sirius_csifingerid: sirius_csifingerid.py annotate

annotate sirius_csifingerid.py @ 0:9e6bf7278257 draft

"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258"

author	computational-metabolomics
date	Wed, 05 Feb 2020 10:41:48 -0500
parents
children	856b3761277d

rev	line source
0 9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	1 from __future__ import absolute_import, print_function
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	2
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	3 import argparse
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	4 import csv
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	5 import glob
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	6 import multiprocessing
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	7 import os
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	8 import re
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	9 import sys
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	10 import tempfile
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	11 import uuid
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	12 from collections import defaultdict
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	13
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	14 import six
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	15
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	16 parser = argparse.ArgumentParser()
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	17 parser.add_argument('--input_pth')
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	18 parser.add_argument('--result_pth')
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	19 parser.add_argument('--database')
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	20 parser.add_argument('--profile')
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	21 parser.add_argument('--candidates')
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	22 parser.add_argument('--ppm_max')
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	23 parser.add_argument('--polarity')
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	24 parser.add_argument('--results_name')
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	25 parser.add_argument('--out_dir')
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	26 parser.add_argument('--tool_directory')
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	27 parser.add_argument('--temp_dir')
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	28
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	29 parser.add_argument('--meta_select_col', default='all')
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	30 parser.add_argument('--cores_top_level', default=1)
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	31 parser.add_argument('--chunks', default=1)
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	32 parser.add_argument('--minMSMSpeaks', default=1)
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	33 parser.add_argument('--schema', default='msp')
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	34 args = parser.parse_args()
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	35 print(args)
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	36 if os.stat(args.input_pth).st_size == 0:
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	37 print('Input file empty')
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	38 exit()
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	39
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	40 if args.temp_dir:
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	41 wd = os.path.join(args.temp_dir, 'temp')
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	42 os.mkdir(wd)
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	43
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	44 if not os.path.exists(wd):
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	45 os.mkdir(wd)
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	46 else:
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	47 td = tempfile.mkdtemp()
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	48 wd = os.path.join(td, str(uuid.uuid4()))
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	49 os.mkdir(wd)
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	50
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	51 ######################################################################
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	52 # Setup regular expressions for MSP parsing dictionary
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	53 ######################################################################
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	54 regex_msp = {}
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	55 regex_msp['name'] = [r'^Name(?:=\|:)(.*)$']
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	56 regex_msp['polarity'] = [r'^ion.mode(?:=\|:)(.)$',
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	57 r'^ionization.mode(?:=\|:)(.)$',
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	58 r'^polarity(?:=\|:)(.*)$']
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	59 regex_msp['precursor_mz'] = [r'^precursor.m/z(?:=\|:)\s(\d[.,]?\d)$',
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	60 r'^precursor.mz(?:=\|:)\s(\d[.,]?\d)$']
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	61 regex_msp['precursor_type'] = [r'^precursor.type(?:=\|:)(.)$',
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	62 r'^adduct(?:=\|:)(.*)$',
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	63 r'^ADDUCTIONNAME(?:=\|:)(.*)$']
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	64 regex_msp['num_peaks'] = [r'^Num.Peaks(?:=\|:)\s(\d*)$']
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	65 regex_msp['msp'] = [r'^Name(?:=\|:)(.*)$'] # Flag for standard MSP format
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	66
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	67 regex_massbank = {}
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	68 regex_massbank['name'] = [r'^RECORD_TITLE:(.*)$']
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	69 regex_massbank['polarity'] = \
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	70 [r'^AC\$MASS_SPECTROMETRY:\s+ION_MODE\s+(.*)$']
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	71 regex_massbank['precursor_mz'] = \
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	72 [r'^MS\$FOCUSED_ION:\s+PRECURSOR_M/Z\s+(\d[.,]?\d)$']
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	73 regex_massbank['precursor_type'] = \
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	74 [r'^MS\$FOCUSED_ION:\s+PRECURSOR_TYPE\s+(.*)$']
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	75 regex_massbank['num_peaks'] = [r'^PK\$NUM_PEAK:\s+(\d*)']
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	76 regex_massbank['cols'] = [r'^PK\$PEAK:\s+(.*)']
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	77 regex_massbank['massbank'] = [r'^RECORD_TITLE:(.*)$'] # Flag for massbank
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	78
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	79 if args.schema == 'msp':
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	80 meta_regex = regex_msp
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	81 elif args.schema == 'massbank':
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	82 meta_regex = regex_massbank
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	83 elif args.schema == 'auto':
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	84 # If auto we just check for all the available paramter names
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	85 # and then determine if Massbank or MSP based on
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	86 # the name parameter
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	87 meta_regex = {}
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	88 meta_regex.update(regex_massbank)
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	89 meta_regex['name'].extend(regex_msp['name'])
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	90 meta_regex['polarity'].extend(regex_msp['polarity'])
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	91 meta_regex['precursor_mz'].extend(regex_msp['precursor_mz'])
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	92 meta_regex['precursor_type'].extend(regex_msp['precursor_type'])
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	93 meta_regex['num_peaks'].extend(regex_msp['num_peaks'])
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	94 meta_regex['msp'] = regex_msp['msp']
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	95
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	96 print(meta_regex)
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	97
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	98 # this dictionary will store the meta data results form the MSp file
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	99 meta_info = {}
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	100
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	101
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	102 # function to extract the meta data using the regular expressions
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	103 def parse_meta(meta_regex, meta_info=None):
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	104 if meta_info is None:
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	105 meta_info = {}
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	106 for k, regexes in six.iteritems(meta_regex):
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	107 for reg in regexes:
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	108 m = re.search(reg, line, re.IGNORECASE)
