metfrag: metfrag.py annotate

annotate metfrag.py @ 2:f151ee133612 draft default tip

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

author	computational-metabolomics
date	Tue, 14 Jul 2020 07:41:53 -0400
parents	9ee2e2ceb2c9
children

rev	line source
0 fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	1 from __future__ import absolute_import, print_function
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	2
2 f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	3 try:
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	4 from configparser import ConfigParser
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	5 except ImportError as e:
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	6 print(e)
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	7 from ConfigParser import ConfigParser
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	8
0 fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	9 import argparse
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	10 import csv
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	11 import glob
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	12 import multiprocessing
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	13 import os
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	14 import re
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	15 import shutil
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	16 import sys
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	17 import tempfile
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	18 from collections import defaultdict
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	19
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	20 import six
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	21
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	22
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	23 # function to extract the meta data using the regular expressions
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	24 def parse_meta(meta_regex, meta_info=None):
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	25 if meta_info is None:
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	26 meta_info = {}
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	27 for k, regexes in six.iteritems(meta_regex):
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	28 for reg in regexes:
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	29 m = re.search(reg, line, re.IGNORECASE)
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	30 if m:
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	31 meta_info[k] = '-'.join(m.groups()).strip()
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	32 return meta_info
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	33
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	34
2 f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	35 def get_meta_regex(schema):
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	36 ######################################################################
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	37 # Setup regular expressions for MSP parsing dictionary
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	38 ######################################################################
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	39 regex_msp = {}
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	40 regex_msp['name'] = [r'^Name(?:=\|:)(.*)$']
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	41 regex_msp['polarity'] = [r'^ion.mode(?:=\|:)(.)$',
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	42 r'^ionization.mode(?:=\|:)(.)$',
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	43 r'^polarity(?:=\|:)(.*)$']
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	44 regex_msp['precursor_mz'] = [r'^precursor.m/z(?:=\|:)\s(\d[.,]?\d)$',
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	45 r'^precursor.mz(?:=\|:)\s(\d[.,]?\d)$']
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	46 regex_msp['precursor_type'] = [r'^precursor.type(?:=\|:)(.)$',
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	47 r'^adduct(?:=\|:)(.*)$',
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	48 r'^ADDUCTIONNAME(?:=\|:)(.*)$']
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	49
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	50 regex_msp['retention_time'] = [r'^RETENTION.TIME(?:=\|:)\s(.*)$',
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	51 r'^rt(?:=\|:)\s(.)$',
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	52 r'^time(?:=\|:)\s(.)$']
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	53 # From example winter_pos.mspy from kristian
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	54 regex_msp['AlignmentID'] = [r'^AlignmentID(?:=\|:)\s(.)$']
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	55
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	56 regex_msp['num_peaks'] = [r'^Num.Peaks(?:=\|:)\s(\d*)$']
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	57 regex_msp['msp'] = [r'^Name(?:=\|:)(.*)$'] # Flag for standard MSP format
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	58
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	59 regex_massbank = {}
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	60 regex_massbank['name'] = [r'^RECORD_TITLE:(.*)$']
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	61 regex_massbank['polarity'] = [
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	62 r'^AC\$MASS_SPECTROMETRY:\s+ION_MODE\s+(.*)$']
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	63 regex_massbank['precursor_mz'] = [
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	64 r'^MS\$FOCUSED_ION:\s+PRECURSOR_M/Z\s+(\d[.,]?\d)$']
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	65 regex_massbank['precursor_type'] = [
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	66 r'^MS\$FOCUSED_ION:\s+PRECURSOR_TYPE\s+(.*)$']
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	67 regex_massbank['retention_time'] = [
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	68 r'^AC\$CHROMATOGRAPHY:\s+RETENTION_TIME\s(\d\.?\d+).*']
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	69
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	70 regex_massbank['num_peaks'] = [r'^PK\$NUM_PEAK:\s+(\d*)']
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	71 regex_massbank['cols'] = [r'^PK\$PEAK:\s+(.*)']
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	72 regex_massbank['massbank'] = [
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	73 r'^RECORD_TITLE:(.*)$'] # Flag for massbank format
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	74
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	75 if schema == 'msp':
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	76 meta_regex = regex_msp
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	77 elif schema == 'massbank':
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	78 meta_regex = regex_massbank
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	79 elif schema == 'auto':
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	80 # If auto we just check for all the available paramter names and then
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	81 # determine if Massbank or MSP based on the name parameter
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	82 meta_regex = {}
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	83 meta_regex.update(regex_massbank)
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	84 meta_regex['name'].extend(regex_msp['name'])
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	85 meta_regex['polarity'].extend(regex_msp['polarity'])
