sirius_csifingerid: sirius_csifingerid.py annotate

annotate sirius_csifingerid.py @ 2:856b3761277d draft

"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d"

author	computational-metabolomics
date	Thu, 02 Jul 2020 11:01:45 -0400
parents	9e6bf7278257
children	4cbfd3d0a4c4

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 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	29 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	30 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	31 parser.add_argument('--minMSMSpeaks', default=1)
2 856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	32 parser.add_argument('--rank_filter', default=0)
0 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')
2 856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	34 parser.add_argument('-a', '--adducts', action='append', nargs=1,
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	35 required=False, default=[], help='Adducts used')
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	36
0 9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	37 args = parser.parse_args()
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	38 print(args)
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	39 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	40 print('Input file empty')
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	41 exit()
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	42
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	43 if args.temp_dir:
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	44 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	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
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	47 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	48 os.mkdir(wd)
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	49 else:
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	50 td = tempfile.mkdtemp()
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	51 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	52 os.mkdir(wd)
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	53
2 856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	54 print(args.adducts)
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	55 if args.adducts:
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	56 adducts_from_cli = [
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	57 a[0].replace('__ob__', '[').replace('__cb__', ']') for a in
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	58 args.adducts
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	59 ]
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	60 else:
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	61 adducts_from_cli = []
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	62
0 9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	63 ######################################################################
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	64 # 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	65 ######################################################################
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	66 regex_msp = {}
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	67 regex_msp['name'] = [r'^Name(?:=\|:)(.*)$']
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	68 regex_msp['polarity'] = [r'^ion.mode(?:=\|:)(.)$',
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	69 r'^ionization.mode(?:=\|:)(.)$',
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	70 r'^polarity(?:=\|:)(.*)$']
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	71 regex_msp['precursor_mz'] = [r'^precursor.m/z(?:=\|:)\s(\d[.,]?\d)$',
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	72 r'^precursor.mz(?:=\|:)\s(\d[.,]?\d)$']
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	73 regex_msp['precursor_type'] = [r'^precursor.type(?:=\|:)(.)$',
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	74 r'^adduct(?:=\|:)(.*)$',
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	75 r'^ADDUCTIONNAME(?:=\|:)(.*)$']
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	76 regex_msp['num_peaks'] = [r'^Num.Peaks(?:=\|:)\s(\d*)$']
2 856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	77 regex_msp['retention_time'] = [r'^RETENTION.TIME(?:=\|:)\s(.*)$',
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	78 r'^rt(?:=\|:)\s(.)$',
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	79 r'^time(?:=\|:)\s(.)$']
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	80 # From example winter_pos.mspy from kristian
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	81 regex_msp['AlignmentID'] = [r'^AlignmentID(?:=\|:)\s(.)$']
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	82
0 9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	83 regex_msp['msp'] = [r'^Name(?:=\|:)(.*)$'] # Flag for standard MSP format
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	84
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	85 regex_massbank = {}
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	86 regex_massbank['name'] = [r'^RECORD_TITLE:(.*)$']
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	87 regex_massbank['polarity'] = \
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	88 [r'^AC\$MASS_SPECTROMETRY:\s+ION_MODE\s+(.*)$']
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	89 regex_massbank['precursor_mz'] = \
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	90 [r'^MS\$FOCUSED_ION:\s+PRECURSOR_M/Z\s+(\d[.,]?\d)$']
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	91 regex_massbank['precursor_type'] = \
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	92 [r'^MS\$FOCUSED_ION:\s+PRECURSOR_TYPE\s+(.*)$']
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	93 regex_massbank['num_peaks'] = [r'^PK\$NUM_PEAK:\s+(\d*)']
2 856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	94 regex_massbank['retention_time'] = [
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	95 r'^AC\$CHROMATOGRAPHY:\s+RETENTION_TIME\s(\d\.?\d+).*']
0 9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	96 regex_massbank['cols'] = [r'^PK\$PEAK:\s+(.*)']
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	97 regex_massbank['massbank'] = [r'^RECORD_TITLE:(.*)$'] # Flag for massbank
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	98
2 856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	99
0 9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	100 if args.schema == 'msp':
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	101 meta_regex = regex_msp
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	102 elif args.schema == 'massbank':
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	103 meta_regex = regex_massbank
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	104 elif args.schema == 'auto':
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	105 # 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	106 # 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	107 # the name parameter
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	108 meta_regex = {}
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	109 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	110 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	111 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	112 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	113 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	114 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	115 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	116
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	117 print(meta_regex)
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	118
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	119 # 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	120 meta_info = {}
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	121
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	122
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	123 # 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	124 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	125 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	126 meta_info = {}
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	127 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	128 for reg in regexes:
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	129 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	130 if m:
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	131 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	132 return meta_info
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 ######################################################################
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	136 # Setup parameter dictionary
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	137 ######################################################################
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	138 def init_paramd(args):
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	139 paramd = defaultdict()
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	140 paramd["cli"] = {}
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	141 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	142 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	143 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	144 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	145 if args.polarity == 'positive':
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	146 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	147 elif args.polarity == 'negative':
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	148 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	149 else:
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	150 paramd["default_ion"] = ''
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	151
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	152 return paramd
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	153
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	154
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	155 ######################################################################
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	156 # 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	157 ######################################################################
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	158 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	159 # 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	160 # 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	161 # 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	162 # 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	163 # 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	164 paramd = init_paramd(args)
2 856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	165 meta_info = {k: v for k, v in meta_info.items() if k
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	166 not in ['msp', 'massbank', 'cols']}
0 9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	167
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	168 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	169 # 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	170 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	171 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	172 # 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	173 # 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	174 paramd['additional_details'] = {
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	175 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	176 meta_info['name'].split("\|")}
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	177 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	178 # 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	179 # 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	180 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	181 else:
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	182 # 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	183 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	184
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	185 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	186
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	187 paramd["cli"]["--output"] = \
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	188 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	189
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	190 # =============== 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	191 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	192 "{}_tmpspec.txt".format(spectrac))
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	193
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	194 # write spec file
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	195 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	196 for p in peaklist:
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	197 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	198
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	199 # =============== 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	200 # 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	201 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	202 paramd["cli"]["--ion"] = meta_info['precursor_type']
