mapalignerposeclustering.py

import os
import shutil
import sys
import openms_workflow as wrkflw

'''
#3 module: map aligner pose clustering
'''
def mapalignerposeclustering(input_port, ini_file, out_port):
    command = "MapAlignerPoseClustering "
    if ini_file is not None:
        command += "-ini " + ini_file + " "
    command += "-in "
    for input_file,file_count in wrkflw.parsefolder(input_port):
        command += input_file + ' '
    command += '-out '
    for input_file,file_count in wrkflw.parsefolder(input_port):
        command += out_port+"/"+out_port+"-"+file_count+".featureXML" + ' '
    command += '> ' + out_port+'/logfile.txt'
    # command += '-log ' + out_port+'/logfile-00000.txt'

    print("COMMAND: " + command + "\n")
    os.system(command)


if __name__ == '__main__':
    print("===MAP ALIGNER POSE CLUSTERING===")

    in_port = sys.argv[4]
    out_port = sys.argv[6]

    # validate previous module's output
    # wrkflw.prevalidation("id-mapper", in_port)

    # 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]


    mapalignerposeclustering(in_port, ini_file, out_port)

    # wrkflw.postvalidation(modulename="map-aligner-pose-clustering", outpath=out_port)