Python read_replicon_names Exemples

Exemple #1

Fichier : process_map.py Projet : ruiqiangxie/Tn-seq

def headers_ok(fasta):
    ok = True
    replicons = common.read_replicon_names(fasta)
    for replicon in replicons.values():
        if "|" in replicon:
            ok = False
    return ok

Exemple #2

Fichier : process_map.py Projet : elijweiss/Tn-seq

def headers_ok(fasta):
    ok = True
    replicons = common.read_replicon_names(fasta)
    for replicon in replicons.values():
        if "|" in replicon:
            ok = False
    return ok

Exemple #3

Fichier : process_annotate_tabulate.py Projet : lg9/Tn-seq

def main():
    # Get command line options
    opts, args = init_options()
    infiles = args

    # Input validation
    for infile in infiles:
        if not os.path.isfile(infile):
            print "Input file " + infile + " not found"
            exit(1)
    annofile_list = opts.annofiles.split(",")
    replicons = common.read_replicon_names(opts.reference_fa)
    if len(replicons) != len(annofile_list):
        print "Number of annotation files must match the number of sequences in the reference fasta"
        exit(1)

    process(infiles, opts, replicons)

Exemple #4

Fichier : process_annotate_tabulate.py Projet : ruiqiangxie/Tn-seq

def main():
    # Get command line options
    opts, args = init_options()
    infiles = args

    # Input validation
    for infile in infiles:
        if not os.path.isfile(infile):
            print "Input file " + infile + " not found"
            exit(1)
    annofile_list = opts.annofiles.split(",")
    replicons = common.read_replicon_names(opts.reference_fa)
    if len(replicons) != len(annofile_list):
        print "Number of annotation files must match the number of sequences in the reference fasta"
        exit(1)

    process(infiles, opts, replicons)

Exemple #5

Fichier : annotate.py Projet : elijweiss/Tn-seq

def main():
    # Get command line options
    opts, args = init_options()
    print "Annotating " + opts.infile

    all_replicons = common.read_replicon_names(opts.fasta)

    # Separate multiple annotation files
    annofile_list = opts.annofiles.split(",")
    if len(annofile_list) != len(all_replicons):
        print "ERROR: wrong number of replicon names for replicon files"
        exit(1)
    print "Using " + str(len(annofile_list)) + " .ptt files"

    annotations = common.read_annotations(annofile_list, all_replicons)

    lines_written = write_annotated(opts.infile, opts.outfile, annotations)
    print str(lines_written) + " lines written to " + opts.outfile

Exemple #6

Fichier : annotate.py Projet : lg9/Tn-seq

def main():
    # Get command line options
    opts, args = init_options()
    print "Annotating " + opts.infile

    all_replicons = common.read_replicon_names(opts.fasta)

    # Separate multiple annotation files
    annofile_list = opts.annofiles.split(",")
    if len(annofile_list) != len(all_replicons):
        print "ERROR: wrong number of replicon names for replicon files"
        exit(1)
    print "Using " + str(len(annofile_list)) + " .ptt files"

    annotations = common.read_annotations(annofile_list, all_replicons)

    lines_written = write_annotated(opts.infile, opts.outfile, annotations)
    print str(lines_written) + " lines written to " + opts.outfile

Exemple #7

Fichier : tabulate.py Projet : elijweiss/Tn-seq

def main():
    # Get command line options
    opts, args = init_options()
    print "Tabulating " + opts.infile

    all_replicons = common.read_replicon_names(opts.fasta)

    # Separate multiple annotation files
    annofile_list = opts.annofiles.split(",")
    if len(annofile_list) != len(all_replicons):
        print "ERROR: wrong number of replicon names for replicon files"
        exit(1)
    print "Using annotation files " + str(annofile_list)

    annotations = common.read_annotations(annofile_list, all_replicons)

    (runs, hits, allhits) = read_hits_file(opts.infile)

    lines_written = write_tabulated(opts.outfile, runs, annotations, hits, allhits)

Exemple #8

def main():
    # Get command line options
    opts, args = init_options()
    print "Tabulating " + opts.infile

    all_replicons = common.read_replicon_names(opts.fasta)

    # Separate multiple annotation files
    annofile_list = opts.annofiles.split(",")
    if len(annofile_list) != len(all_replicons):
        print "ERROR: wrong number of replicon names for replicon files"
        exit(1)
    print "Using annotation files " + str(annofile_list)

    annotations = common.read_annotations(annofile_list, all_replicons)

    (runs, hits, allhits) = read_hits_file(opts.infile)

    lines_written = write_tabulated(opts.outfile, runs, annotations, hits,
                                    allhits)