Exemple #1
0
def load(filepath, db, action=None):
    samfile = _load_sam(filepath, db)

    sam_data = Sam(db)
    chromosome_data = Chromosome(db)

    chromosomes = []
    for ref in samfile.references:
        name = trim_chromosome_name(ref)

        c = chromosome_data.get_by_name(name)
        c['ref'] = ref

        chromosomes.append(c)

    filename = os.path.basename(filepath)
    sam = sam_data.get_by_filename(filename)

    if sam is None:
        logging.error('Error : please load "%s" first' % filename)

    samId = sam['id']

    # cypileup
    cypileup.pileup(samfile, chromosomes, samId, db, action)

    samfile.close()
Exemple #2
0
def load(filepath, db):
    filename = os.path.basename(filepath)
    base, ext = os.path.splitext(filepath)
    if not re.match('^\.(sam|bam)', ext):
        raise UnsupportedFileError('ERROR: Not supported file format')

    sam_data = Sam(db)
    chr_data = Chromosome(db)

    if sam_data.get_by_filename(filename) is not None:
        raise AlreadyLoadedError('WARNING: Already loaded "%s"' % filename)

    logging.info("Begin to load '%s'" % filename)

    # Convert sam to bam
    if ext == '.sam':
        insam = pysam.Samfile(filepath, 'r')
        filepath = base + '.bam'
        outbam = pysam.Samfile(filepath, 'wb', template=insam)
        for s in insam:
            outbam.write(s)

    # Create index if not exist
    bai = filepath + '.bai'
    if not os.path.isfile(bai):
        logging.info("Create index '%s'" % os.path.basename(bai))
        pysam.index(filepath)

    # load sam
    samfile = pysam.Samfile(filepath)
    sam_data.append(filename,
                    samfile.header, samfile.lengths,
                    samfile.mapped,
                    samfile.nreferences, samfile.references)

    # load chromosome
    for ref in samfile.references:
        chr_data.append(trim_chromosome_name(ref))