--- a/translate_bed_sequences.py	Thu Dec 15 18:41:21 2016 -0500
+++ b/translate_bed_sequences.py	Tue Apr 07 11:45:53 2020 -0400
@@ -10,366 +10,390 @@
 #  James E Johnson
 #
 #------------------------------------------------------------------------------
-"""
 
-"""
 Input:  BED file (12 column) + 13th sequence column appended by extract_genomic_dna
 Output: Fasta of 3-frame translations of the spliced sequence
-  
 """
 
-import sys,re,os.path
+import optparse
+import os.path
+import sys
 import tempfile
-import optparse
-from optparse import OptionParser
-from Bio.Seq import reverse_complement, transcribe, back_transcribe, translate
+
+from Bio.Seq import (
+    reverse_complement,
+    translate
+)
+
+
+class BedEntry(object):
+    def __init__(self, line):
+        self.line = line
+        try:
+            fields = line.rstrip('\r\n').split('\t')
+            (chrom, chromStart, chromEnd, name, score, strand, thickStart, thickEnd, itemRgb, blockCount, blockSizes, blockStarts) = fields[0:12]
+            seq = fields[12] if len(fields) > 12 else None
+            self.chrom = chrom
+            self.chromStart = int(chromStart)
+            self.chromEnd = int(chromEnd)
+            self.name = name
+            self.score = int(score)
+            self.strand = strand
+            self.thickStart = int(thickStart)
+            self.thickEnd = int(thickEnd)
+            self.itemRgb = itemRgb
+            self.blockCount = int(blockCount)
+            self.blockSizes = [int(x) for x in blockSizes.split(',')]
+            self.blockStarts = [int(x) for x in blockStarts.split(',')]
+            self.seq = seq
+        except Exception as e:
+            sys.stderr.write("Unable to read Bed entry %s\n" % e)
+            exit(1)
+
+    def __str__(self):
+        return '%s\t%d\t%d\t%s\t%d\t%s\t%d\t%d\t%s\t%d\t%s\t%s%s' % (
+               self.chrom, self.chromStart, self.chromEnd, self.name, self.score, self.strand, self.thickStart, self.thickEnd, self.itemRgb, self.blockCount,
+               ','.join([str(x) for x in self.blockSizes]),
+               ','.join([str(x) for x in self.blockStarts]),
+               '\t%s' % self.seq if self.seq else '')
+
+    def get_splice_junctions(self):
+        splice_juncs = []
+        for i in range(self.blockCount - 1):
+            splice_junc = "%s:%d_%d" % (self.chrom, self.chromStart + self.blockSizes[i], self.chromStart + self.blockStarts[i + 1])
+            splice_juncs.append(splice_junc)
+        return splice_juncs
+
+    def get_exon_seqs(self):
+        exons = []
+        for i in range(self.blockCount):
+            # splice_junc = "%s:%d_%d" % (self.chrom, self.chromStart + self.blockSizes[i], self.chromStart + self.blockStarts[i+1])
+            exons.append(self.seq[self.blockStarts[i]:self.blockStarts[i] + self.blockSizes[i]])
+        if self.strand == '-':  # reverse complement
+            exons.reverse()
+            for i, s in enumerate(exons):
+                exons[i] = reverse_complement(s)
+        return exons
+
+    def get_spliced_seq(self):
+        seq = ''.join(self.get_exon_seqs())
+        return seq
+
+    def get_translation(self, sequence=None):
+        translation = None
+        seq = sequence if sequence else self.get_spliced_seq()
+        if seq:
+            seqlen = int(len(seq) / 3) * 3
+            if seqlen >= 3:
+                translation = translate(seq[:seqlen])
+        return translation
+
+    def get_translations(self):
+        translations = []
+        seq = self.get_spliced_seq()
+        if seq:
+            for i in range(3):
+                translation = self.get_translation(sequence=seq[i:])
+                if translation:
+                    translations.append(translation)
+        return translations
+
+    def get_subrange(self, tstart, tstop):
+        """
+        (start, end)
+        """
+        chromStart = self.chromStart
+        chromEnd = self.chromEnd
+        r = range(self.blockCount)
+        if self.strand == '-':
+            r = list(r)
+            r.reverse()
+        bStart = 0