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	86 meta_regex['precursor_mz'].extend(regex_msp['precursor_mz'])
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	87 meta_regex['precursor_type'].extend(regex_msp['precursor_type'])
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	88 meta_regex['num_peaks'].extend(regex_msp['num_peaks'])
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	89 meta_regex['retention_time'].extend(regex_msp['retention_time'])
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	90 meta_regex['AlignmentID'] = regex_msp['AlignmentID']
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	91 meta_regex['msp'] = regex_msp['msp']
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	92
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	93 else:
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	94 sys.exit("No schema selected")
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	95
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	96 return meta_regex
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	97
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	98
0 fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	99 ######################################################################
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	100 # Setup parameter dictionary
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	101 ######################################################################
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	102 def init_paramd(args):
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	103 paramd = defaultdict()
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	104
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	105 paramd["MetFragDatabaseType"] = args.MetFragDatabaseType
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	106
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	107 if args.MetFragDatabaseType == "LocalCSV":
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	108 paramd["LocalDatabasePath"] = args.LocalDatabasePath
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	109 elif args.MetFragDatabaseType == "MetChem":
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	110 paramd["LocalMetChemDatabase"] = \
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	111 config.get('MetChem', 'LocalMetChemDatabase')
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	112 paramd["LocalMetChemDatabasePortNumber"] = \
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	113 config.get('MetChem', 'LocalMetChemDatabasePortNumber')
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	114 paramd["LocalMetChemDatabaseServerIp"] = \
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	115 args.LocalMetChemDatabaseServerIp
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	116 paramd["LocalMetChemDatabaseUser"] = \
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	117 config.get('MetChem', 'LocalMetChemDatabaseUser')
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	118 paramd["LocalMetChemDatabasePassword"] = \
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	119 config.get('MetChem', 'LocalMetChemDatabasePassword')
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	120
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	121 paramd["FragmentPeakMatchAbsoluteMassDeviation"] = \
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	122 args.FragmentPeakMatchAbsoluteMassDeviation
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	123 paramd["FragmentPeakMatchRelativeMassDeviation"] = \
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	124 args.FragmentPeakMatchRelativeMassDeviation
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	125 paramd["DatabaseSearchRelativeMassDeviation"] = \
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	126 args.DatabaseSearchRelativeMassDeviation
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	127 paramd["SampleName"] = ''
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	128 paramd["ResultsPath"] = os.path.join(wd)
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	129
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	130 if args.polarity == "pos":
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	131 paramd["IsPositiveIonMode"] = True
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	132 paramd["PrecursorIonModeDefault"] = "1"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	133 paramd["PrecursorIonMode"] = "1"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	134 paramd["nm_mass_diff_default"] = 1.007276
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	135 else:
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	136 paramd["IsPositiveIonMode"] = False
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	137 paramd["PrecursorIonModeDefault"] = "-1"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	138 paramd["PrecursorIonMode"] = "-1"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	139 paramd["nm_mass_diff_default"] = -1.007276
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	140
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	141 paramd["MetFragCandidateWriter"] = "CSV"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	142 paramd["NumberThreads"] = args.NumberThreads
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	143
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	144 if args.ScoreSuspectLists:
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	145 paramd["ScoreSuspectLists"] = args.ScoreSuspectLists
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	146
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	147 paramd["MetFragScoreTypes"] = args.MetFragScoreTypes
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	148 paramd["MetFragScoreWeights"] = args.MetFragScoreWeights
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	149
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	150 dct_filter = defaultdict()
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	151 filterh = []
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	152
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	153 if args.UnconnectedCompoundFilter:
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	154 filterh.append('UnconnectedCompoundFilter')
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	155
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	156 if args.IsotopeFilter:
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	157 filterh.append('IsotopeFilter')
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	158
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	159 if args.FilterMinimumElements:
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	160 filterh.append('MinimumElementsFilter')
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	161 dct_filter['FilterMinimumElements'] = args.FilterMinimumElements
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	162
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	163 if args.FilterMaximumElements:
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	164 filterh.append('MaximumElementsFilter')
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	165 dct_filter['FilterMaximumElements'] = args.FilterMaximumElements
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	166
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	167 if args.FilterSmartsInclusionList:
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	168 filterh.append('SmartsSubstructureInclusionFilter')
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	169 dct_filter[
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	170 'FilterSmartsInclusionList'] = args.FilterSmartsInclusionList
