view metfrag.py @ 4:eb581a101672 draft

planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4

from __future__ import absolute_import, print_function
import argparse
import csv
import os
import sys
import six
import re
import random
import string
import shutil
import glob
import tempfile
import multiprocessing

from subprocess import call
from collections import defaultdict

print(sys.version)

parser = argparse.ArgumentParser()
parser.add_argument('--input_pth')
parser.add_argument('--result_pth', default='metfrag_result.csv')

parser.add_argument('--temp_dir')
parser.add_argument('--polarity', default='pos')
parser.add_argument('--minMSMSpeaks', default=1)

parser.add_argument('--MetFragDatabaseType', default='PubChem')
parser.add_argument('--LocalDatabasePath', default='')
parser.add_argument('--LocalMetChemDatabaseServerIp', default='')

parser.add_argument('--DatabaseSearchRelativeMassDeviation', default=5)
parser.add_argument('--FragmentPeakMatchRelativeMassDeviation', default=10)
parser.add_argument('--FragmentPeakMatchAbsoluteMassDeviation', default=0.001)
parser.add_argument('--NumberThreads', default=1)
parser.add_argument('--UnconnectedCompoundFilter', action='store_true')
parser.add_argument('--IsotopeFilter', action='store_true')

parser.add_argument('--FilterMinimumElements', default='')
parser.add_argument('--FilterMaximumElements', default='')
parser.add_argument('--FilterSmartsInclusionList', default='')
parser.add_argument('--FilterSmartsExclusionList', default='')
parser.add_argument('--FilterIncludedElements', default='')
parser.add_argument('--FilterExcludedElements', default='')
parser.add_argument('--FilterIncludedExclusiveElements', default='')

parser.add_argument('--score_thrshld', default=0)
parser.add_argument('--pctexplpeak_thrshld', default=0)
parser.add_argument('--schema')
parser.add_argument('--cores_top_level', default=1)
parser.add_argument('--chunks', default=1)
parser.add_argument('--meta_select_col', default='name')
parser.add_argument('--skip_invalid_adducts',  action='store_true')

parser.add_argument('--ScoreSuspectLists', default='')
parser.add_argument('--MetFragScoreTypes', default="FragmenterScore,OfflineMetFusionScore")
parser.add_argument('--MetFragScoreWeights', default="1.0,1.0")


args = parser.parse_args()
print(args)

if os.stat(args.input_pth).st_size == 0:
    exit('Input file empty')


# Create temporary working directory
if args.temp_dir:
    wd = args.temp_dir
else:
    wd = tempfile.mkdtemp()

if os.path.exists(wd):
    shutil.rmtree(wd)
    os.makedirs(wd)
else:
    os.makedirs(wd)

######################################################################
# Setup regular expressions for MSP parsing dictionary
######################################################################
regex_msp = {}
regex_msp['name'] = ['^Name(?:=|:)(.*)$']
regex_msp['polarity'] = ['^ion.*mode(?:=|:)(.*)$', '^ionization.*mode(?:=|:)(.*)$', '^polarity(?:=|:)(.*)$']
regex_msp['precursor_mz'] = ['^precursor.*m/z(?:=|:)\s*(\d*[.,]?\d*)$', '^precursor.*mz(?:=|:)\s*(\d*[.,]?\d*)$']
regex_msp['precursor_type'] = ['^precursor.*type(?:=|:)(.*)$', '^adduct(?:=|:)(.*)$', '^ADDUCTIONNAME(?:=|:)(.*)$']
regex_msp['num_peaks'] = ['^Num.*Peaks(?:=|:)\s*(\d*)$']
regex_msp['msp'] = ['^Name(?:=|:)(.*)$']  # Flag for standard MSP format

regex_massbank = {}
regex_massbank['name'] = ['^RECORD_TITLE:(.*)$']
regex_massbank['polarity'] = ['^AC\$MASS_SPECTROMETRY:\s+ION_MODE\s+(.*)$']
regex_massbank['precursor_mz'] = ['^MS\$FOCUSED_ION:\s+PRECURSOR_M/Z\s+(\d*[.,]?\d*)$']
regex_massbank['precursor_type'] = ['^MS\$FOCUSED_ION:\s+PRECURSOR_TYPE\s+(.*)$']
regex_massbank['num_peaks'] = ['^PK\$NUM_PEAK:\s+(\d*)']
regex_massbank['cols'] = ['^PK\$PEAK:\s+(.*)']
regex_massbank['massbank'] = ['^RECORD_TITLE:(.*)$']  # Flag for massbank format