+        for x in r:
+            bEnd = bStart + self.blockSizes[x]
+            if bStart <= tstart < bEnd:
+                if self.strand == '+':
+                    chromStart = self.chromStart + self.blockStarts[x] + (tstart - bStart)
+                else:
+                    chromEnd = self.chromStart + self.blockStarts[x] + (tstart - bStart)
+            if bStart <= tstop < bEnd:
+                if self.strand == '+':
+                    chromEnd = self.chromStart + self.blockStarts[x] + (tstop - bStart)
+                else:
+                    chromStart = self.chromStart + self.blockStarts[x] + self.blockSizes[x] - (tstop - bStart)
+            bStart += self.blockSizes[x]
+        return(chromStart, chromEnd)
 
-class BedEntry( object ):
-  def __init__(self, line):
-    self.line = line
-    try:
-      fields = line.rstrip('\r\n').split('\t')
-      (chrom,chromStart,chromEnd,name,score,strand,thickStart,thickEnd,itemRgb,blockCount,blockSizes,blockStarts) = fields[0:12]
-      seq = fields[12] if len(fields) > 12 else None
-      self.chrom = chrom
-      self.chromStart = int(chromStart)
-      self.chromEnd = int(chromEnd)
-      self.name = name
-      self.score = int(score)
-      self.strand = strand
-      self.thickStart = int(thickStart)
-      self.thickEnd = int(thickEnd)
-      self.itemRgb = itemRgb
-      self.blockCount = int(blockCount)
-      self.blockSizes = [int(x) for x in blockSizes.split(',')]
-      self.blockStarts = [int(x) for x in blockStarts.split(',')]
-      self.seq = seq
-    except Exception, e:
-      print >> sys.stderr, "Unable to read Bed entry" % e
-      exit(1)
-  def __str__(self):
-    return '%s\t%d\t%d\t%s\t%d\t%s\t%d\t%d\t%s\t%d\t%s\t%s%s' % (
-      self.chrom, self.chromStart, self.chromEnd, self.name, self.score, self.strand, self.thickStart, self.thickEnd, self.itemRgb, self.blockCount, 
-      ','.join([str(x) for x in self.blockSizes]), 
-      ','.join([str(x) for x in self.blockStarts]), 
-      '\t%s' % self.seq if self.seq else '')
-  def get_splice_junctions(self): 
-    splice_juncs = []
-    for i in range(self.blockCount  - 1):
-      splice_junc = "%s:%d_%d" % (self.chrom, self.chromStart + self.blockSizes[i], self.chromStart + self.blockStarts[i+1])
-      splice_juncs.append(splice_junc)
-    return splice_juncs
-  def get_exon_seqs(self):
-    exons = []
-    for i in range(self.blockCount):
-      # splice_junc = "%s:%d_%d" % (self.chrom, self.chromStart + self.blockSizes[i], self.chromStart + self.blockStarts[i+1])
-      exons.append(self.seq[self.blockStarts[i]:self.blockStarts[i] + self.blockSizes[i]])
-    if self.strand == '-':  #reverse complement
-      exons.reverse()
-      for i,s in enumerate(exons):
-        exons[i] = reverse_complement(s)
-    return exons
-  def get_spliced_seq(self):
-    seq = ''.join(self.get_exon_seqs())
-    return seq
-  def get_translation(self,sequence=None):
-    translation = None
-    seq = sequence if sequence else self.get_spliced_seq()
-    if seq:
-      seqlen = len(seq) / 3 * 3;
-      if seqlen >= 3:
-        translation = translate(seq[:seqlen])
-    return translation
-  def get_translations(self):
-    translations = []
-    seq = self.get_spliced_seq()
-    if seq:
-      for i in range(3):
-        translation = self.get_translation(sequence=seq[i:])
-        if translation:
-          translations.append(translation)
-    return translations
-  ## (start,end)
-  def get_subrange(self,tstart,tstop):
-    chromStart = self.chromStart
-    chromEnd = self.chromEnd
-    r = range(self.blockCount)
-    if self.strand == '-':
-      r.reverse()
-    bStart = 0
-    for x in r:
-      bEnd = bStart + self.blockSizes[x]
-      if bStart <= tstart < bEnd:
-        if self.strand == '+':
-          chromStart = self.chromStart + self.blockStarts[x] + (tstart - bStart)
-        else:
-          chromEnd = self.chromStart + self.blockStarts[x] + (tstart - bStart)
-      if bStart <= tstop < bEnd:
-        if self.strand == '+':
-          chromEnd = self.chromStart + self.blockStarts[x] + (tstop - bStart)
