument('--pctexplpeak_thrshld', default=0)
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	48 parser.add_argument('--schema')
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	49 parser.add_argument('--cores_top_level', default=1)
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	50 parser.add_argument('--chunks', default=1)
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	51 parser.add_argument('--meta_select_col', default='name')
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	52 parser.add_argument('--skip_invalid_adducts', action='store_true')
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	53
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	54 parser.add_argument('--ScoreSuspectLists', default='')
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	55 parser.add_argument('--MetFragScoreTypes',
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	56 default="FragmenterScore,OfflineMetFusionScore")
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	57 parser.add_argument('--MetFragScoreWeights', default="1.0,1.0")
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	58
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	59 args = parser.parse_args()
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	60 print(args)
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	61
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	62 config = ConfigParser.ConfigParser()
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	63 config.read(
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	64 os.path.join(os.path.dirname(os.path.abspath(__file__)), 'config.ini'))
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	65
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	66 if os.stat(args.input_pth).st_size == 0:
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	67 print('Input file empty')
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	68 exit()
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	69
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	70 # Create temporary working directory
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	71 if args.temp_dir:
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	72 wd = args.temp_dir
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	73 else:
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	74 wd = tempfile.mkdtemp()
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	75
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	76 if os.path.exists(wd):
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	77 shutil.rmtree(wd)
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	78 os.makedirs(wd)
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	79 else:
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	80 os.makedirs(wd)
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	81
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	82 ######################################################################
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	83 # Setup regular expressions for MSP parsing dictionary
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	84 ######################################################################
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	85 regex_msp = {}
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	86 regex_msp['name'] = [r'^Name(?:=\|:)(.*)$']
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	87 regex_msp['polarity'] = [r'^ion.mode(?:=\|:)(.)$',
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	88 r'^ionization.mode(?:=\|:)(.)$',
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	89 r'^polarity(?:=\|:)(.*)$']
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	90 regex_msp['precursor_mz'] = [r'^precursor.m/z(?:=\|:)\s(\d[.,]?\d)$',
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	91 r'^precursor.mz(?:=\|:)\s(\d[.,]?\d)$']
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	92 regex_msp['precursor_type'] = [r'^precursor.type(?:=\|:)(.)$',
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	93 r'^adduct(?:=\|:)(.*)$',
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	94 r'^ADDUCTIONNAME(?:=\|:)(.*)$']
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	95 regex_msp['num_peaks'] = [r'^Num.Peaks(?:=\|:)\s(\d*)$']
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	96 regex_msp['msp'] = [r'^Name(?:=\|:)(.*)$'] # Flag for standard MSP format
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	97
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	98 regex_massbank = {}
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	99 regex_massbank['name'] = [r'^RECORD_TITLE:(.*)$']
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	100 regex_massbank['polarity'] = [r'^AC\$MASS_SPECTROMETRY:\s+ION_MODE\s+(.*)$']
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	101 regex_massbank['precursor_mz'] = [
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	102 r'^MS\$FOCUSED_ION:\s+PRECURSOR_M/Z\s+(\d[.,]?\d)$']
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	103 regex_massbank['precursor_type'] = [
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	104 r'^MS\$FOCUSED_ION:\s+PRECURSOR_TYPE\s+(.*)$']
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	105 regex_massbank['num_peaks'] = [r'^PK\$NUM_PEAK:\s+(\d*)']
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	106 regex_massbank['cols'] = [r'^PK\$PEAK:\s+(.*)']
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	107 regex_massbank['massbank'] = [
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	108 r'^RECORD_TITLE:(.*)$'] # Flag for massbank format
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	109
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	110 if args.schema == 'msp':
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	111 meta_regex = regex_msp
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	112 elif args.schema == 'massbank':
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	113 meta_regex = regex_massbank
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	114 elif args.schema == 'auto':
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	115 # If auto we just check for all the available paramter names and then
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	116 # determine if Massbank or MSP based on the name parameter
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	117 meta_regex = {}
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	118 meta_regex.update(regex_massbank)
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	119 meta_regex['name'].extend(regex_msp['name'])
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	120 meta_regex['polarity'].extend(regex_msp['polarity'])
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	121 meta_regex['precursor_mz'].extend(regex_msp['precursor_mz'])
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	122 meta_regex['precursor_type'].extend(regex_msp['precursor_type'])
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	123 meta_regex['num_peaks'].extend(regex_msp['num_peaks'])
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	124 meta_regex['msp'] = regex_msp['msp']
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	125 else:
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	126 sys.exit("No schema selected")
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	127
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	128 adduct_types = {
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	129 '[M+H]+': 1.007276,
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	130 '[M+NH4]+': 18.034374,
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	131 '[M+Na]+': 22.989218,
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	132 '[M+K]+': 38.963158,
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	133 '[M+CH3OH+H]+': 33.033489,
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	134 '[M+ACN+H]+': 42.033823,
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	135 '[M+ACN+Na]+': 64.015765,
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	136 '[M+2ACN+H]+': 83.06037,
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	137 '[M-H]-': -1.007276,
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	138 '[M+Cl]-': 34.969402,
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	139 '[M+HCOO]-': 44.99819,
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	140 '[M-H+HCOOH]-': 44.99819,
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	141 # same as above but different style of writing adduct