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	171
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	172 if args.FilterSmartsExclusionList:
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	173 filterh.append('SmartsSubstructureExclusionFilter')
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	174 dct_filter[
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	175 'FilterSmartsExclusionList'] = args.FilterSmartsExclusionList
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	176
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	177 # My understanding is that both 'ElementInclusionExclusiveFilter'
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	178 # and 'ElementExclusionFilter' use 'FilterIncludedElements'
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	179 if args.FilterIncludedExclusiveElements:
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	180 filterh.append('ElementInclusionExclusiveFilter')
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	181 dct_filter[
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	182 'FilterIncludedElements'] = args.FilterIncludedExclusiveElements
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	183
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	184 if args.FilterIncludedElements:
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	185 filterh.append('ElementInclusionFilter')
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	186 dct_filter['FilterIncludedElements'] = args.FilterIncludedElements
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	187
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	188 if args.FilterExcludedElements:
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	189 filterh.append('ElementExclusionFilter')
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	190 dct_filter['FilterExcludedElements'] = args.FilterExcludedElements
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	191
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	192 if filterh:
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	193 fcmds = ','.join(filterh) + ' '
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	194 for k, v in six.iteritems(dct_filter):
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	195 fcmds += "{0}={1} ".format(str(k), str(v))
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	196
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	197 paramd["MetFragPreProcessingCandidateFilter"] = fcmds
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	198
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	199 return paramd
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	200
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	201
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	202 ######################################################################
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	203 # Function to run metfrag when all metainfo and peaks have been parsed
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	204 ######################################################################
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	205 def run_metfrag(meta_info, peaklist, args, wd, spectrac, adduct_types):
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	206 # Get sample details (if possible to extract) e.g. if created as part of
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	207 # the msPurity pipeline) choose between getting additional details to add
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	208 # as columns as either all meta data from msp, just details from the
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	209 # record name (i.e. when using msPurity and we have the columns coded into
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	210 # the name) or just the spectra index (spectrac)].
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	211 # Returns the parameters used and the command line call
2 f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	212 meta_info = {k: v for k, v in meta_info.items() if k
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	213 not in ['msp', 'massbank', 'cols']}
0 fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	214
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	215 paramd = init_paramd(args)
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	216 if args.meta_select_col == 'name':
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	217 # have additional column of just the name
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	218 paramd['additional_details'] = {'name': meta_info['name']}
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	219 elif args.meta_select_col == 'name_split':
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	220 # have additional columns split by "\|" and
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	221 # then on ":" e.g. MZ:100.2 \| RT:20 \| xcms_grp_id:1
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	222 paramd['additional_details'] = {
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	223 sm.split(":")[0].strip(): sm.split(":")[1].strip() for sm in
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	224 meta_info['name'].split("\|")}
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	225 elif args.meta_select_col == 'all':
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	226 # have additional columns based on all the meta information
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	227 # extracted from the MSP
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	228 paramd['additional_details'] = meta_info
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	229 else:
2 f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	230 # Just have an index of the spectra in the MSP file
0 fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	231 paramd['additional_details'] = {'spectra_idx': spectrac}
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	232
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	233 paramd["SampleName"] = "{}_metfrag_result".format(spectrac)
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	234
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	235 # =============== Output peaks to txt file ==============================
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	236 paramd["PeakListPath"] = os.path.join(wd,
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	237 "{}_tmpspec.txt".format(spectrac))
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	238
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	239 # write spec file
2 f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	240
0 fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	241 with open(paramd["PeakListPath"], 'w') as outfile:
2 f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	242 pls = ''
0 fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	243 for p in peaklist:
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	244 outfile.write(p[0] + "\t" + p[1] + "\n")
2 f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	245 pls = pls + '{}_{};'.format(p[0], p[1])
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	246
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	247 if args.output_cl:
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	248 peaklist_str = pls[:-1]
0 fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	249
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	250 # =============== Update param based on MSP metadata ======================
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	251 # Replace param details with details from MSP if required
