sirius_csifingerid: sirius_csifingerid.py annotate

annotate sirius_csifingerid.py @ 7:e29e64ff50bb draft

"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit a2dd58962ce65259d79c7647efef1f0b18dce48c"

author	computational-metabolomics
date	Thu, 10 Feb 2022 16:05:47 +0000 (2022-02-10)
parents	96b077221201
children	8dac4cef0a22

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 import argparse
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	2 import csv
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	3 import glob
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	4 import multiprocessing
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	5 import os
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	6 import re
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	7 import sys
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	8 import tempfile
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	9 import uuid
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	10 from collections import defaultdict
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	11
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	12
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	13 parser = argparse.ArgumentParser()
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	14 parser.add_argument('--input_pth')
3 4cbfd3d0a4c4 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac" computational-metabolomics parents: 2 diff changeset	15 parser.add_argument('--canopus_result_pth')
4cbfd3d0a4c4 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac" computational-metabolomics parents: 2 diff changeset	16 parser.add_argument('--annotations_result_pth')
0 9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	17 parser.add_argument('--database')
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	18 parser.add_argument('--profile')
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	19 parser.add_argument('--candidates')
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	20 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	21 parser.add_argument('--polarity')
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	22 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	23 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	24 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	25 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	26 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	27 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	28 parser.add_argument('--chunks', default=1)
3 4cbfd3d0a4c4 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac" computational-metabolomics parents: 2 diff changeset	29 parser.add_argument('--min_MSMS_peaks', default=1)
2 856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	30 parser.add_argument('--rank_filter', default=0)
3 4cbfd3d0a4c4 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac" computational-metabolomics parents: 2 diff changeset	31 parser.add_argument('--confidence_filter', default=0)
0 9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	32 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	33 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	34 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	35
0 9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	36 args = parser.parse_args()
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	37 print(args)
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	38 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	39 print('Input file empty')
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	40 exit()
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	41
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	42 if args.temp_dir:
6 96b077221201 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit a1dfcf9fe850298b80f3738611835a3ef53e820a" computational-metabolomics parents: 4 diff changeset	43 wd = os.path.join(args.temp_dir, 'temp_'+str(uuid.uuid4()))
0 9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	44 os.mkdir(wd)
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	45
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	46 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	47 os.mkdir(wd)
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	48 else:
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	49 td = tempfile.mkdtemp()
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	50 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	51 os.mkdir(wd)
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	52
2 856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	53 print(args.adducts)
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	54 if args.adducts:
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	55 adducts_from_cli = [
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	56 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	57 args.adducts
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	58 ]
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	59 else:
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	60 adducts_from_cli = []
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	61
0 9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	62 ######################################################################
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	63 # 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	64 ######################################################################
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	65 regex_msp = {}
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	66 regex_msp['name'] = [r'^Name(?:=\|:)(.*)$']
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	67 regex_msp['polarity'] = [r'^ion.mode(?:=\|:)(.)$',
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	68 r'^ionization.mode(?:=\|:)(.)$',
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	69 r'^polarity(?:=\|:)(.*)$']
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	70 regex_msp['precursor_mz'] = [r'^precursor.m/z(?:=\|:)\s(\d[.,]?\d)$',
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	71 r'^precursor.mz(?:=\|:)\s(\d[.,]?\d)$']
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	72 regex_msp['precursor_type'] = [r'^precursor.type(?:=\|:)(.)$',
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	73 r'^adduct(?:=\|:)(.*)$',
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	74 r'^ADDUCTIONNAME(?:=\|:)(.*)$']
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	75 regex_msp['num_peaks'] = [r'^Num.Peaks(?:=\|:)\s(\d*)$']
2 856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	76 regex_msp['retention_time'] = [r'^RETENTION.TIME(?:=\|:)\s(.*)$',
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	77 r'^rt(?:=\|:)\s(.)$',
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	78 r'^time(?:=\|:)\s(.)$']
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	79 # From example winter_pos.mspy from kristian
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	80 regex_msp['AlignmentID'] = [r'^AlignmentID(?:=\|:)\s(.)$']
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	81
0 9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	82 regex_msp['msp'] = [r'^Name(?:=\|:)(.*)$'] # Flag for standard MSP format
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	83
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	84 regex_massbank = {}
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	85 regex_massbank['name'] = [r'^RECORD_TITLE:(.*)$']
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	86 regex_massbank['polarity'] = \