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	142 '[M+CH3COO]-': 59.01385,
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	143 '[M-H+CH3COOH]-': 59.01385
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	144 # same as above but different style of writing adduct
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	145 }
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	146 inv_adduct_types = {int(round(v, 0)): k for k, v in adduct_types.iteritems()}
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	147
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	148
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	149 # function to extract the meta data using the regular expressions
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	150 def parse_meta(meta_regex, meta_info=None):
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	151 if meta_info is None:
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	152 meta_info = {}
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	153 for k, regexes in six.iteritems(meta_regex):
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	154 for reg in regexes:
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	155 m = re.search(reg, line, re.IGNORECASE)
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	156 if m:
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	157 meta_info[k] = '-'.join(m.groups()).strip()
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	158 return meta_info
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	159
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	160
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	161 ######################################################################
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	162 # Setup parameter dictionary
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	163 ######################################################################
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	164 def init_paramd(args):
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	165 paramd = defaultdict()
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	166
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	167 paramd["MetFragDatabaseType"] = args.MetFragDatabaseType
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	168
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	169 if args.MetFragDatabaseType == "LocalCSV":
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	170 paramd["LocalDatabasePath"] = args.LocalDatabasePath
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	171 elif args.MetFragDatabaseType == "MetChem":
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	172 paramd["LocalMetChemDatabase"] = \
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	173 config.get('MetChem', 'LocalMetChemDatabase')
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	174 paramd["LocalMetChemDatabasePortNumber"] = \
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	175 config.get('MetChem', 'LocalMetChemDatabasePortNumber')
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	176 paramd["LocalMetChemDatabaseServerIp"] = \
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	177 args.LocalMetChemDatabaseServerIp
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	178 paramd["LocalMetChemDatabaseUser"] = \
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	179 config.get('MetChem', 'LocalMetChemDatabaseUser')
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	180 paramd["LocalMetChemDatabasePassword"] = \
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	181 config.get('MetChem', 'LocalMetChemDatabasePassword')
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	182
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	183 paramd["FragmentPeakMatchAbsoluteMassDeviation"] = \
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	184 args.FragmentPeakMatchAbsoluteMassDeviation
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	185 paramd["FragmentPeakMatchRelativeMassDeviation"] = \
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	186 args.FragmentPeakMatchRelativeMassDeviation
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	187 paramd["DatabaseSearchRelativeMassDeviation"] = \
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	188 args.DatabaseSearchRelativeMassDeviation
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	189 paramd["SampleName"] = ''
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	190 paramd["ResultsPath"] = os.path.join(wd)
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	191
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	192 if args.polarity == "pos":
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	193 paramd["IsPositiveIonMode"] = True
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	194 paramd["PrecursorIonModeDefault"] = "1"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	195 paramd["PrecursorIonMode"] = "1"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	196 paramd["nm_mass_diff_default"] = 1.007276
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	197 else:
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	198 paramd["IsPositiveIonMode"] = False
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	199 paramd["PrecursorIonModeDefault"] = "-1"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	200 paramd["PrecursorIonMode"] = "-1"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	201 paramd["nm_mass_diff_default"] = -1.007276
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	202
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	203 paramd["MetFragCandidateWriter"] = "CSV"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	204 paramd["NumberThreads"] = args.NumberThreads
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	205
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	206 if args.ScoreSuspectLists:
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	207 paramd["ScoreSuspectLists"] = args.ScoreSuspectLists
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	208
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	209 paramd["MetFragScoreTypes"] = args.MetFragScoreTypes
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	210 paramd["MetFragScoreWeights"] = args.MetFragScoreWeights
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	211
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	212 dct_filter = defaultdict()
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	213 filterh = []
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	214
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	215 if args.UnconnectedCompoundFilter:
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	216 filterh.append('UnconnectedCompoundFilter')
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	217
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	218 if args.IsotopeFilter:
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	219 filterh.append('IsotopeFilter')
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	220
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	221 if args.FilterMinimumElements:
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	222 filterh.append('MinimumElementsFilter')
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	223 dct_filter['FilterMinimumElements'] = args.FilterMinimumElements
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	224
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	225 if args.FilterMaximumElements:
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	226 filterh.append('MaximumElementsFilter')
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	227 dct_filter['FilterMaximumElements'] = args.FilterMaximumElements
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	228
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	229 if args.FilterSmartsInclusionList:
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	230 filterh.append('SmartsSubstructureInclusionFilter')
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	231 dct_filter[
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	232 'FilterSmartsInclusionList'] = args.FilterSmartsInclusionList
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	233
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	234 if args.FilterSmartsExclusionList:
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	235 filterh.append('SmartsSubstructureExclusionFilter')