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	252 if 'precursor_type' in meta_info and \
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	253 meta_info['precursor_type'] in adduct_types:
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	254 adduct = meta_info['precursor_type']
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	255 nm = float(meta_info['precursor_mz']) - adduct_types[
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	256 meta_info['precursor_type']]
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	257 paramd["PrecursorIonMode"] = \
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	258 int(round(adduct_types[meta_info['precursor_type']], 0))
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	259 elif not args.skip_invalid_adducts:
2 f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	260 inv_adduct_types = {int(round(v, 0)): k for k, v in
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	261 six.iteritems(adduct_types)}
0 fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	262 adduct = inv_adduct_types[int(paramd['PrecursorIonModeDefault'])]
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	263 paramd["PrecursorIonMode"] = paramd['PrecursorIonModeDefault']
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	264 nm = float(meta_info['precursor_mz']) - paramd['nm_mass_diff_default']
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	265 else:
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	266 print('Skipping {}'.format(paramd["SampleName"]))
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	267 return '', ''
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	268
2 f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	269 if not ('precursor_type' in paramd['additional_details'] or 'adduct'
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	270 in paramd['additional_details']):
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	271 paramd['additional_details']['adduct'] = adduct
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	272
0 fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	273 paramd["NeutralPrecursorMass"] = nm
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	274
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	275 # ============== Create CLI cmd for metfrag ===============================
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	276 cmd = "metfrag"
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	277 for k, v in six.iteritems(paramd):
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	278 if k not in ['PrecursorIonModeDefault', 'nm_mass_diff_default',
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	279 'additional_details']:
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	280 cmd += " {}={}".format(str(k), str(v))
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	281
2 f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	282 if args.output_cl:
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	283 cli_str = '{} PeakListString={}'.format(cmd, peaklist_str)
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	284 paramd['additional_details']['MetFragCLIString'] = cli_str
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	285
0 fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	286 # ============== Run metfrag ==============================================
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	287 # print(cmd)
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	288 # Filter before process with a minimum number of MS/MS peaks
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	289 if plinesread >= float(args.minMSMSpeaks):
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	290
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	291 if int(args.cores_top_level) == 1:
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	292 os.system(cmd)
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	293
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	294 return paramd, cmd
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	295
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	296
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	297 def work(cmds):
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	298 return [os.system(cmd) for cmd in cmds]
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	299
fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	300
2 f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	301 if __name__ == "__main__":
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	302 print(sys.version)
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	303
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	304 parser = argparse.ArgumentParser()
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	305 parser.add_argument('--input_pth')
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	306 parser.add_argument('--result_pth', default='metfrag_result.csv')
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	307
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	308 parser.add_argument('--temp_dir')
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	309 parser.add_argument('--polarity', default='pos')
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	310 parser.add_argument('--minMSMSpeaks', default=1)
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	311
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	312 parser.add_argument('--MetFragDatabaseType', default='PubChem')
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	313 parser.add_argument('--LocalDatabasePath', default='')
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	314 parser.add_argument('--LocalMetChemDatabaseServerIp', default='')
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	315
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	316 parser.add_argument('--DatabaseSearchRelativeMassDeviation', default=5)
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	317 parser.add_argument('--FragmentPeakMatchRelativeMassDeviation', default=10)
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	318 parser.add_argument('--FragmentPeakMatchAbsoluteMassDeviation',
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	319 default=0.001)
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	320 parser.add_argument('--NumberThreads', default=1)
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	321 parser.add_argument('--UnconnectedCompoundFilter', action='store_true')
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	322 parser.add_argument('--IsotopeFilter', action='store_true')
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	323
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	324 parser.add_argument('--FilterMinimumElements', default='')
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	325 parser.add_argument('--FilterMaximumElements', default='')
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	326 parser.add_argument('--FilterSmartsInclusionList', default='')
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	327 parser.add_argument('--FilterSmartsExclusionList', default='')
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	328 parser.add_argument('--FilterIncludedElements', default='')
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	329 parser.add_argument('--FilterExcludedElements', default='')
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	330 parser.add_argument('--FilterIncludedExclusiveElements', default='')
0 fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	331
2 f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	332 parser.add_argument('--score_thrshld', default=0)