if args.schema == 'msp':
    meta_regex = regex_msp
elif args.schema == 'massbank':
    meta_regex = regex_massbank
elif args.schema == 'auto':
    # If auto we just check for all the available paramter names and then determine if Massbank or MSP based on
    # the name parameter
    meta_regex = {}
    meta_regex.update(regex_massbank)
    meta_regex['name'].extend(regex_msp['name'])
    meta_regex['polarity'].extend(regex_msp['polarity'])
    meta_regex['precursor_mz'].extend(regex_msp['precursor_mz'])
    meta_regex['precursor_type'].extend(regex_msp['precursor_type'])
    meta_regex['num_peaks'].extend(regex_msp['num_peaks'])
    meta_regex['msp'] = regex_msp['msp']

    print(meta_regex)

adduct_types = {
    '[M+H]+': 1.007276,
    '[M+NH4]+': 18.034374,
    '[M+Na]+': 22.989218,
    '[M+K]+': 38.963158,
    '[M+CH3OH+H]+': 33.033489,
    '[M+ACN+H]+': 42.033823,
    '[M+ACN+Na]+': 64.015765,
    '[M+2ACN+H]+': 83.06037,
    '[M-H]-': -1.007276,
    '[M+Cl]-': 34.969402,
    '[M+HCOO]-': 44.99819,
    '[M-H+HCOOH]-': 44.99819,  # same as above but different style of writing adduct
    '[M+CH3COO]-': 59.01385,
    '[M-H+CH3COOH]-': 59.01385  # same as above but different style of writing adduct
}

# function to extract the meta data using the regular expressions
def parse_meta(meta_regex, meta_info={}):
    for k, regexes in six.iteritems(meta_regex):
        for reg in regexes:
            m = re.search(reg, line, re.IGNORECASE)
            if m:
                meta_info[k] = '-'.join(m.groups()).strip()
    return meta_info



######################################################################
# Setup parameter dictionary
######################################################################
def init_paramd(args):
    paramd = defaultdict()

    paramd["MetFragDatabaseType"] = args.MetFragDatabaseType

    if args.MetFragDatabaseType == "LocalCSV":
        paramd["LocalDatabasePath"] = args.LocalDatabasePath
    elif args.MetFragDatabaseType == "MetChem":
        paramd["LocalMetChemDatabase"] = "metchem"
        paramd["LocalMetChemDatabasePortNumber"] = 5432
        paramd["LocalMetChemDatabaseServerIp"] = args.LocalMetChemDatabaseServerIp
        paramd["LocalMetChemDatabaseUser"] = "metchemro"
        paramd["LocalMetChemDatabasePassword"] = "metchemro"

    paramd["FragmentPeakMatchAbsoluteMassDeviation"] = args.FragmentPeakMatchAbsoluteMassDeviation
    paramd["FragmentPeakMatchRelativeMassDeviation"] = args.FragmentPeakMatchRelativeMassDeviation
    paramd["DatabaseSearchRelativeMassDeviation"] = args.DatabaseSearchRelativeMassDeviation
    paramd["SampleName"] = ''
    paramd["ResultsPath"] = os.path.join(wd)

    if args.polarity == "pos":
        paramd["IsPositiveIonMode"] = True
        paramd["PrecursorIonModeDefault"] = "1"
        paramd["PrecursorIonMode"] = "1"
        paramd["nm_mass_diff_default"] = 1.007276
    else:
        paramd["IsPositiveIonMode"] = False
        paramd["PrecursorIonModeDefault"] = "-1"
        paramd["PrecursorIonMode"] = "-1"
        paramd["nm_mass_diff_default"] = -1.007276

    paramd["MetFragCandidateWriter"] = "CSV"
    paramd["NumberThreads"] = args.NumberThreads

    if args.ScoreSuspectLists:
        paramd["ScoreSuspectLists"] = args.ScoreSuspectLists

    paramd["MetFragScoreTypes"] = args.MetFragScoreTypes
    paramd["MetFragScoreWeights"] = args.MetFragScoreWeights

    dct_filter = defaultdict()
    filterh = []

    if args.UnconnectedCompoundFilter:
        filterh.append('UnconnectedCompoundFilter')

    if args.IsotopeFilter:
        filterh.append('IsotopeFilter')

    if args.FilterMinimumElements:
        filterh.append('MinimumElementsFilter')
        dct_filter['FilterMinimumElements'] = args.FilterMinimumElements

    if args.FilterMaximumElements:
        filterh.append('MaximumElementsFilter')
        dct_filter['FilterMaximumElements'] = args.FilterMaximumElements

    if args.FilterSmartsInclusionList:
        filterh.append('SmartsSubstructureInclusionFilter')
        dct_filter['FilterSmartsInclusionList'] = args.FilterSmartsInclusionList

    if args.FilterSmartsExclusionList:
        filterh.append('SmartsSubstructureExclusionFilter')
        dct_filter['FilterSmartsExclusionList'] = args.FilterSmartsExclusionList