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	236 dct_filter[
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	237 'FilterSmartsExclusionList'] = args.FilterSmartsExclusionList
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	238
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	239 # My understanding is that both 'ElementInclusionExclusiveFilter'
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	240 # and 'ElementExclusionFilter' use 'FilterIncludedElements'
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	241 if args.FilterIncludedExclusiveElements:
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	242 filterh.append('ElementInclusionExclusiveFilter')
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	243 dct_filter[
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	244 'FilterIncludedElements'] = args.FilterIncludedExclusiveElements
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	245
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	246 if args.FilterIncludedElements:
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	247 filterh.append('ElementInclusionFilter')
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	248 dct_filter['FilterIncludedElements'] = args.FilterIncludedElements
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	249
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	250 if args.FilterExcludedElements:
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	251 filterh.append('ElementExclusionFilter')
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	252 dct_filter['FilterExcludedElements'] = args.FilterExcludedElements
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	253
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	254 if filterh:
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	255 fcmds = ','.join(filterh) + ' '
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	256 for k, v in six.iteritems(dct_filter):
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	257 fcmds += "{0}={1} ".format(str(k), str(v))
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	258
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	259 paramd["MetFragPreProcessingCandidateFilter"] = fcmds
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	260
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	261 return paramd
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	262
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	263
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	264 ######################################################################
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	265 # Function to run metfrag when all metainfo and peaks have been parsed
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	266 ######################################################################
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	267 def run_metfrag(meta_info, peaklist, args, wd, spectrac, adduct_types):
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	268 # Get sample details (if possible to extract) e.g. if created as part of
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	269 # the msPurity pipeline) choose between getting additional details to add
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	270 # as columns as either all meta data from msp, just details from the
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	271 # record name (i.e. when using msPurity and we have the columns coded into
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	272 # the name) or just the spectra index (spectrac)].
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	273 # Returns the parameters used and the command line call
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	274
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	275 paramd = init_paramd(args)
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	276 if args.meta_select_col == 'name':
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	277 # have additional column of just the name
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	278 paramd['additional_details'] = {'name': meta_info['name']}
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	279 elif args.meta_select_col == 'name_split':
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	280 # have additional columns split by "\|" and
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	281 # then on ":" e.g. MZ:100.2 \| RT:20 \| xcms_grp_id:1
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	282 paramd['additional_details'] = {
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	283 sm.split(":")[0].strip(): sm.split(":")[1].strip() for sm in
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	284 meta_info['name'].split("\|")}
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	285 elif args.meta_select_col == 'all':
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	286 # have additional columns based on all the meta information
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	287 # extracted from the MSP
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	288 paramd['additional_details'] = meta_info
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	289 else:
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	290 # Just have and index of the spectra in the MSP file
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	291 paramd['additional_details'] = {'spectra_idx': spectrac}
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	292
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	293 paramd["SampleName"] = "{}_metfrag_result".format(spectrac)
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	294
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	295 # =============== Output peaks to txt file ==============================
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	296 paramd["PeakListPath"] = os.path.join(wd,
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	297 "{}_tmpspec.txt".format(spectrac))
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	298
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	299 # write spec file
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	300 with open(paramd["PeakListPath"], 'w') as outfile:
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	301 for p in peaklist:
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	302 outfile.write(p[0] + "\t" + p[1] + "\n")
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	303
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	304 # =============== Update param based on MSP metadata ======================
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	305 # Replace param details with details from MSP if required
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	306 if 'precursor_type' in meta_info and \
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	307 meta_info['precursor_type'] in adduct_types:
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	308 adduct = meta_info['precursor_type']
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	309 nm = float(meta_info['precursor_mz']) - adduct_types[
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	310 meta_info['precursor_type']]
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	311 paramd["PrecursorIonMode"] = \
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	312 int(round(adduct_types[meta_info['precursor_type']], 0))
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	313 elif not args.skip_invalid_adducts:
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	314 adduct = inv_adduct_types[int(paramd['PrecursorIonModeDefault'])]
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	315 paramd["PrecursorIonMode"] = paramd['PrecursorIonModeDefault']
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	316 nm = float(meta_info['precursor_mz']) - paramd['nm_mass_diff_default']
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	317 else:
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	318 print('Skipping {}'.format(paramd["SampleName"]))
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	319 return '', ''
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	320
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	321 paramd['additional_details']['adduct'] = adduct
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	322 paramd["NeutralPrecursorMass"] = nm
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	323