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	87 [r'^AC\$MASS_SPECTROMETRY:\s+ION_MODE\s+(.*)$']
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	88 regex_massbank['precursor_mz'] = \
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	89 [r'^MS\$FOCUSED_ION:\s+PRECURSOR_M/Z\s+(\d[.,]?\d)$']
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	90 regex_massbank['precursor_type'] = \
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	91 [r'^MS\$FOCUSED_ION:\s+PRECURSOR_TYPE\s+(.*)$']
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	92 regex_massbank['num_peaks'] = [r'^PK\$NUM_PEAK:\s+(\d*)']
2 856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	93 regex_massbank['retention_time'] = [
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	94 r'^AC\$CHROMATOGRAPHY:\s+RETENTION_TIME\s(\d\.?\d+).*']
0 9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	95 regex_massbank['cols'] = [r'^PK\$PEAK:\s+(.*)']
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	96 regex_massbank['massbank'] = [r'^RECORD_TITLE:(.*)$'] # Flag for massbank
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	97
2 856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	98
0 9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	99 if args.schema == 'msp':
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	100 meta_regex = regex_msp
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	101 elif args.schema == 'massbank':
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	102 meta_regex = regex_massbank
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	103 elif args.schema == 'auto':
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	104 # 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	105 # 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	106 # the name parameter
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	107 meta_regex = {}
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	108 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	109 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	110 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	111 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	112 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	113 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	114 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	115
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	116 print(meta_regex)
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	117
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	118 # 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	119 meta_info = {}
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	120
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 # 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	123 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	124 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	125 meta_info = {}
3 4cbfd3d0a4c4 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac" computational-metabolomics parents: 2 diff changeset	126 for k, regexes in meta_regex.items():
0 9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	127 for reg in regexes:
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	128 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	129 if m:
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	130 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	131 return meta_info
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	132
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	133
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	134 ######################################################################
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	135 # Setup parameter dictionary
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	136 ######################################################################
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	137 def init_paramd(args):
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	138 paramd = defaultdict()
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	139 paramd["cli"] = {}
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	140 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	141 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	142 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	143 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	144 if args.polarity == 'positive':
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	145 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	146 elif args.polarity == 'negative':
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	147 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	148 else:
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	149 paramd["default_ion"] = ''
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	150
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	151 return paramd
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	152
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 # 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	156 ######################################################################
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	157 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	158 # 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	159 # 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	160 # 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	161 # 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	162 # 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	163 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	164 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	165 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	166
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	167 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	168 # 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	169 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	170 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	171 # 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	172 # 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	173 paramd['additional_details'] = {
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	174 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	175 meta_info['name'].split("\|")}
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	176 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	177 # 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	178 # 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	179 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	180 else:
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	181 # 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	182 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	183
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	184 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	185
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	186 paramd["cli"]["--output"] = \
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	187 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	188
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	189 # =============== 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	190 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	191 "{}_tmpspec.txt".format(spectrac))
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	192
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	193 # write spec file
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	194 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	195 for p in peaklist:
