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

Initial upload

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/BSseeker2/bs_align/output.py	Fri Jul 12 18:47:28 2013 -0400
@@ -0,0 +1,83 @@
+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)