def gnpsexport(input_port, inputFiles_port, ini_file, out_port):
for input_file, file_count in list(
wrkflw.parsefolder(input_port, whitelist=['consensusXML'])):
output = out_port + '/' + out_port + "-" + file_count + ".mgf"
command = "GNPSExport"
if ini_file is not None:
command += " -ini " + ini_file
command += " -in_cm " + input_file + " -in_mzml"
# command = "GNPSExport -ini " + ini_file + " -in_cm " + input_file + " -in_mzml "
file_maps = dict()
with open(input_file, 'r') as fp:
params = xtd.parse(fp.read())
for map in params['consensusXML']['mapList']['map']:
# print (map['@id'], map['@name'])
file_maps[int(map['@id'])] = map['@name']
for input_file, file_count in sorted(
list(wrkflw.parsefolder(inputFiles_port, whitelist=['mzML']))):
command += " " + input_file
command += " -out " + output
command += '> ' + out_port + '/logfile-00000.txt'
# command += ' -log ' + out_port+'/logfile-00000.txt'
print("COMMAND: " + command + "\n")
os.system(command)
def fix_filenames(out_port, mapping_file):
print("correcting filenames in featurelinker step...")
files = dict()
with open(mapping_file) as f:
file_dict = xtd.parse(f.read())
for map_line in file_dict['parameters']['parameter']:
if "upload_file_mapping" in map_line[
'@name'] and "inputFiles" in map_line['#text']:
map = map_line['#text'].split('|')
raw_file_path = os.path.splitext(map[0])[0].split('-')[1]
print("mapping", raw_file_path, "->", map[1])
files[int(raw_file_path)] = map[1]
# print(list(wrkflw.parsefolder(out_port)))
for input_file, file_count in wrkflw.parsefolder(out_port,
blacklist=['log']):
with open(input_file) as f:
file_dict = xtd.parse(f.read())
for map in file_dict['consensusXML']['mapList']['map']:
print("\tid:", map['@id'], '\t', map['@name'], '\t-->\t',
files[int(map['@id'])])
map['@name'] = files[int(map['@id'])]
# export file_dict
out = xtd.unparse(file_dict, pretty=True)
with open(input_file, 'w') as file:
file.write(out)
print("out port dir:", os.listdir(out_port))
def featurefindermetabo(input_port, ini_file, out_port):
commands = []
for input_file,file_count in wrkflw.parsefolder(input_port, blacklist=['log']):
cmd = get_exec_cmd(input_file,file_count,ini_file,out_port)
commands.append(cmd)
mpl.run_parallel_shellcommands(commands,8)
def textexporter(input_port, ini_file, out_port):
for input_file, file_count in list(
wrkflw.parsefolder(input_port, blacklist=['log'])):
# command = "TextExporter -ini " + ini_file + " -in " + input_file + " -out " + out_port+'/'+out_port+'-'+file_count+'.csv' + ' >> ' + out_port+'/logfile-00000.txt'
command = "TextExporter -ini " + ini_file + " -in " + input_file + " -out " + out_port + '/' + out_port + '-' + file_count + '.csv' + ' -log ' + out_port + '/logfile-00000.txt'
print("COMMAND: " + command + "\n")
os.system(command)
def filefilter(input_port, out_port):
#only one job
for input_file,file_count in wrkflw.parsefolder(input_port, blacklist=['log']):
# in_cm = in_port+'/'+get_port_outputs(in_port)[0]
output = out_port+'/'+out_port+"-"+file_count+".consensusXML"
command = "FileFilter -id:remove_unannotated_features -in " + input_file + " "
command += "-out " + output + ' '
command += '> ' + out_port+'/logfile-00000.txt'
# command += '-log ' + out_port+'/logfile-00000.txt'
print("COMMAND: " + command + "\n")