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	333 parser.add_argument('--pctexplpeak_thrshld', default=0)
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	334 parser.add_argument('--schema')
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	335 parser.add_argument('--cores_top_level', default=1)
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	336 parser.add_argument('--chunks', default=1)
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	337 parser.add_argument('--meta_select_col', default='name')
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	338 parser.add_argument('--skip_invalid_adducts', action='store_true')
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	339 parser.add_argument('--output_cl', action='store_true')
0 fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	340
2 f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	341 parser.add_argument('--ScoreSuspectLists', default='')
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	342 parser.add_argument('--MetFragScoreTypes',
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	343 default="FragmenterScore,OfflineMetFusionScore")
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	344 parser.add_argument('--MetFragScoreWeights', default="1.0,1.0")
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	345 parser.add_argument('-a', '--adducts', action='append', nargs=1,
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	346 required=False, default=[], help='Adducts used')
0 fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	347
2 f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	348 args = parser.parse_args()
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	349 print(args)
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	350 config = ConfigParser()
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	351 config.read(
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	352 os.path.join(os.path.dirname(os.path.abspath(__file__)), 'config.ini'))
0 fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	353
2 f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	354 if os.stat(args.input_pth).st_size == 0:
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	355 print('Input file empty')
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	356 exit()
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	357
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	358 # Create temporary working directory
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	359 if args.temp_dir:
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	360 wd = args.temp_dir
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	361 else:
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	362 wd = tempfile.mkdtemp()
0 fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	363
2 f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	364 if os.path.exists(wd):
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	365 shutil.rmtree(wd)
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	366 os.makedirs(wd)
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	367 else:
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	368 os.makedirs(wd)
0 fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	369
2 f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	370 meta_regex = get_meta_regex(args.schema)
0 fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	371
2 f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	372 adduct_types = {
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	373 '[M+H]+': 1.007276,
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	374 '[M+NH4]+': 18.034374,
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	375 '[M+Na]+': 22.989218,
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	376 '[M+K]+': 38.963158,
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	377 '[M+CH3OH+H]+': 33.033489,
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	378 '[M+ACN+H]+': 42.033823,
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	379 '[M+ACN+Na]+': 64.015765,
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	380 '[M+2ACN+H]+': 83.06037,
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	381 '[M-H]-': -1.007276,
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	382 '[M+Cl]-': 34.969402,
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	383 '[M+HCOO]-': 44.99819,
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	384 '[M-H+HCOOH]-': 44.99819,
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	385 # same as above but different style of writing adduct
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	386 '[M+CH3COO]-': 59.01385,
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	387 '[M-H+CH3COOH]-': 59.01385
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	388 # same as above but different style of writing adduct
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	389 }
0 fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	390
2 f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	391 ######################################################################
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	392 # Parse MSP file and run metfrag CLI
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	393 ######################################################################
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	394 # keep list of commands if performing in CLI in parallel
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	395 cmds = []
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	396 # keep a dictionary of all params
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	397 paramds = {}
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	398 # keep count of spectra (for uid)
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	399 spectrac = 0
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	400 # this dictionary will store the meta data results form the MSp file
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	401 meta_info = {}
0 fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	402
2 f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	403 if args.adducts:
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	404 adducts_from_cli = [
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	405 a[0].replace('__ob__', '[').replace('__cb__', ']') for a in
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	406 args.adducts
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	407 ]
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	408 else:
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	409 adducts_from_cli = []
0 fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	410
2 f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	411 with open(args.input_pth, "r") as infile:
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	412 # number of lines for the peaks
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	413 pnumlines = 0
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	414 # number of lines read for the peaks
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	415 plinesread = 0
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	416 for line in infile:
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	417 line = line.strip()
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	418
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	419 if pnumlines == 0:
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	420 # ============== Extract metadata from MSP ====================
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	421 meta_info = parse_meta(meta_regex, meta_info)