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	196 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	197
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	198 # =============== 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	199 # 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	200 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	201 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	202 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	203 else:
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	204 if paramd["default_ion"]:
3 4cbfd3d0a4c4 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac" computational-metabolomics parents: 2 diff changeset	205 paramd["cli"]["--adduct"] = 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	206 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	207 else:
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	208 paramd["cli"]["--auto-charge"] = ''
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	209
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	210 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	211 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	212
2 856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	213 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	214 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	215 # 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	216 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	217
0 9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	218 # ============== Create CLI cmd for metfrag ===============================
3 4cbfd3d0a4c4 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac" computational-metabolomics parents: 2 diff changeset	219 cmd = "sirius --no-citations --ms2 {} --adduct {} --precursor {} -o {} " \
4cbfd3d0a4c4 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac" computational-metabolomics parents: 2 diff changeset	220 "formula -c {} --ppm-max {} --profile {} " \
4cbfd3d0a4c4 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac" computational-metabolomics parents: 2 diff changeset	221 "structure --database {} canopus".format(
4cbfd3d0a4c4 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac" computational-metabolomics parents: 2 diff changeset	222 paramd["cli"]["--ms2"],
4cbfd3d0a4c4 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac" computational-metabolomics parents: 2 diff changeset	223 adduct,
4cbfd3d0a4c4 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac" computational-metabolomics parents: 2 diff changeset	224 paramd["cli"]["--precursor"],
4cbfd3d0a4c4 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac" computational-metabolomics parents: 2 diff changeset	225 paramd["cli"]["--output"],
4cbfd3d0a4c4 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac" computational-metabolomics parents: 2 diff changeset	226 paramd["cli"]["--candidates"],
4cbfd3d0a4c4 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac" computational-metabolomics parents: 2 diff changeset	227 paramd["cli"]["--ppm-max"],
4cbfd3d0a4c4 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac" computational-metabolomics parents: 2 diff changeset	228 paramd["cli"]["--profile"],
4cbfd3d0a4c4 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac" computational-metabolomics parents: 2 diff changeset	229 paramd["cli"]["--database"]
4cbfd3d0a4c4 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac" computational-metabolomics parents: 2 diff changeset	230 )
4cbfd3d0a4c4 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac" computational-metabolomics parents: 2 diff changeset	231 print(cmd)
0 9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	232 paramds[paramd["SampleName"]] = paramd
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 # =============== Run srius ==============================================
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	235 # Filter before process with a minimum number of MS/MS peaks
3 4cbfd3d0a4c4 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac" computational-metabolomics parents: 2 diff changeset	236 if plinesread >= float(args.min_MSMS_peaks):
0 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 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	239 os.system(cmd)
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	240
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	241 return paramd, cmd
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	242
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	243
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	244 def work(cmds):
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	245 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	246
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	247
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 # 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	250 ######################################################################
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	251 # 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	252 cmds = []
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	253 # 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	254 paramds = {}
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	255 # 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	256 spectrac = 0
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 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	259 # 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	260 pnumlines = 0
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	261 # 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	262 plinesread = 0
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	263 for line in infile:
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	264
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	265 line = line.strip()
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	266
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	267 if pnumlines == 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 # ============== Extract metadata from MSP ========================
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	270 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	271
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	272 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	273 ('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	274 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	275 peaklist = []
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	276 plinesread = 0
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	277
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	278 elif plinesread < pnumlines:
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	279 # =============== Extract peaks from MSP ==========================
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	280 # .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	281 line = tuple(line.split())
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	282 # 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	283 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	284 plinesread += 1
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	285
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	286 peaklist.append(save_line)
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	287
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	288 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	289 # ======= 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	290 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	291 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	292 print(adduct)