    # My understanding is that both 'ElementInclusionExclusiveFilter' and 'ElementExclusionFilter' use
    # 'FilterIncludedElements'
    if args.FilterIncludedExclusiveElements:
        filterh.append('ElementInclusionExclusiveFilter')
        dct_filter['FilterIncludedElements'] = args.FilterIncludedExclusiveElements

    if args.FilterIncludedElements:
        filterh.append('ElementInclusionFilter')
        dct_filter['FilterIncludedElements'] = args.FilterIncludedElements

    if args.FilterExcludedElements:
        filterh.append('ElementExclusionFilter')
        dct_filter['FilterExcludedElements'] = args.FilterExcludedElements

    if filterh:
        fcmds = ','.join(filterh) + ' '
        for k, v in six.iteritems(dct_filter):
            fcmds += "{0}={1} ".format(str(k), str(v))

        paramd["MetFragPreProcessingCandidateFilter"] = fcmds

    return paramd


######################################################################
# Function to run metfrag when all metainfo and peaks have been parsed
######################################################################
def run_metfrag(meta_info, peaklist, args, wd, spectrac, adduct_types):
    # Get sample details (if possible to extract) e.g. if created as part of the msPurity pipeline)
    # choose between getting additional details to add as columns as either all meta data from msp, just
    # details from the record name (i.e. when using msPurity and we have the columns coded into the name) or
    # just the spectra index (spectrac)]
    # Returns the parameters used and the command line call

    paramd = init_paramd(args)
    if args.meta_select_col == 'name':
        # have additional column of just the name
        paramd['additional_details'] = {'name': meta_info['name']}
    elif args.meta_select_col == 'name_split':
        # have additional columns split by "|" and then on ":" e.g. MZ:100.2 | RT:20 | xcms_grp_id:1
        paramd['additional_details'] = {sm.split(":")[0].strip(): sm.split(":")[1].strip() for sm in
                   meta_info['name'].split("|")}
    elif args.meta_select_col == 'all':
        # have additional columns based on all the meta information extracted from the MSP
        paramd['additional_details'] = meta_info
    else:
        # Just have and index of the spectra in the MSP file
        paramd['additional_details'] = {'spectra_idx': spectrac}

    paramd["SampleName"] = "{}_metfrag_result".format(spectrac)

    # =============== Output peaks to txt file  ==============================
    paramd["PeakListPath"] = os.path.join(wd, "{}_tmpspec.txt".format(spectrac))

    # write spec file
    with open(paramd["PeakListPath"], 'w') as outfile:
        for p in peaklist:
            outfile.write(p[0] + "\t" + p[1] + "\n")

    # =============== Update param based on MSP metadata ======================
    # Replace param details with details from MSP if required
    if 'precursor_type' in meta_info and meta_info['precursor_type'] in adduct_types:
        nm = float(meta_info['precursor_mz']) - adduct_types[meta_info['precursor_type']]
        paramd["PrecursorIonMode"] = int(round(adduct_types[meta_info['precursor_type']], 0))
    elif not args.skip_invalid_adducts:
        paramd["PrecursorIonMode"] = paramd['PrecursorIonModeDefault']
        nm = float(meta_info['precursor_mz']) - paramd['nm_mass_diff_default']
    else:
        print('Skipping {}'.format(paramd["SampleName"]))
        return '', ''

    paramd["NeutralPrecursorMass"] = nm

    # =============== Create CLI cmd for metfrag ===============================
    cmd = "metfrag"
    for k, v in six.iteritems(paramd):
        if not k in ['PrecursorIonModeDefault', 'nm_mass_diff_default', 'additional_details']:
            cmd += " {}={}".format(str(k), str(v))

    # =============== Run metfrag ==============================================
    print(cmd)
    # Filter before process with a minimum number of MS/MS peaks
    if plinesread >= float(args.minMSMSpeaks):

        if int(args.cores_top_level) == 1:
            os.system(cmd)

    return paramd, cmd


def work(cmds):
    return [os.system(cmd) for cmd in cmds]



