annotate BSseeker2/bs_align/output.py @ 0:e6df770c0e58 draft

Initial upload

try :
    import pysam
except ImportError :
    print "[Error] It seems that you haven't install \"pysam\" package.. Please do it before you run this script."
    exit(-1)

import sys
from bs_align_utils import *

BAM = 'bam'
SAM = 'sam'
BS_SEEKER1 = 'bs_seeker1'

formats = [BAM, SAM, BS_SEEKER1]

class outfile:
    def __init__(self, filename, format, chrom_len, cmd_line, suppress_SAM_header):
        self.filename = filename
        self.format = format
        self.chrom_ids = dict((k, i) for i, k in enumerate(sorted(chrom_len)))

        if format == BS_SEEKER1:
            self.f = open(filename, 'w')
        elif format in [SAM, BAM]:
            header = { 'HD' : { 'VN': '1.0'},
                       'SQ' : [ {'LN' : chrom_len[c], 'SN' : c} for c in sorted(chrom_len) ],
                       'PG' : [ { 'ID' : 1, 'PN' : 'BS Seeker 2', 'CL' : cmd_line} ]
                     }
            self.f = pysam.Samfile(filename, 'w' + ('b' if format == BAM else ('' if suppress_SAM_header else 'h')), header = header)



    def close(self):
        self.f.close()

    def store(self, qname, N_mismatch, FR, refname, strand, pos, cigar, original_BS, methy, STEVE, rnext = -1, pnext = -1, qual = None, output_genome = None,
              rrbs = False, my_region_serial = -1, my_region_start = 0, my_region_end = 0):

        if self.format == BS_SEEKER1:

            # remove the soft clipped bases from the read
            # this is done for backwards compatibility with the old format
            r_start, r_end, _ = get_read_start_end_and_genome_length(cigar)
            original_BS = original_BS[r_start : r_end]

            if rrbs:
                self.f.write('%s\t%2d\t%s\t%s%s%s\t%s\t%s\t%s\t%d\n' % (qname, N_mismatch, FR, refname, strand, str(pos+1).zfill(10), output_genome, original_BS, methy, STEVE))
            else:
                self.f.write('%s\t%2d\t%s\t%s%s%s\t%s\t%s\t%s\t%d\t%d\t%d\t%d\n' % (qname, N_mismatch, FR, refname, strand, str(pos+1).zfill(10), output_genome, original_BS, methy, my_region_serial, my_region_start, my_region_end, STEVE))


        elif self.format == BAM or self.format == SAM:

            a = pysam.AlignedRead()
            a.qname = qname
            a.seq = original_BS if strand == '+' else reverse_compl_seq(original_BS)
            a.flag =  0x10 if strand == '-' else 0
            a.tid = self.chrom_ids[refname]
            a.pos = pos
            a.mapq = 255
            a.cigar = cigar if strand == '+' else list(reversed(cigar))
            a.rnext = rnext if rnext == -1 else self.chrom_ids[rnext]
            a.pnext = pnext
            a.qual= qual
            if rrbs:
                a.tags = (('XO', FR),
                          ('XS', STEVE),
                          ('NM', N_mismatch),
                          ('XM', methy),
                          ('XG', output_genome),
                          ('YR', my_region_serial),
                          ('YS', my_region_start),
                          ('YE', my_region_end)
                          )

            else:
                a.tags = (('XO', FR),
                          ('XS', STEVE),
                          ('NM', N_mismatch),
                          ('XM', methy),
                          ('XG', output_genome))

            self.f.write(a)