comparison spring_cross.py @ 38:80a4b98121b6 draft

"planemo upload commit 22cd6b0fa88ce0ddc4052beab306f5ba10754f12"

37:0be0af9e695d

from spring_package.DBKit import createFile
from spring_package.Molecule import Molecule


def getId(line):
    line = line.split()[0]
    return line[:4].upper() + line[4:6]


def main(args):
    logFile = open(args.log, "w")

if __name__ == "__main__":
    parser = argparse.ArgumentParser(description='List filtering.')
    parser.add_argument('-l', '--list', help='List of PDB chains [PDB_CHAIN]', required=True)
    parser.add_argument('-i', '--index', help='PDB Database Index file (dbkit_index)', required=True)
    parser.add_argument('-d', '--database', help='PDB Database files (dbkit)', required=True)
    parser.add_argument('-o', '--output', help='Output file', required=True)
    parser.add_argument('-t', '--temp', help='Temporary Directory', required=True)
    parser.add_argument('-g', '--log', help='Log File', required=True)
    args = parser.parse_args()
    main(args)

38:80a4b98121b6

from spring_package.DBKit import createFile
from spring_package.Molecule import Molecule


def getId(line):
    line = line.strip()
    if len(line) != 6 or line[4:5] != "_":
        raise Exception("Invalid list entry (`PDB_CHAIN`): %s." % line)
    return line[:4].upper() + line[4:6]


def main(args):
    logFile = open(args.log, "w")

if __name__ == "__main__":
    parser = argparse.ArgumentParser(description='List filtering.')
    parser.add_argument('-l', '--list', help='List of PDB chains [PDB_CHAIN]', required=True)
    parser.add_argument('-i', '--index', help='PDB Database Index file (ffindex)', required=True)
    parser.add_argument('-d', '--database', help='PDB Database files (ffdata)', required=True)
    parser.add_argument('-o', '--output', help='Output file', required=True)
    parser.add_argument('-t', '--temp', help='Temporary Directory', required=True)
    parser.add_argument('-g', '--log', help='Log File', required=True)
    args = parser.parse_args()
    main(args)