2 856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	203 adduct = meta_info['precursor_type']
0 9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	204 else:
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	205 if paramd["default_ion"]:
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	206 paramd["cli"]["--ion"] = paramd["default_ion"]
2 856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	207 adduct = paramd["default_ion"]
0 9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	208 else:
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	209 paramd["cli"]["--auto-charge"] = ''
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	210
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	211 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	212 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	213
2 856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	214 if not ('precursor_type' in paramd['additional_details'] or 'adduct'
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	215 in paramd['additional_details']):
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	216 # If possible always good to have the adduct in output as a column
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	217 paramd['additional_details']['adduct'] = adduct
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	218
0 9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	219 # ============== 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	220 cmd = "sirius --fingerid"
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	221 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	222 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	223 paramds[paramd["SampleName"]] = paramd
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	224
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	225 # =============== Run srius ==============================================
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	226 # 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	227 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	228
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	229 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	230 os.system(cmd)
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	231
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	232 return paramd, cmd
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	233
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	234
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	235 def work(cmds):
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	236 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	237
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 ######################################################################
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	240 # 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	241 ######################################################################
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	242 # 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	243 cmds = []
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	244 # 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	245 paramds = {}
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	246 # 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	247 spectrac = 0
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 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	250 # 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	251 pnumlines = 0
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	252 # 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	253 plinesread = 0
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	254 for line in infile:
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	255
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	256 line = line.strip()
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	257
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	258 if pnumlines == 0:
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	259
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	260 # ============== Extract metadata from MSP ========================
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	261 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	262
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	263 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	264 ('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	265 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	266 peaklist = []
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	267 plinesread = 0
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	268
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	269 elif plinesread < pnumlines:
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	270 # =============== Extract peaks from MSP ==========================
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	271 # .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	272 line = tuple(line.split())
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	273 # 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	274 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	275 plinesread += 1
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	276
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	277 peaklist.append(save_line)
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 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	280 # ======= Get sample name and additional details for output =======
2 856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	281 if adducts_from_cli:
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	282 for adduct in adducts_from_cli:
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	283 print(adduct)
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	284 spectrac += 1
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	285 meta_info['precursor_type'] = adduct
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	286 paramd, cmd = run_sirius(meta_info, peaklist, args, wd,
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	287 spectrac)
0 9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	288
2 856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	289 paramds[paramd["SampleName"]] = paramd
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	290 cmds.append(cmd)
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	291 else:
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	292 spectrac += 1
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	293 paramd, cmd = run_sirius(meta_info, peaklist, args, wd,
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	294 spectrac)
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	295
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	296 paramds[paramd["SampleName"]] = paramd
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	297 cmds.append(cmd)
0 9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	298
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	299 meta_info = {}
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	300 pnumlines = 0
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	301 plinesread = 0
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	302
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	303 # 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	304 # run metfrag on still
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	305
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	306 if plinesread and plinesread == pnumlines:
2 856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	307 if adducts_from_cli:
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	308 for adduct in adducts_from_cli:
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	309 print(adduct)
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	310 spectrac += 1
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	311 meta_info['precursor_type'] = adduct
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	312 paramd, cmd = run_sirius(meta_info, peaklist, args, wd,
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	313 spectrac)
0 9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	314
2 856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	315 paramds[paramd["SampleName"]] = paramd
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	316 cmds.append(cmd)
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	317 else:
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	318 spectrac += 1
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	319 paramd, cmd = run_sirius(meta_info, peaklist, args, wd,
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	320 spectrac)
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	321
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	322 paramds[paramd["SampleName"]] = paramd
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	323 cmds.append(cmd)
0 9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	324
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	325 # 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	326 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	327 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	328 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	329 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	330 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	331 pool.close()
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	332 pool.join()
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	333
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	334 ######################################################################
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	335 # 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	336 ######################################################################
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	337 # 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	338 # 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	339 # 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	340 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	341
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	342 # sort files nicely
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	343 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	344 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	345 s).group(1)))
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	346 print(outfiles)
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	347
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	348 if len(outfiles) == 0:
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	349 print('No results')
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	350 sys.exit()
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	351
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	352 headers = []
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	353 c = 0
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	354 for fn in outfiles:
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	355 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	356 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	357 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	358 headers.extend(next(reader))
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	359 else:
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	360 headers.extend(reader.next())
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	361 break
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	362
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	363 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	364
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	365 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	366 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	367 fieldnames=headers, delimiter='\t')
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	368 dwriter.writeheader()
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	369
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	370 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	371 print(fn)
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	372
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	373 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	374 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	375
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	376 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	377
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	378 for line in reader:
2 856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	379 if 0 < int(args.rank_filter) < int(line['rank']):
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	380 # filter out those annotations greater than rank filter
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	381 # If rank_filter is zero then skip
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	382 continue
0 9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	383 line.update(ad)
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	384 # 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	385 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	386
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	387 dwriter.writerow(line)

Mercurial > repos > computational-metabolomics > sirius_csifingerid

annotate sirius_csifingerid.py @ 2:856b3761277d draft