Example #1
0
def main():
    logging.basicConfig(format='%(levelname)s: %(asctime)s %(message)s',
                        level=logging.INFO)
    description = "Add estimated start and stop codons to a GTF file."
    parser = ArgumentParser(description = description)
    parser.add_argument("fasta_file", metavar="seq_file", type=str, 
                        help="sequence of transcripts in fasta format")
    parser.add_argument("gtf_file", metavar="gtf_file", type=str, 
                        help="gtf file")

    samtools = which("samtools")

    if samtools is None:
        print "samtools must be executable, add it to your path or " \
              "download it from http://samtools.sourceforge.net/"
        exit(-1)
    
    args = parser.parse_args()

    if not os.path.exists(args.gtf_file):
        parser.help()
        exit(-1)
    if not os.path.exists(args.fasta_file):
        parser.help()
        exit(-1)

    gtflines = GTFtoDict(args.gtf_file)
    
    x = aggregateFeaturesByTranscript(gtflines)
    x = addFeatureCoordinatesToTranscripts(x)
    for transcript in x:
        seq = get_sequence_of_transcript(samtools, args.fasta_file, x[transcript])
        orf = find_longest_orf(seq)
        z = add_start_and_stop_codons(orf, x[transcript])
        outputGTFout(z)
Example #2
0
    def __init__(self, parser: ArgumentParser):
        self.log = logging.getLogger(
            "{}.{}".format(self.__module__, self.__class__.__name__), )

        if self.help:
            parser.help = self.help

        if self.description:
            parser.description = self.description
Example #3
0
def main():
    logging.basicConfig(format='%(levelname)s: %(asctime)s %(message)s',
                        level=logging.INFO)
    description = "Add estimated start and stop codons to a GTF file."
    parser = ArgumentParser(description=description)
    parser.add_argument("fasta_file",
                        metavar="seq_file",
                        type=str,
                        help="sequence of transcripts in fasta format")
    parser.add_argument("gtf_file",
                        metavar="gtf_file",
                        type=str,
                        help="gtf file")

    samtools = which("samtools")

    if samtools is None:
        print "samtools must be executable, add it to your path or " \
              "download it from http://samtools.sourceforge.net/"
        exit(-1)

    args = parser.parse_args()

    if not os.path.exists(args.gtf_file):
        parser.help()
        exit(-1)
    if not os.path.exists(args.fasta_file):
        parser.help()
        exit(-1)

    gtflines = GTFtoDict(args.gtf_file)

    x = aggregateFeaturesByTranscript(gtflines)
    x = addFeatureCoordinatesToTranscripts(x)
    for transcript in x:
        seq = get_sequence_of_transcript(samtools, args.fasta_file,
                                         x[transcript])
        orf = find_longest_orf(seq)
        z = add_start_and_stop_codons(orf, x[transcript])
        outputGTFout(z)
Example #4
0

if __name__ == "__main__":
    basicConfig(level=DEBUG)
    debug("Staring up")
    parser = ArgumentParser(
        description='Program to search and display ical files')
    parser.add_argument('-y', '--year', help='year to search')
    parser.add_argument('-f', '--faculty', help='faculty to search')
    parser.add_argument('-s', '--subject', help='subject to search')
    parser.add_argument('-n', '--number', help='course number to search')
    parser.add_argument('-c', '--code', help='course code to parse')
    args = parser.parse_args()
    debug("Args: %s" % args)
    if args.year or args.faculty or args.subject:
        errs = []
        if not args.year:
            errs.append("A year is requried")
        if not args.faculty:
            errs.append("A faculty is requried")
        if not args.subject:
            errs.append("A subject is requried")
        if errs:
            print "Error: %s" % ','.join(errs)
            parser.help()
            exit(1)
        else:
            search(args)
    if args.code:
        display(args.code)