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	324 # ============== Create CLI cmd for metfrag ===============================
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	325 cmd = "metfrag"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	326 for k, v in six.iteritems(paramd):
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	327 if k not in ['PrecursorIonModeDefault', 'nm_mass_diff_default',
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	328 'additional_details']:
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	329 cmd += " {}={}".format(str(k), str(v))
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	330
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	331 # ============== Run metfrag ==============================================
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	332 # print(cmd)
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	333 # Filter before process with a minimum number of MS/MS peaks
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	334 if plinesread >= float(args.minMSMSpeaks):
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	335
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	336 if int(args.cores_top_level) == 1:
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	337 os.system(cmd)
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	338
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	339 return paramd, cmd
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	340
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	341
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	342 def work(cmds):
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	343 return [os.system(cmd) for cmd in cmds]
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	344
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	345
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	346 ######################################################################
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	347 # Parse MSP file and run metfrag CLI
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	348 ######################################################################
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	349 # keep list of commands if performing in CLI in parallel
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	350 cmds = []
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	351 # keep a dictionary of all params
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	352 paramds = {}
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	353 # keep count of spectra (for uid)
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	354 spectrac = 0
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	355 # this dictionary will store the meta data results form the MSp file
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	356 meta_info = {}
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	357
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	358 with open(args.input_pth, "r") as infile:
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	359 # number of lines for the peaks
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	360 pnumlines = 0
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	361 # number of lines read for the peaks
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	362 plinesread = 0
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	363 for line in infile:
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	364 line = line.strip()
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	365
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	366 if pnumlines == 0:
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	367 # ============== Extract metadata from MSP ========================
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	368 meta_info = parse_meta(meta_regex, meta_info)
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	369
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	370 if ('massbank' in meta_info and 'cols' in meta_info) or (
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	371 'msp' in meta_info and 'num_peaks' in meta_info):
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	372 pnumlines = int(meta_info['num_peaks'])
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	373 plinesread = 0
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	374 peaklist = []
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	375
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	376 elif plinesread < pnumlines:
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	377 # ============== Extract peaks from MSP ==========================
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	378 # .split() will split on any empty space (i.e. tab and space)
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	379 line = tuple(line.split())
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	380 # Keep only m/z and intensity, not relative intensity
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	381 save_line = tuple(line[0].split() + line[1].split())
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	382 plinesread += 1
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	383 peaklist.append(save_line)
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	384
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	385 elif plinesread and plinesread == pnumlines:
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	386 # ======= Get sample name and additional details for output =======
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	387 spectrac += 1
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	388 paramd, cmd = run_metfrag(meta_info, peaklist, args, wd, spectrac,
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	389 adduct_types)
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	390
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	391 if paramd:
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	392 paramds[paramd["SampleName"]] = paramd
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	393 cmds.append(cmd)
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	394
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	395 meta_info = {}
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	396 pnumlines = 0
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	397 plinesread = 0
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	398
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	399 # end of file. Check if there is a MSP spectra to run metfrag on still
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	400 if plinesread and plinesread == pnumlines:
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	401
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	402 paramd, cmd = run_metfrag(meta_info, peaklist, args, wd, spectrac + 1,
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	403 adduct_types)
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	404
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	405 if paramd:
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	406 paramds[paramd["SampleName"]] = paramd
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	407 cmds.append(cmd)
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	408
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	409 # Perform multiprocessing on command line call level
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	410 if int(args.cores_top_level) > 1:
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	411 cmds_chunks = [cmds[x:x + int(args.chunks)] for x in
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	412 list(range(0, len(cmds), int(args.chunks)))]
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	413 pool = multiprocessing.Pool(processes=int(args.cores_top_level))
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	414 pool.map(work, cmds_chunks)
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	415 pool.close()
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	416 pool.join()
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	417
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	418 ######################################################################
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	419 # Concatenate and filter the output
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	420 ######################################################################
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	421 # outputs might have different headers. Need to get a list of all the
