--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PEsortedSAM2readprofile.py	Wed Apr 01 17:05:51 2015 -0400
@@ -0,0 +1,101 @@
+#!/usr/bin/env python
+
+import sys
+from galaxy import eggs
+import pkg_resources
+pkg_resources.require( "bx-python" )
+import bx.seq.twobit
+
+##output columns: read_name chr prefix_start    prefix_end  TR_start    TR_end  suffix_start    suffix_end  TR_length   TR_sequence
+
+samf = open(sys.argv[1],'r') #assumes sam file is sorted by readname
+seq_path = sys.argv[2] #Path to the reference genome in 2bit format
+
+##maxTRlength=int(sys.argv[4])
+##maxoriginalreadlength=int(sys.argv[5])
+maxTRlength=int(sys.argv[3])
+maxoriginalreadlength=int(sys.argv[4])
+outfile=sys.argv[5]
+fout = open(outfile,'w')
+
+twobitfile = bx.seq.twobit.TwoBitFile( file( seq_path ) )
+
+skipped=0
+while True:
+    read = samf.readline().strip()
+    if not(read): #EOF reached
+        break
+    if read[0] == "@":
+        #print read
+        continue
+    mate = samf.readline().strip()
+    if not(mate): #EOF reached
+        break
+    read_elems = read.split()
+    mate_elems = mate.split()
+    read_name = read_elems[0].strip()
+    mate_name = mate_elems[0].strip()
+    while True:
+        if read_name == mate_name:
+            break
+        elif read_name != mate_name:
+            #print >>sys.stderr, "Input SAM file doesn't seem to be sorted by readname. Please sort and retry."
+            #break
+            skipped += 1
+            read = mate
+            read_elems = mate_elems
+            mate = samf.readline().strip()
+            read_name = read_elems[0].strip()
+            mate_name = mate_elems[0].strip()
+            if not(mate): #EOF reached
+                break
+            mate_elems = mate.split()
+    #extract XT:A tag
+    #for e in  read_elems:
+    #    if e.startswith('XT:A'):
+    #        read_xt = e
+    #for e in  mate_elems:
+    #    if e.startswith('XT:A'):
+    #        mate_xt = e
+    #if 'XT:A:U' not in read_elems or 'XT:A:U' not in mate_elems:   #both read and it's mate need to be mapped uniquely
+    #    continue
+    read_chr = read_elems[2]
+    read_start = int(read_elems[3])
+    read_cigar = read_elems[5]
+    if len(read_cigar.split('M')) != 2:     #we want perfect matches only..cigar= <someInt>M
+        continue
+    read_len = int(read_cigar.split('M')[0])
+    mate_chr = mate_elems[2]
+    mate_start = int(mate_elems[3])
+    mate_cigar = mate_elems[5]
+    if len(mate_cigar.split('M')) != 2:     #we want perfect matches only..cigar= <someInt>M
+        continue
+    mate_len = int(mate_cigar.split('M')[0])
+    if read_chr != mate_chr:            # check that they were mapped to the same chromosome
+        continue
+    if abs(read_start - mate_start) > (maxoriginalreadlength+maxTRlength):
+        continue
+    if read_start < mate_start:
+        pre_s = read_start-1
+        pre_e = read_start-1+read_len
+        tr_s = read_start-1+read_len
+        tr_e = mate_start-1
+        suf_s = mate_start-1
+        suf_e = mate_start-1+mate_len
+    else:
+        pre_s = mate_start-1
+        pre_e = mate_start-1+mate_len
+        tr_s = mate_start-1+mate_len
+        tr_e = read_start-1
+        suf_s = read_start-1
+        suf_e = read_start-1+read_len
+    tr_len = abs(tr_e - tr_s)
+    if tr_len > maxTRlength:
+        continue
+    if pre_e >= suf_s:  #overlapping prefix and suffix
+        continue
+    tr_ref_seq = twobitfile[read_chr][tr_s:tr_e]
+    ##print >>fout, "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s" %(read_name,read_chr,pre_s,pre_e,tr_s,tr_e,suf_s,suf_e,tr_len,tr_ref_seq)
+    fout.writelines('\t'.join(map(str,[read_name,read_chr,pre_s,pre_e,tr_s,tr_e,suf_s,suf_e,tr_len,tr_ref_seq]))+'\n')
+
+print  "Skipped %d unpaired reads" %(skipped)