######################################################################
# Parse MSP file and run metfrag CLI
######################################################################
# keep list of commands if performing in CLI in parallel
cmds = []
# keep a dictionary of all params
paramds = {}
# keep count of spectra (for uid)
spectrac = 0
# this dictionary will store the meta data results form the MSp file
meta_info = {}

with open(args.input_pth, "r") as infile:
    # number of lines for the peaks
    pnumlines = 0
    # number of lines read for the peaks
    plinesread = 0
    for line in infile:
        line = line.strip()

        if pnumlines == 0:
            # =============== Extract metadata from MSP ========================
            meta_info = parse_meta(meta_regex, meta_info)

            if ('massbank' in meta_info and 'cols' in meta_info) or ('msp' in meta_info and 'num_peaks' in meta_info):

                pnumlines = int(meta_info['num_peaks'])
                plinesread = 0
                peaklist = []

        elif plinesread < pnumlines:
            # =============== Extract peaks from MSP ==========================
            line = tuple(line.split())  # .split() will split on any empty space (i.e. tab and space)
            # Keep only m/z and intensity, not relative intensity
            save_line = tuple(line[0].split() + line[1].split())
            plinesread += 1
            peaklist.append(save_line)

        elif plinesread and plinesread == pnumlines:
            # =============== Get sample name and additional details for output =======
            spectrac += 1
            paramd, cmd = run_metfrag(meta_info, peaklist, args, wd, spectrac, adduct_types)

            if paramd:
                paramds[paramd["SampleName"]] = paramd
                cmds.append(cmd)

            meta_info = {}
            pnumlines = 0
            plinesread = 0

    # end of file. Check if there is a MSP spectra to run metfrag on still
    if plinesread and plinesread == pnumlines:

        paramd, cmd = run_metfrag(meta_info, peaklist, args, wd, spectrac+1, adduct_types)

        if paramd:
            paramds[paramd["SampleName"]] = paramd
            cmds.append(cmd)




# Perform multiprocessing on command line call level
if int(args.cores_top_level) > 1:
    cmds_chunks = [cmds[x:x + int(args.chunks)] for x in list(range(0, len(cmds), int(args.chunks)))]
    pool = multiprocessing.Pool(processes=int(args.cores_top_level))
    pool.map(work, cmds_chunks)
    pool.close()
    pool.join()

######################################################################
# Concatenate and filter the output
######################################################################
# outputs might have different headers. Need to get a list of all the headers before we start merging the files
# outfiles = [os.path.join(wd, f) for f in glob.glob(os.path.join(wd, "*_metfrag_result.csv"))]
outfiles = glob.glob(os.path.join(wd, "*_metfrag_result.csv"))

headers = []
c = 0
for fn in outfiles:
    with open(fn, 'r') as infile:
        reader = csv.reader(infile)
        if sys.version_info >= (3, 0):
            headers.extend(next(reader))
        else:
            headers.extend(reader.next())
        # check if file has any data rows 
        for i, row in enumerate(reader):
            c += 1
            if i == 1:
                break

# if no data rows (e.g. matches) then do not save an output and leave the program        
if c == 0:
    sys.exit()

additional_detail_headers = ['sample_name']
for k, paramd in six.iteritems(paramds):
    additional_detail_headers = list(set(additional_detail_headers + list(paramd['additional_details'].keys())))

headers = additional_detail_headers + sorted(list(set(headers)))


# Sort files nicely
outfiles.sort(key = lambda s: int(re.match('^.*/(\d+)_metfrag_result.csv', s).group(1)))

print(outfiles)


# merge outputs
with open(args.result_pth, 'a') as merged_outfile:
    dwriter = csv.DictWriter(merged_outfile, fieldnames=headers, delimiter='\t', quotechar='"')
    dwriter.writeheader()

    for fn in outfiles:

        with open(fn) as infile:
            reader = csv.DictReader(infile, delimiter=',', quotechar='"')
            for line in reader:
                bewrite = True
                for key, value in line.items():
                    # Filter when no MS/MS peak matched
                    if key == "ExplPeaks":
                        if float(args.pctexplpeak_thrshld) > 0 and "NA" in value:
                            bewrite = False
                    # Filter with a score threshold
                    elif key == "Score":
                        if float(value) <= float(args.score_thrshld):
                            bewrite = False
                    elif key == "NoExplPeaks":
                        nbfindpeak = float(value)
                    elif key == "NumberPeaksUsed":
                        totpeaks = float(value)
                # Filter with a relative number of peak matched
                try:
                    pctexplpeak = nbfindpeak / totpeaks * 100
                except ZeroDivisionError:
                    bewrite = False
                else:
                    if pctexplpeak < float(args.pctexplpeak_thrshld):
                        bewrite = False

                # Write the line if it pass all filters
                if bewrite:
                    bfn = os.path.basename(fn)
                    bfn = bfn.replace(".csv", "")
                    ad = paramds[bfn]['additional_details']
                    line.update(ad)
                    line['sample_name'] = paramds[bfn]['SampleName']

                    dwriter.writerow(line)