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	109 if m:
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	110 meta_info[k] = '-'.join(m.groups()).strip()
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	111 return meta_info
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	112
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	113
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	114 ######################################################################
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	115 # Setup parameter dictionary
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	116 ######################################################################
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	117 def init_paramd(args):
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	118 paramd = defaultdict()
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	119 paramd["cli"] = {}
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	120 paramd["cli"]["--database"] = args.database
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	121 paramd["cli"]["--profile"] = args.profile
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	122 paramd["cli"]["--candidates"] = args.candidates
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	123 paramd["cli"]["--ppm-max"] = args.ppm_max
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	124 if args.polarity == 'positive':
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	125 paramd["default_ion"] = "[M+H]+"
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	126 elif args.polarity == 'negative':
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	127 paramd["default_ion"] = "[M-H]-"
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	128 else:
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	129 paramd["default_ion"] = ''
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	130
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	131 return paramd
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	132
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	133
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	134 ######################################################################
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	135 # Function to run sirius when all meta and spectra is obtained
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	136 ######################################################################
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	137 def run_sirius(meta_info, peaklist, args, wd, spectrac):
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	138 # Get sample details (if possible to extract) e.g. if created as part of
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	139 # the msPurity pipeline) choose between getting additional details to
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	140 # add as columns as either all meta data from msp, just details from the
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	141 # record name (i.e. when using msPurity and we have the columns
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	142 # coded into the name) or just the spectra index (spectrac)
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	143 paramd = init_paramd(args)
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	144
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	145 if args.meta_select_col == 'name':
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	146 # have additional column of just the name
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	147 paramd['additional_details'] = {'name': meta_info['name']}
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	148 elif args.meta_select_col == 'name_split':
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	149 # have additional columns split by "\|" and
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	150 # then on ":" e.g. MZ:100.2 \| RT:20 \| xcms_grp_id:1
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	151 paramd['additional_details'] = {
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	152 sm.split(":")[0].strip(): sm.split(":")[1].strip() for sm in
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	153 meta_info['name'].split("\|")}
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	154 elif args.meta_select_col == 'all':
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	155 # have additional columns based on all
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	156 # the meta information extracted from the MSP
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	157 paramd['additional_details'] = meta_info
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	158 else:
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	159 # Just have and index of the spectra in the MSP file
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	160 paramd['additional_details'] = {'spectra_idx': spectrac}
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	161
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	162 paramd["SampleName"] = "{}_sirius_result".format(spectrac)
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	163
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	164 paramd["cli"]["--output"] = \
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	165 os.path.join(wd, "{}_sirius_result".format(spectrac))
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	166
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	167 # =============== Output peaks to txt file ==============================
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	168 paramd["cli"]["--ms2"] = os.path.join(wd,
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	169 "{}_tmpspec.txt".format(spectrac))
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	170
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	171 # write spec file
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	172 with open(paramd["cli"]["--ms2"], 'w') as outfile:
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	173 for p in peaklist:
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	174 outfile.write(p[0] + "\t" + p[1] + "\n")
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	175
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	176 # =============== Update param based on MSP metadata ======================
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	177 # Replace param details with details from MSP if required
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	178 if 'precursor_type' in meta_info and meta_info['precursor_type']:
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	179 paramd["cli"]["--ion"] = meta_info['precursor_type']
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	180 else:
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	181 if paramd["default_ion"]:
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	182 paramd["cli"]["--ion"] = paramd["default_ion"]
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	183 else:
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	184 paramd["cli"]["--auto-charge"] = ''
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	185
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	186 if 'precursor_mz' in meta_info and meta_info['precursor_mz']:
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	187 paramd["cli"]["--precursor"] = meta_info['precursor_mz']
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	188
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	189 # ============== Create CLI cmd for metfrag ===============================
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	190 cmd = "sirius --fingerid"
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	191 for k, v in six.iteritems(paramd["cli"]):
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	192 cmd += " {} {}".format(str(k), str(v))
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	193 paramds[paramd["SampleName"]] = paramd
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	194
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	195 # =============== Run srius ==============================================
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	196 # Filter before process with a minimum number of MS/MS peaks
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	197 if plinesread >= float(args.minMSMSpeaks):
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	198
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	199 if int(args.cores_top_level) == 1:
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	200 os.system(cmd)
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	201
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	202 return paramd, cmd
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	203
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	204
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	205 def work(cmds):
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	206 return [os.system(cmd) for cmd in cmds]
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	207
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	208
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	209 ######################################################################
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	210 # Parse MSP file and run SIRIUS CLI
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	211 ######################################################################
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	212 # keep list of commands if performing in CLI in parallel
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	213 cmds = []
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	214 # keep a dictionary of all params