-        else:
-          chromStart = self.chromStart + self.blockStarts[x] + self.blockSizes[x] - (tstop - bStart)
-      bStart += self.blockSizes[x]
-    return(chromStart,chromEnd)
-  #get the blocks for sub range
-  def get_blocks(self,chromStart,chromEnd):
-    tblockCount = 0
-    tblockSizes = []
-    tblockStarts = []
-    for x in range(self.blockCount):
-      bStart = self.chromStart + self.blockStarts[x]
-      bEnd = bStart + self.blockSizes[x]
-      if bStart > chromEnd:
-        break
-      if bEnd < chromStart:
-              continue
-      cStart = max(chromStart,bStart)
-      tblockStarts.append(cStart - chromStart)
-      tblockSizes.append(min(chromEnd,bEnd) - cStart)
-      tblockCount += 1
-      ## print >> sys.stderr, "tblockCount: %d  tblockStarts: %s  tblockSizes: %s" % (tblockCount,tblockStarts,tblockSizes)
-    return (tblockCount,tblockSizes,tblockStarts)
-  ## [(start,end,seq,blockCount,blockSizes,blockStarts),(start,end,seq,blockCount,blockSizes,blockStarts),(start,end,seq,blockCount,blockSizes,blockStarts)]
-  ## filter: ignore translation if stop codon in first exon after ignore_left_bp
-  def get_filterd_translations(self,untrimmed=False,filtering=True,ignore_left_bp=0,ignore_right_bp=0,debug=False):
-    translations = [None,None,None,None,None,None]
-    seq = self.get_spliced_seq()
-    ignore = (ignore_left_bp if self.strand == '+' else ignore_right_bp) / 3
-    block_sum = sum(self.blockSizes)
-    exon_sizes = [x for x in self.blockSizes]
-    if self.strand == '-':
-      exon_sizes.reverse()
-    splice_sites = [sum(exon_sizes[:x]) / 3 for x in range(1,len(exon_sizes))]
-    if debug:
-      print >> sys.stderr, "splice_sites: %s" % splice_sites
-    junc = splice_sites[0] if len(splice_sites) > 0 else exon_sizes[0]
-    if seq:
-      for i in range(3):
-        translation = self.get_translation(sequence=seq[i:])
-        if translation:
-          tstart = 0
-          tstop = len(translation)
-          offset = (block_sum - i) % 3
-          if debug:
-            print >> sys.stderr, "frame: %d\ttstart: %d  tstop: %d  offset: %d\t%s" % (i,tstart,tstop,offset,translation)
-          if not untrimmed:
-            tstart = translation.rfind('*',0,junc) + 1
-            stop = translation.find('*',junc)
-            tstop = stop if stop >= 0 else len(translation)
-          offset = (block_sum - i) % 3
-          trimmed = translation[tstart:tstop]
-          if debug:
-            print >> sys.stderr, "frame: %d\ttstart: %d  tstop: %d  offset: %d\t%s" % (i,tstart,tstop,offset,trimmed)
-          if filtering and tstart > ignore:
-            continue
-          #get genomic locations for start and end 
-          if self.strand == '+':
-            chromStart = self.chromStart + i + (tstart * 3)
-            chromEnd = self.chromEnd - offset - (len(translation) - tstop) * 3
-          else:
-            chromStart = self.chromStart + offset + (len(translation) - tstop) * 3
-            chromEnd = self.chromEnd - i - (tstart * 3)
-          #get the blocks for this translation
-          (tblockCount,tblockSizes,tblockStarts) = self.get_blocks(chromStart,chromEnd)
-          translations[i] = (chromStart,chromEnd,trimmed,tblockCount,tblockSizes,tblockStarts)
-          if debug:
-            print >> sys.stderr, "tblockCount: %d  tblockStarts: %s  tblockSizes: %s" % (tblockCount,tblockStarts,tblockSizes)
-          # translations[i] = (chromStart,chromEnd,trimmed,tblockCount,tblockSizes,tblockStarts)
-    return translations
-  def get_seq_id(self,seqtype='unk:unk',reference='',frame=None):
-    ## Ensembl fasta ID format
-    # >ID SEQTYPE:STATUS LOCATION GENE TRANSCRIPT
-    # >ENSP00000328693 pep:splice chromosome:NCBI35:1:904515:910768:1 gene:ENSG00000158815:transcript:ENST00000328693 gene_biotype:protein_coding transcript_biotype:protein_coding
-    frame_name = ''
-    chromStart = self.chromStart
-    chromEnd = self.chromEnd
-    strand = 1 if self.strand == '+' else -1
-    if frame != None:
-      block_sum = sum(self.blockSizes)
-      offset = (block_sum - frame) % 3