0 fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	422
2 f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	423 if ('massbank' in meta_info and 'cols' in meta_info) or (
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	424 'msp' in meta_info and 'num_peaks' in meta_info):
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	425 pnumlines = int(meta_info['num_peaks'])
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	426 plinesread = 0
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	427 peaklist = []
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	428
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	429 elif plinesread < pnumlines:
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	430 # ============== Extract peaks from MSP =======================
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	431 # .split() will split on any empty space (i.e. tab and space)
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	432 line = tuple(line.split())
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	433 # Keep only m/z and intensity, not relative intensity
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	434 save_line = tuple(line[0].split() + line[1].split())
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	435 plinesread += 1
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	436 peaklist.append(save_line)
0 fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	437
2 f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	438 elif plinesread and plinesread == pnumlines:
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	439 # =Get sample name and additional details for output and RUN ==
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	440 if adducts_from_cli:
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	441 for adduct in adducts_from_cli:
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	442 spectrac += 1
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	443 meta_info['precursor_type'] = adduct
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	444 paramd, cmd = run_metfrag(meta_info, peaklist, args,
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	445 wd, spectrac, adduct_types)
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	446 if paramd:
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	447 paramds[paramd["SampleName"]] = paramd
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	448 cmds.append(cmd)
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	449 else:
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	450 spectrac += 1
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	451 paramd, cmd = run_metfrag(meta_info, peaklist, args,
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	452 wd, spectrac, adduct_types)
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	453 if paramd:
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	454 paramds[paramd["SampleName"]] = paramd
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	455 cmds.append(cmd)
0 fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	456
2 f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	457 meta_info = {}
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	458 pnumlines = 0
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	459 plinesread = 0
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	460
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	461 # end of file. Check if there is a MSP spectra to run metfrag on
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	462 if plinesread and plinesread == pnumlines:
0 fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	463
2 f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	464 if adducts_from_cli:
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	465 for adduct in adducts_from_cli:
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	466 spectrac += 1
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	467 meta_info['precursor_type'] = adduct
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	468 paramd, cmd = run_metfrag(meta_info, peaklist, args,
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	469 wd, spectrac, adduct_types)
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	470 if paramd:
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	471 paramds[paramd["SampleName"]] = paramd
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	472 cmds.append(cmd)
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	473 else:
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	474 spectrac += 1
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	475 paramd, cmd = run_metfrag(meta_info, peaklist, args,
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	476 wd, spectrac, adduct_types)
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	477 if paramd:
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	478 paramds[paramd["SampleName"]] = paramd
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	479 cmds.append(cmd)
0 fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	480
2 f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	481 # Perform multiprocessing on command line call level
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	482 if int(args.cores_top_level) > 1:
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	483 cmds_chunks = [cmds[x:x + int(args.chunks)] for x in
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	484 list(range(0, len(cmds), int(args.chunks)))]
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	485 pool = multiprocessing.Pool(processes=int(args.cores_top_level))
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	486 pool.map(work, cmds_chunks)
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	487 pool.close()
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	488 pool.join()
0 fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	489
2 f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	490 ######################################################################
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	491 # Concatenate and filter the output
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	492 ######################################################################
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	493 # outputs might have different headers. Need to get a list of all the
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	494 # headers before we start merging the files
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	495 # outfiles = [os.path.join(wd, f) for f in glob.glob(os.path.join(wd,
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	496 # "*_metfrag_result.csv"))]
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	497 outfiles = glob.glob(os.path.join(wd, "*_metfrag_result.csv"))
0 fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	498
2 f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	499 if len(outfiles) == 0:
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	500 print('No results')
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	501 sys.exit()
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	502
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	503 headers = []
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	504 c = 0
0 fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	505 for fn in outfiles:
2 f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	506 with open(fn, 'r') as infile:
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	507 reader = csv.reader(infile)
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	508 if sys.version_info >= (3, 0):
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	509 headers.extend(next(reader))