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	293 spectrac += 1
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	294 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	295 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	296 spectrac)
0 9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	297
2 856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	298 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	299 cmds.append(cmd)
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	300 else:
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	301 spectrac += 1
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	302 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	303 spectrac)
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	304
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	305 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	306 cmds.append(cmd)
0 9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	307
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	308 meta_info = {}
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	309 pnumlines = 0
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	310 plinesread = 0
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	311
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	312 # 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	313 # run metfrag on still
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	314
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	315 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	316 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	317 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	318 print(adduct)
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	319 spectrac += 1
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	320 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	321 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	322 spectrac)
0 9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	323
2 856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	324 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	325 cmds.append(cmd)
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	326 else:
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	327 spectrac += 1
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	328 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	329 spectrac)
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	330
856b3761277d "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 3e3dee9a853b6133cf089b3c063f53c52b39463d" computational-metabolomics parents: 0 diff changeset	331 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	332 cmds.append(cmd)
0 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 # 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	335 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	336 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	337 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	338 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	339 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	340 pool.close()
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	341 pool.join()
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	342
3 4cbfd3d0a4c4 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac" computational-metabolomics parents: 2 diff changeset	343
0 9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	344 ######################################################################
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	345 # 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	346 ######################################################################
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	347 # 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	348 # 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	349 # glob.glob(os.path.join(wd, "*_metfrag_result.csv"))]
3 4cbfd3d0a4c4 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac" computational-metabolomics parents: 2 diff changeset	350 def concat_output(filename, result_pth,
7 e29e64ff50bb "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit a2dd58962ce65259d79c7647efef1f0b18dce48c" computational-metabolomics parents: 6 diff changeset	351 rank_filter, confidence_filter):
3 4cbfd3d0a4c4 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac" computational-metabolomics parents: 2 diff changeset	352 outfiles = glob.glob(os.path.join(wd, '', '{}'.format(filename)))
0 9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	353
3 4cbfd3d0a4c4 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac" computational-metabolomics parents: 2 diff changeset	354 # sort files nicely
4cbfd3d0a4c4 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac" computational-metabolomics parents: 2 diff changeset	355 outfiles.sort(key=lambda s: int(re.match(r'^.*/('
4cbfd3d0a4c4 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac" computational-metabolomics parents: 2 diff changeset	356 r'\d+).*{}'.format(filename),
4cbfd3d0a4c4 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac" computational-metabolomics parents: 2 diff changeset	357 s).group(1)))
4cbfd3d0a4c4 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac" computational-metabolomics parents: 2 diff changeset	358 print(outfiles)
4cbfd3d0a4c4 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac" computational-metabolomics parents: 2 diff changeset	359
4cbfd3d0a4c4 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac" computational-metabolomics parents: 2 diff changeset	360 if len(outfiles) == 0:
4cbfd3d0a4c4 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac" computational-metabolomics parents: 2 diff changeset	361 print('No results')
4cbfd3d0a4c4 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac" computational-metabolomics parents: 2 diff changeset	362 sys.exit()
4cbfd3d0a4c4 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac" computational-metabolomics parents: 2 diff changeset	363
4cbfd3d0a4c4 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac" computational-metabolomics parents: 2 diff changeset	364 headers = []
0 9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	365
3 4cbfd3d0a4c4 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac" computational-metabolomics parents: 2 diff changeset	366 for fn in outfiles:
4cbfd3d0a4c4 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac" computational-metabolomics parents: 2 diff changeset	367 with open(fn, 'r') as infile:
4cbfd3d0a4c4 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac" computational-metabolomics parents: 2 diff changeset	368 reader = csv.reader(infile, delimiter='\t')
4cbfd3d0a4c4 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac" computational-metabolomics parents: 2 diff changeset	369 if sys.version_info >= (3, 0):
4cbfd3d0a4c4 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac" computational-metabolomics parents: 2 diff changeset	370 headers.extend(next(reader))
4cbfd3d0a4c4 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac" computational-metabolomics parents: 2 diff changeset	371 else:
4cbfd3d0a4c4 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac" computational-metabolomics parents: 2 diff changeset	372 headers.extend(reader.next())
4cbfd3d0a4c4 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac" computational-metabolomics parents: 2 diff changeset	373 break
4cbfd3d0a4c4 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac" computational-metabolomics parents: 2 diff changeset	374