os.system(command)
def featurelinkerunlabeledqt(input_port, ini_file, out_port):
command = "FeatureLinkerUnlabeledQT "
if ini_file is not None:
command += "-ini " + ini_file + " "
command += "-in "
for input_file, file_count in wrkflw.parsefolder(input_port,
whitelist=["featureXML"]):
command += input_file + " "
command += "-out " + out_port + "/" + out_port + "-00000.consensusXML "
command += '-log ' + out_port + '/logfile-00000.txt'
print("COMMAND: " + command + "\n")
os.system(command)
def fileconverter(input_port, out_port):
commands = []
for input_file,file_count in wrkflw.parsefolder(input_port, blacklist=["log"]):
if any([ext.lower() in input_file.lower() for ext in ['mzData', 'mzXML',\
'cachedMzML', 'dta', 'dta2d', 'mgf', 'featureXML',\
'consensusXML', 'ms2', 'fid', 'tsv', 'peplist', 'kroenik',\
'edta']]):
cmd = get_exec_cmd(input_file,file_count,out_port)
commands.append(cmd)
elif "mzml" in input_file.lower():
shutil.copyfile(input_file, out_port+"/"+out_port+"-"+file_count+".mzML")
os.system("echo \"original file format for {} is mzml\" >> {}".format(input_file,out_port+"/logfile-"+file_count+".txt"))
else:
continue
mpl.run_parallel_shellcommands(commands,8)
def idmapper(input_port, ini_file, idxml_path, featurefinder_port, out_port):
commands = []
for input_file, file_count in wrkflw.parsefolder(featurefinder_port,
blacklist=['log']):
cmd = get_exec_cmd( \
input_file, \
file_count, \
ini_file, \
idxml_path, \
input_port, \
out_port
)
commands.append(cmd)
mpl.run_parallel_shellcommands(commands, 8)
def mapalignerposeclustering(input_port, ini_file, out_port):
command = "MapAlignerPoseClustering "
if ini_file is not None:
command += "-ini " + ini_file + " "
command += "-in "
outputs = []
for input_file, file_count in wrkflw.parsefolder(input_port,
blacklist=['log']):
command += '{} '.format(input_file)
outputs.append("{out}/{out}-{filec}.featureXML ".format(
out=out_port, filec=file_count))
# command += input_file + ' '
command += '-out '
command += ' '.join(outputs)
# for input_file,file_count in wrkflw.parsefolder(input_port, blacklist=['log']):
# command += out_port+"/"+out_port+"-"+file_count+".featureXML" + ' '
command += '> ' + out_port + '/logfile-00000.txt'
# command += '-log ' + out_port+'/logfile-00000.txt'
print("COMMAND: " + command + "\n")
os.system(command)
#6 module: text export
'''
def textexporter(input_port, ini_file, out_port):
for input_file, file_count in list(
wrkflw.parsefolder(input_port, blacklist=['log'])):
# command = "TextExporter -ini " + ini_file + " -in " + input_file + " -out " + out_port+'/'+out_port+'-'+file_count+'.csv' + ' >> ' + out_port+'/logfile-00000.txt'
command = "TextExporter -ini " + ini_file + " -in " + input_file + " -out " + out_port + '/' + out_port + '-' + file_count + '.csv' + ' -log ' + out_port + '/logfile-00000.txt'
print("COMMAND: " + command + "\n")
os.system(command)
if __name__ == '__main__':
print("===TEXT EXPORTER===")
# set env
os.environ["LD_LIBRARY_PATH"] = sys.argv[1]
os.environ["PATH"] = sys.argv[2]
os.environ["OPENMS_DATA_PATH"] = os.path.abspath(sys.argv[3])
# ini file
ini_file = None
if os.path.exists('iniFiles'):
ini_dir = list(wrkflw.parsefolder('iniFiles'))
if len(ini_dir) > 0:
ini_file = ini_dir[0][0]
textexporter(sys.argv[4], ini_file, sys.argv[6])