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	510 else:
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	511 headers.extend(reader.next())
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	512 # check if file has any data rows
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	513 for i, row in enumerate(reader):
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	514 c += 1
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	515 if i == 1:
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	516 break
0 fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	517
2 f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	518 # if no data rows (e.g. matches) then do not save an
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	519 # output and leave the program
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	520 if c == 0:
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	521 print('No results')
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	522 sys.exit()
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	523
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	524 additional_detail_headers = ['sample_name']
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	525 for k, paramd in six.iteritems(paramds):
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	526 additional_detail_headers = list(set(
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	527 additional_detail_headers + list(
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	528 paramd['additional_details'].keys())))
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	529
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	530 # add inchikey if not already present (missing in metchem output)
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	531 if 'InChIKey' not in headers:
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	532 headers.append('InChIKey')
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	533
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	534 additional_detail_headers = sorted(additional_detail_headers)
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	535 headers = additional_detail_headers + sorted(list(set(headers)))
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	536
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	537 # Sort files nicely
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	538 outfiles.sort(
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	539 key=lambda s: int(
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	540 re.match(r'^.*/(\d+)_metfrag_result.csv', s).group(1)))
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	541
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	542 print(outfiles)
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	543
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	544 # merge outputs
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	545 with open(args.result_pth, 'a') as merged_outfile:
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	546 dwriter = csv.DictWriter(merged_outfile, fieldnames=headers,
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	547 delimiter='\t', quotechar='"')
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	548 dwriter.writeheader()
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	549
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	550 for fn in outfiles:
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	551 with open(fn) as infile:
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	552 reader = csv.DictReader(infile, delimiter=',', quotechar='"')
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	553 for line in reader:
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	554 bewrite = True
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	555 for key, value in line.items():
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	556 # Filter when no MS/MS peak matched
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	557 if key == "ExplPeaks":
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	558 if float(args.pctexplpeak_thrshld) > 0 \
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	559 and value and "NA" in value:
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	560 bewrite = False
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	561 # Filter with a score threshold
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	562 elif key == "Score":
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	563 if value and float(value) <= float(
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	564 args.score_thrshld):
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	565 bewrite = False
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	566 elif key == "NoExplPeaks":
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	567 nbfindpeak = float(value)
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	568 elif key == "NumberPeaksUsed":
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	569 totpeaks = float(value)
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	570 # Filter with a relative number of peak matched
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	571 try:
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	572 pctexplpeak = nbfindpeak / totpeaks * 100
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	573 except ZeroDivisionError:
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	574 bewrite = False
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	575 else:
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	576 if pctexplpeak < float(args.pctexplpeak_thrshld):
0 fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	577 bewrite = False
2 f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	578
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	579 # Write the line if it pass all filters
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	580 if bewrite:
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	581 bfn = os.path.basename(fn)
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	582 bfn = bfn.replace(".csv", "")
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	583 line['sample_name'] = paramds[bfn]['SampleName']
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	584 ad = paramds[bfn]['additional_details']
0 fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	585
2 f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	586 if args.MetFragDatabaseType == "MetChem":
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	587 # for some reason the metchem database option does
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	588 # not report the full inchikey (at least in the
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	589 # Bham setup. This ensures we always get
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	590 # the fully inchikey
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	591 line['InChIKey'] = '{}-{}-{}'.format(
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	592 line['InChIKey1'],
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	593 line['InChIKey2'],
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	594 line['InChIKey3'])
0 fd5c0b39569a "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d" computational-metabolomics parents: diff changeset	595
2 f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	596 line.update(ad)
f151ee133612 "planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a" computational-metabolomics parents: 1 diff changeset	597 dwriter.writerow(line)

Mercurial > repos > computational-metabolomics > metfrag

annotate metfrag.py @ 2:f151ee133612 draft default tip