diff tools/samtools/pileup_interval.py @ 0:9071e359b9a3

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/samtools/pileup_interval.py	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,117 @@
+#!/usr/bin/env python
+
+"""
+Condenses pileup format into ranges of bases.
+
+usage: %prog [options]
+   -i, --input=i: Input pileup file
+   -o, --output=o: Output pileup
+   -c, --coverage=c: Coverage
+   -f, --format=f: Pileup format
+   -b, --base=b: Base to select
+   -s, --seq_column=s: Sequence column
+   -l, --loc_column=l: Base location column
+   -r, --base_column=r: Reference base column
+   -C, --cvrg_column=C: Coverage column
+"""
+
+from galaxy import eggs
+import pkg_resources; pkg_resources.require( "bx-python" )
+from bx.cookbook import doc_optparse
+import sys
+
+def stop_err( msg ):
+    sys.stderr.write( msg )
+    sys.exit()
+
+def __main__():
+    strout = ''
+    #Parse Command Line
+    options, args = doc_optparse.parse( __doc__ )
+    coverage = int(options.coverage)
+    fin = file(options.input, 'r')
+    fout = file(options.output, 'w')
+    inLine = fin.readline()
+    if options.format == 'six':
+        seqIndex = 0
+        locIndex = 1
+        baseIndex = 2
+        covIndex = 3
+    elif options.format == 'ten':
+        seqIndex = 0
+        locIndex = 1
+        if options.base == 'first':
+            baseIndex = 2
+        else:
+            baseIndex = 3
+        covIndex = 7
+    else:
+        seqIndex = int(options.seq_column) - 1
+        locIndex = int(options.loc_column) - 1
+        baseIndex = int(options.base_column) - 1
+        covIndex = int(options.cvrg_column) - 1
+    lastSeq = ''
+    lastLoc = -1
+    locs = []
+    startLoc = -1
+    bases = []
+    while inLine.strip() != '':
+        lineParts = inLine.split('\t')
+        try:
+            seq, loc, base, cov = lineParts[seqIndex], int(lineParts[locIndex]), lineParts[baseIndex], int(lineParts[covIndex])
+        except IndexError, ei:
+            if options.format == 'ten':
+                stop_err( 'It appears that you have selected 10 columns while your file has 6. Make sure that the number of columns you specify matches the number in your file.\n' + str( ei ) )
+            else:
+                stop_err( 'There appears to be something wrong with your column index values.\n' + str( ei ) )
+        except ValueError, ev:
+            if options.format == 'six':
+                stop_err( 'It appears that you have selected 6 columns while your file has 10. Make sure that the number of columns you specify matches the number in your file.\n' + str( ev ) )
+            else:
+                stop_err( 'There appears to be something wrong with your column index values.\n' + str( ev ) )
+#        strout += str(startLoc) + '\n'
+#        strout += str(bases) + '\n'
+#        strout += '%s\t%s\t%s\t%s\n' % (seq, loc, base, cov)
+        if loc == lastLoc+1 or lastLoc == -1:
+            if cov >= coverage:
+                if seq == lastSeq or lastSeq == '':
+                    if startLoc == -1:
+                        startLoc = loc
+                    locs.append(loc)
+                    bases.append(base)
+                else:
+                    if len(bases) > 0:
+                        fout.write('%s\t%s\t%s\t%s\n' % (lastSeq, startLoc-1, lastLoc, ''.join(bases)))
+                    startLoc = loc
+                    locs = [loc]
+                    bases = [base]
+            else:
+                if len(bases) > 0:
+                    fout.write('%s\t%s\t%s\t%s\n' % (lastSeq, startLoc-1, lastLoc, ''.join(bases)))
+                startLoc = -1
+                locs = []
+                bases = []
+        else:
+            if len(bases) > 0:
+                fout.write('%s\t%s\t%s\t%s\n' % (lastSeq, startLoc-1, lastLoc, ''.join(bases)))
+            if cov >= coverage:
+                startLoc = loc
+                locs = [loc]
+                bases = [base]
+            else:
+                startLoc = -1
+                locs = []
+                bases = []
+        lastSeq = seq
+        lastLoc = loc
+        inLine = fin.readline()
+    if len(bases) > 0:
+        fout.write('%s\t%s\t%s\t%s\n' % (lastSeq, startLoc-1, lastLoc, ''.join(bases)))
+    fout.close()
+    fin.close()
+    
+#    import sys
+#    strout += file(fout.name,'r').read()
+#    sys.stderr.write(strout)
+
+if __name__ == "__main__" : __main__()