--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bed_to_protein_map.py	Mon Nov 20 14:58:18 2017 -0500
@@ -0,0 +1,120 @@
+#!/usr/bin/env python
+"""
+"""
+import sys
+import os.path
+import optparse
+
+"""
+X	276352	291629	ENST00000430923	20	+	284187	291629	80,80,80	5	42,148,137,129,131	0,7814,12380,14295,15146
+X	304749	318819	ENST00000326153	20	-	305073	318787	80,80,80	10	448,153,149,209,159,68,131,71,138,381	0,2610,2982,6669,8016,9400,10140,10479,12164,13689
+grep ENST bed_to_protein_map.py | grep -v grep | ./bed_to_protein_map.py
+"""
+
+def __main__():
+    #Parse Command Line
+    parser = optparse.OptionParser()
+    #I/O
+    parser.add_option( '-i', '--input', dest='input', default=None, help='Tabular file with peptide_sequence column' )
+    parser.add_option( '-c', '--column', type='int', dest='column', default=1, help='column ordinal with Ensembl transcript ID' )
+    parser.add_option( '-g', '--gtf', dest='gtf', default=None, help='GTF gene model file. Used to annotate NSJ peptide entries.')
+    parser.add_option( '-2', '--twobit', dest='twobit', default=None, help='Reference genome in UCSC twobit format')
+    parser.add_option( '-C', '--coding', dest='coding', action='store_true', default=False, help='Output coding BED line')
+    parser.add_option( '-o', '--output', dest='output', default=None, help='The output bed (else write to stdout)' )
+    parser.add_option( '-s', '--sqlitedb', dest='sqlitedb', default=None, help='The sqlitedb' )
+    parser.add_option( '--debug', dest='debug', action='store_true', default=False, help='Print debugging messages')
+    (options, args) = parser.parse_args()
+    ##INPUTS##
+    if options.input != None:
+        try:
+            inputPath = os.path.abspath(options.input)
+            inputFile = open(inputPath, 'r')
+        except Exception, e:
+            print >> sys.stderr, "failed: %s" % e
+            exit(2)
+    else:
+        inputFile = sys.stdin
+
+    if options.output != None:
+        try:
+            outputPath = os.path.abspath(options.output)
+            outputFile = open(outputPath, 'w')
+        except Exception, e:
+            print >> sys.stderr, "failed: %s" % e
+            exit(3)
+    else:
+        outputFile = sys.stdout
+
+    dbFile = None
+    if options.sqlitedb != None:
+        try:
+            dbPath = os.path.abspath(options.sqlitedb)
+            dbFile = open(dbPath, 'w')
+        except Exception, e:
+            print >> sys.stderr, "failed: %s" % e
+            exit(3)
+
+
+    try:
+        for linenum,line in enumerate(inputFile):
+            if options.debug:
+                print >> sys.stderr, "%d: %s\n" % (linenum,line)
+            if line.startswith('#'):
+                continue
+            if line.strip() == '':
+                continue
+            fields = line.rstrip('\r\n').split('\t')
+            if len(fields) < 12:
+                print >> sys.stderr, "%d: %s\n" % (linenum,line)
+                continue
+            (chrom,_chromStart,_chromEnd,name,score,strand,_thickStart,_thickEnd,itemRgb,_blockCount,blockSizes,blockStarts) = fields[0:12]
+            chromStart = int(_chromStart)
+            chromEnd = int(_chromEnd)
+            thickStart = int(_thickStart)
+            thickEnd = int(_thickEnd)
+            blockCount = int(_blockCount)
+            blockSizes = [int(x) for x in blockSizes.split(',')]
+            blockStarts = [int(x) for x in blockStarts.split(',')]
+            if strand == '+':
+                cds_start = 0
+                cds_end = 0
+                for i in range(blockCount):
+                    start = chromStart + blockStarts[i]
+                    end = start + blockSizes[i]
+                    if end < thickStart:
+                        continue
+                    if start > thickEnd:
+                        break
+                    if start < thickStart:  
+                        start = thickStart
+                    if end > thickEnd:
+                        end = thickEnd
+                    cds_end = cds_start + (end - start)
+                    ##dbFile.write('%s\t%s\t%d\t%d\t%s\t%d\t%d\n' % (name,chrom,start,end,strand,cds_start,cds_end))
+                    outputFile.write('%s\t%s\t%d\t%d\t%s\t%d\t%d\n' % (name,chrom,start,end,strand,cds_start,cds_end))
+                    cds_start = cds_end
+            elif strand == '-':
+                cds_start = 0
+                cds_end = 0
+                for i in reversed(range(blockCount)):
+                    start = chromStart + blockStarts[i]
+                    end = start + blockSizes[i]
+                    if end < thickStart:
+                        break
+                    if start > thickEnd:
+                        continue
+                    if start < thickStart:  
+                        start = thickStart
+                    if end > thickEnd:
+                        end = thickEnd
+                    cds_end = cds_start + (end - start)
+                    outputFile.write('%s\t%s\t%d\t%d\t%s\t%d\t%d\n' % (name,chrom,start,end,strand,cds_start,cds_end))
+                    cds_start = cds_end
+                pass
+    except Exception, e:
+        print >> sys.stderr, "failed: %s" % e
+        exit(1)
+
+
+if __name__ == "__main__" : __main__()
+