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	215 paramds = {}
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	216 # keep count of spectra (for uid)
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	217 spectrac = 0
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	218
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	219 with open(args.input_pth, "r") as infile:
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	220 # number of lines for the peaks
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	221 pnumlines = 0
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	222 # number of lines read for the peaks
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	223 plinesread = 0
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	224 for line in infile:
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	225
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	226 line = line.strip()
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	227
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	228 if pnumlines == 0:
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	229
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	230 # ============== Extract metadata from MSP ========================
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	231 meta_info = parse_meta(meta_regex, meta_info)
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	232
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	233 if ('massbank' in meta_info and 'cols' in meta_info) or \
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	234 ('msp' in meta_info and 'num_peaks' in meta_info):
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	235 pnumlines = int(meta_info['num_peaks'])
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	236 peaklist = []
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	237 plinesread = 0
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	238
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	239 elif plinesread < pnumlines:
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	240 # =============== Extract peaks from MSP ==========================
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	241 # .split() will split on any empty space (i.e. tab and space)
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	242 line = tuple(line.split())
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	243 # Keep only m/z and intensity, not relative intensity
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	244 save_line = tuple(line[0].split() + line[1].split())
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	245 plinesread += 1
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	246
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	247 peaklist.append(save_line)
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	248
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	249 elif plinesread and plinesread == pnumlines:
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	250 # ======= Get sample name and additional details for output =======
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	251 spectrac += 1
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	252 paramd, cmd = run_sirius(meta_info, peaklist, args, wd, spectrac)
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	253
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	254 paramds[paramd["SampleName"]] = paramd
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	255 cmds.append(cmd)
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	256
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	257 meta_info = {}
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	258 pnumlines = 0
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	259 plinesread = 0
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	260
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	261 # end of file. Check if there is a MSP spectra to
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	262 # run metfrag on still
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	263
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	264 if plinesread and plinesread == pnumlines:
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	265 paramd, cmd = run_sirius(meta_info, peaklist, args, wd, spectrac + 1)
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	266
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	267 paramds[paramd["SampleName"]] = paramd
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	268 cmds.append(cmd)
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	269
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	270 # Perform multiprocessing on command line call level
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	271 if int(args.cores_top_level) > 1:
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	272 cmds_chunks = [cmds[x:x + int(args.chunks)]
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	273 for x in list(range(0, len(cmds), int(args.chunks)))]
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	274 pool = multiprocessing.Pool(processes=int(args.cores_top_level))
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	275 pool.map(work, cmds_chunks)
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	276 pool.close()
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	277 pool.join()
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	278
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	279 ######################################################################
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	280 # Concatenate and filter the output
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	281 ######################################################################
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	282 # outputs might have different headers. Need to get a list of all the headers
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	283 # before we start merging the files outfiles = [os.path.join(wd, f) for f in
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	284 # glob.glob(os.path.join(wd, "*_metfrag_result.csv"))]
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	285 outfiles = glob.glob(os.path.join(wd, '', '', 'summary_csi_fingerid.csv'))
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	286
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	287 # sort files nicely
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	288 outfiles.sort(key=lambda s: int(re.match(r'^.*/('
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	289 r'\d+)././summary_csi_fingerid.csv',
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	290 s).group(1)))
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	291 print(outfiles)
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	292
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	293 if len(outfiles) == 0:
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	294 print('No results')
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	295 sys.exit()
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	296
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	297 headers = []
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	298 c = 0
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	299 for fn in outfiles:
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	300 with open(fn, 'r') as infile:
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	301 reader = csv.reader(infile, delimiter='\t')
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	302 if sys.version_info >= (3, 0):
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	303 headers.extend(next(reader))
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	304 else:
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	305 headers.extend(reader.next())
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	306 break
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	307
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	308 headers = list(paramd['additional_details'].keys()) + headers
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	309
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	310 with open(args.result_pth, 'a') as merged_outfile:
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	311 dwriter = csv.DictWriter(merged_outfile,
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	312 fieldnames=headers, delimiter='\t')
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	313 dwriter.writeheader()
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	314
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	315 for fn in sorted(outfiles):
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	316 print(fn)
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	317
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	318 with open(fn) as infile:
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	319 reader = csv.DictReader(infile, delimiter='\t')
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	320
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	321 ad = paramds[fn.split(os.sep)[-3]]['additional_details']
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	322
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	323 for line in reader:
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	324 line.update(ad)
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	325 # round score to 5 d.p.
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	326 line['score'] = round(float(line['score']), 5)
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	327
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	328 dwriter.writerow(line)

Mercurial > repos > computational-metabolomics > sirius_csifingerid

annotate sirius_csifingerid.py @ 0:9e6bf7278257 draft