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	422 # headers before we start merging the files
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	423 # outfiles = [os.path.join(wd, f) for f in glob.glob(os.path.join(wd,
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	424 # "*_metfrag_result.csv"))]
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	425 outfiles = glob.glob(os.path.join(wd, "*_metfrag_result.csv"))
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	426
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	427 if len(outfiles) == 0:
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	428 print('No results')
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	429 sys.exit()
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	430
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	431 headers = []
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	432 c = 0
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	433 for fn in outfiles:
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	434 with open(fn, 'r') as infile:
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	435 reader = csv.reader(infile)
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	436 if sys.version_info >= (3, 0):
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	437 headers.extend(next(reader))
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	438 else:
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	439 headers.extend(reader.next())
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	440 # check if file has any data rows
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	441 for i, row in enumerate(reader):
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	442 c += 1
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	443 if i == 1:
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	444 break
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	445
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	446 # if no data rows (e.g. matches) then do not save an
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	447 # output and leave the program
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	448 if c == 0:
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	449 print('No results')
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	450 sys.exit()
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	451
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	452 additional_detail_headers = ['sample_name']
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	453 for k, paramd in six.iteritems(paramds):
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	454 additional_detail_headers = list(set(
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	455 additional_detail_headers + list(paramd['additional_details'].keys())))
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	456
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	457 # add inchikey if not already present (missing in metchem output)
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	458 if 'InChIKey' not in headers:
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	459 headers.append('InChIKey')
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	460
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	461 headers = additional_detail_headers + sorted(list(set(headers)))
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	462
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	463 # Sort files nicely
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	464 outfiles.sort(
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	465 key=lambda s: int(re.match(r'^.*/(\d+)_metfrag_result.csv', s).group(1)))
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	466
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	467 print(outfiles)
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	468
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	469 # merge outputs
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	470 with open(args.result_pth, 'a') as merged_outfile:
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	471 dwriter = csv.DictWriter(merged_outfile, fieldnames=headers,
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	472 delimiter='\t', quotechar='"')
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	473 dwriter.writeheader()
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	474
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	475 for fn in outfiles:
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	476
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	477 with open(fn) as infile:
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	478 reader = csv.DictReader(infile, delimiter=',', quotechar='"')
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	479 for line in reader:
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	480 bewrite = True
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	481 for key, value in line.items():
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	482 # Filter when no MS/MS peak matched
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	483 if key == "ExplPeaks":
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	484 if float(args.pctexplpeak_thrshld) > 0 and \
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	485 "NA" in value:
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	486 bewrite = False
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	487 # Filter with a score threshold
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	488 elif key == "Score":
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	489 if float(value) <= float(args.score_thrshld):
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	490 bewrite = False
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	491 elif key == "NoExplPeaks":
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	492 nbfindpeak = float(value)
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	493 elif key == "NumberPeaksUsed":
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	494 totpeaks = float(value)
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	495 # Filter with a relative number of peak matched
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	496 try:
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	497 pctexplpeak = nbfindpeak / totpeaks * 100
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	498 except ZeroDivisionError:
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	499 bewrite = False
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	500 else:
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	501 if pctexplpeak < float(args.pctexplpeak_thrshld):
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	502 bewrite = False
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	503
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	504 # Write the line if it pass all filters
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	505 if bewrite:
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	506 bfn = os.path.basename(fn)
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	507 bfn = bfn.replace(".csv", "")
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	508 line['sample_name'] = paramds[bfn]['SampleName']
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	509 ad = paramds[bfn]['additional_details']
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	510
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	511 if args.MetFragDatabaseType == "MetChem":
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	512 # for some reason the metchem database option does
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	513 # not report the full inchikey (at least in the Bham
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	514 # setup. This ensures we always get the fully inchikey
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	515 line['InChIKey'] = '{}-{}-{}'.format(line['InChIKey1'],
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	516 line['InChIKey2'],
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	517 line['InChIKey3'])
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	518
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	519 line.update(ad)
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	520 dwriter.writerow(line)

Mercurial > repos > computational-metabolomics > metfrag

annotate metfrag.py @ 0:fd5c0b39569a draft