4cbfd3d0a4c4 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac" computational-metabolomics parents: 2 diff changeset	375 headers = list(paramd['additional_details'].keys()) + headers
0 9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	376
3 4cbfd3d0a4c4 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac" computational-metabolomics parents: 2 diff changeset	377 with open(result_pth, 'a') as merged_outfile:
4cbfd3d0a4c4 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac" computational-metabolomics parents: 2 diff changeset	378 dwriter = csv.DictWriter(merged_outfile,
4cbfd3d0a4c4 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac" computational-metabolomics parents: 2 diff changeset	379 fieldnames=headers, delimiter='\t')
4cbfd3d0a4c4 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac" computational-metabolomics parents: 2 diff changeset	380 dwriter.writeheader()
4cbfd3d0a4c4 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac" computational-metabolomics parents: 2 diff changeset	381
4cbfd3d0a4c4 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac" computational-metabolomics parents: 2 diff changeset	382 for fn in sorted(outfiles):
4cbfd3d0a4c4 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac" computational-metabolomics parents: 2 diff changeset	383 print(fn)
4cbfd3d0a4c4 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac" computational-metabolomics parents: 2 diff changeset	384
4cbfd3d0a4c4 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac" computational-metabolomics parents: 2 diff changeset	385 with open(fn) as infile:
4cbfd3d0a4c4 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac" computational-metabolomics parents: 2 diff changeset	386 reader = csv.DictReader(infile, delimiter='\t')
0 9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	387
3 4cbfd3d0a4c4 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac" computational-metabolomics parents: 2 diff changeset	388 ad = paramds[fn.split(os.sep)[-2]]['additional_details']
4cbfd3d0a4c4 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac" computational-metabolomics parents: 2 diff changeset	389
4cbfd3d0a4c4 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac" computational-metabolomics parents: 2 diff changeset	390 for line in reader:
4 8fb51147d15e "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit fdeefc696443bc3aadf08d4df7226cb6f91d0388" computational-metabolomics parents: 3 diff changeset	391 if 'rank' in line \
8fb51147d15e "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit fdeefc696443bc3aadf08d4df7226cb6f91d0388" computational-metabolomics parents: 3 diff changeset	392 and 0 < int(rank_filter) < int(line['rank']):
3 4cbfd3d0a4c4 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac" computational-metabolomics parents: 2 diff changeset	393 # filter out those annotations greater than rank filter
4cbfd3d0a4c4 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac" computational-metabolomics parents: 2 diff changeset	394 # If rank_filter is zero then skip
4cbfd3d0a4c4 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac" computational-metabolomics parents: 2 diff changeset	395 continue
0 9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	396
6 96b077221201 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit a1dfcf9fe850298b80f3738611835a3ef53e820a" computational-metabolomics parents: 4 diff changeset	397 if 'ConfidenceScore' in line:
96b077221201 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit a1dfcf9fe850298b80f3738611835a3ef53e820a" computational-metabolomics parents: 4 diff changeset	398 if isinstance(line['ConfidenceScore'], str):
96b077221201 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit a1dfcf9fe850298b80f3738611835a3ef53e820a" computational-metabolomics parents: 4 diff changeset	399 # Value is NA or N/A
96b077221201 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit a1dfcf9fe850298b80f3738611835a3ef53e820a" computational-metabolomics parents: 4 diff changeset	400 continue
96b077221201 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit a1dfcf9fe850298b80f3738611835a3ef53e820a" computational-metabolomics parents: 4 diff changeset	401
96b077221201 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit a1dfcf9fe850298b80f3738611835a3ef53e820a" computational-metabolomics parents: 4 diff changeset	402 if (0 < float(confidence_filter)
96b077221201 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit a1dfcf9fe850298b80f3738611835a3ef53e820a" computational-metabolomics parents: 4 diff changeset	403 and float(line['ConfidenceScore'])
96b077221201 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit a1dfcf9fe850298b80f3738611835a3ef53e820a" computational-metabolomics parents: 4 diff changeset	404 < float(confidence_filter)):
96b077221201 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit a1dfcf9fe850298b80f3738611835a3ef53e820a" computational-metabolomics parents: 4 diff changeset	405 # filter out those annotations that are less than
96b077221201 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit a1dfcf9fe850298b80f3738611835a3ef53e820a" computational-metabolomics parents: 4 diff changeset	406 # the confidence filter value
96b077221201 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit a1dfcf9fe850298b80f3738611835a3ef53e820a" computational-metabolomics parents: 4 diff changeset	407 continue
3 4cbfd3d0a4c4 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac" computational-metabolomics parents: 2 diff changeset	408 line.update(ad)
0 9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	409
3 4cbfd3d0a4c4 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac" computational-metabolomics parents: 2 diff changeset	410 dwriter.writerow(line)
0 9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	411
9e6bf7278257 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit 1d1b37a070f895c94069819237199c768da27258" computational-metabolomics parents: diff changeset	412
4 8fb51147d15e "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit fdeefc696443bc3aadf08d4df7226cb6f91d0388" computational-metabolomics parents: 3 diff changeset	413 concat_output('compound_identifications.tsv',
8fb51147d15e "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit fdeefc696443bc3aadf08d4df7226cb6f91d0388" computational-metabolomics parents: 3 diff changeset	414 args.annotations_result_pth,
3 4cbfd3d0a4c4 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac" computational-metabolomics parents: 2 diff changeset	415 args.rank_filter,
6 96b077221201 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit a1dfcf9fe850298b80f3738611835a3ef53e820a" computational-metabolomics parents: 4 diff changeset	416 args.confidence_filter)
4 8fb51147d15e "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit fdeefc696443bc3aadf08d4df7226cb6f91d0388" computational-metabolomics parents: 3 diff changeset	417 concat_output('canopus_summary.tsv',
8fb51147d15e "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit fdeefc696443bc3aadf08d4df7226cb6f91d0388" computational-metabolomics parents: 3 diff changeset	418 args.canopus_result_pth,
3 4cbfd3d0a4c4 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit e4bc02f97a21da7556d1b76e5338ede3a9031fac" computational-metabolomics parents: 2 diff changeset	419 0,
6 96b077221201 "planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit a1dfcf9fe850298b80f3738611835a3ef53e820a" computational-metabolomics parents: 4 diff changeset	420 0)

Mercurial > repos > computational-metabolomics > sirius_csifingerid

annotate sirius_csifingerid.py @ 7:e29e64ff50bb draft