-      frame_name = '_' + str(frame + 1)
-      if self.strand == '+':
-        chromStart += frame
-        chromEnd -= offset
-      else:
-        chromStart += offset
-        chromEnd -= frame
-    location = "chromosome:%s:%s:%s:%s:%s" % (reference,self.chrom,chromStart,chromEnd,strand)
-    seq_id = "%s%s %s %s" % (self.name,frame_name,seqtype,location)
-    return seq_id
-  def get_line(self, start_offset = 0, end_offset = 0):
-    if start_offset or end_offset:
-      s_offset = start_offset if start_offset else 0
-      e_offset = end_offset if end_offset else 0
-      if s_offset > self.chromStart:
-        s_offset = self.chromStart
-      chrStart = self.chromStart - s_offset
-      chrEnd = self.chromEnd + e_offset
-      blkSizes = self.blockSizes
-      blkSizes[0] += s_offset
-      blkSizes[-1] += e_offset
-      blkStarts = self.blockStarts
-      for i in range(1,self.blockCount):
-        blkStarts[i] += s_offset
-      items = [str(x) for x in [self.chrom,chrStart,chrEnd,self.name,self.score,self.strand,self.thickStart,self.thickEnd,self.itemRgb,self.blockCount,','.join([str(x) for x in blkSizes]),','.join([str(x) for x in blkStarts])]]
-      return '\t'.join(items) + '\n'
-    return self.line
+    def get_blocks(self, chromStart, chromEnd):
+        """
+        get the blocks for sub range
+        """
+        tblockCount = 0
+        tblockSizes = []
+        tblockStarts = []
+        for x in range(self.blockCount):
+            bStart = self.chromStart + self.blockStarts[x]
+            bEnd = bStart + self.blockSizes[x]
+            if bStart > chromEnd:
+                break
+            if bEnd < chromStart:
+                continue
+            cStart = max(chromStart, bStart)
+            tblockStarts.append(cStart - chromStart)
+            tblockSizes.append(min(chromEnd, bEnd) - cStart)
+            tblockCount += 1
+            # print >> sys.stderr, "tblockCount: %d  tblockStarts: %s  tblockSizes: %s" % (tblockCount, tblockStarts, tblockSizes)
+        return (tblockCount, tblockSizes, tblockStarts)
+
+    def get_filterd_translations(self, untrimmed=False, filtering=True, ignore_left_bp=0, ignore_right_bp=0, debug=False):
+        """
+        [(start, end, seq, blockCount, blockSizes, blockStarts), (start, end, seq, blockCount, blockSizes, blockStarts), (start, end, seq, blockCount, blockSizes, blockStarts)]
+        filter: ignore translation if stop codon in first exon after ignore_left_bp
+        """
+        translations = [None, None, None, None, None, None]
+        seq = self.get_spliced_seq()
+        ignore = int((ignore_left_bp if self.strand == '+' else ignore_right_bp) / 3)
+        block_sum = sum(self.blockSizes)
+        exon_sizes = [x for x in self.blockSizes]
+        if self.strand == '-':
+            exon_sizes.reverse()
+        splice_sites = [int(sum(exon_sizes[:x]) / 3) for x in range(1, len(exon_sizes))]
+        if debug:
+            sys.stderr.write("splice_sites: %s\n" % splice_sites)
+        junc = splice_sites[0] if len(splice_sites) > 0 else exon_sizes[0]
+        if seq:
+            for i in range(3):
+                translation = self.get_translation(sequence=seq[i:])
+                if translation:
+                    tstart = 0
+                    tstop = len(translation)
+                    offset = (block_sum - i) % 3
+                    if debug:
+                        sys.stderr.write("frame: %d\ttstart: %d  tstop: %d  offset: %d\t%s\n" % (i, tstart, tstop, offset, translation))
+                    if not untrimmed:
+                        tstart = translation.rfind('*', 0, junc) + 1
+                        stop = translation.find('*', junc)
+                        tstop = stop if stop >= 0 else len(translation)
+                    offset = (block_sum - i) % 3
+                    trimmed = translation[tstart:tstop]
+                    if debug:
+                        sys.stderr.write("frame: %d\ttstart: %d  tstop: %d  offset: %d\t%s\n" % (i, tstart, tstop, offset, trimmed))
+                    if filtering and tstart > ignore:
+                        continue
+                    # get genomic locations for start and end
+                    if self.strand == '+':
+                        chromStart = self.chromStart + i + (tstart * 3)
+                        chromEnd = self.chromEnd - offset - (len(translation) - tstop) * 3
+                    else:
+                        chromStart = self.chromStart + offset + (len(translation) - tstop) * 3
+                        chromEnd = self.chromEnd - i - (tstart * 3)
+                    # get the blocks for this translation
+                    (tblockCount, tblockSizes, tblockStarts) = self.get_blocks(chromStart, chromEnd)
+                    translations[i] = (chromStart, chromEnd, trimmed, tblockCount, tblockSizes, tblockStarts)
+                    if debug:
+                        sys.stderr.write("tblockCount: %d  tblockStarts: %s  tblockSizes: %s\n" % (tblockCount, tblockStarts, tblockSizes))
+                    # translations[i] = (chromStart, chromEnd, trimmed, tblockCount, tblockSizes, tblockStarts)
+        return translations
+
+    def get_seq_id(self, seqtype='unk:unk', reference='', frame=None):
+        """
+        # Ensembl fasta ID format
+        >ID SEQTYPE:STATUS LOCATION GENE TRANSCRIPT
+        >ENSP00000328693 pep:splice chromosome:NCBI35:1:904515:910768:1 gene:ENSG00000158815:transcript:ENST00000328693 gene_biotype:protein_coding transcript_biotype:protein_coding
+        """
+        frame_name = ''
+        chromStart = self.chromStart
+        chromEnd = self.chromEnd
+        strand = 1 if self.strand == '+' else -1
+        if frame is not None:
+            block_sum = sum(self.blockSizes)
+            offset = (block_sum - frame) % 3
+            frame_name = '_' + str(frame + 1)
+            if self.strand == '+':
+                chromStart += frame
+                chromEnd -= offset
+            else:
+                chromStart += offset
+                chromEnd -= frame
+        location = "chromosome:%s:%s:%s:%s:%s" % (reference, self.chrom, chromStart, chromEnd, strand)
+        seq_id = "%s%s %s %s" % (self.name, frame_name, seqtype, location)
+        return seq_id
+
+    def get_line(self, start_offset=0, end_offset=0):
+        if start_offset or end_offset:
+            s_offset = start_offset if start_offset else 0
+            e_offset = end_offset if end_offset else 0
+            if s_offset > self.chromStart:
+                s_offset = self.chromStart
+            chrStart = self.chromStart - s_offset
+            chrEnd = self.chromEnd + e_offset
+            blkSizes = self.blockSizes
+            blkSizes[0] += s_offset
+            blkSizes[-1] += e_offset
+            blkStarts = self.blockStarts
+            for i in range(1, self.blockCount):
+                blkStarts[i] += s_offset
+            items = [str(x) for x in [self.chrom, chrStart, chrEnd, self.name, self.score, self.strand, self.thickStart, self.thickEnd, self.itemRgb, self.blockCount, ','.join([str(x) for x in blkSizes]), ','.join([str(x) for x in blkStarts])]]
+            return '\t'.join(items) + '\n'
+        return self.line
+
 
 def __main__():
-  #Parse Command Line
-  parser = optparse.OptionParser()
-  parser.add_option( '-i', '--input', dest='input', help='BED file (tophat junctions.bed) with sequence column added' )
-  parser.add_option( '-o', '--output', dest='output', help='Translations of spliced sequence')
-  parser.add_option( '-b', '--bed_format', dest='bed_format', action='store_true', default=False, help='Append translations to bed file instead of fasta'  )
-  parser.add_option( '-D', '--fa_db', dest='fa_db', default=None, help='Prefix DB identifier for fasta ID line, e.g. generic'  )
-  parser.add_option( '-s', '--fa_sep', dest='fa_sep', default='|', help='fasta ID separator defaults to pipe char, e.g. generic|ProtID|description'  )
-  parser.add_option( '-B', '--bed', dest='bed', default=None, help='Output a bed file with added 13th column having translation'  )
-  parser.add_option( '-G', '--gff3', dest='gff', default=None, help='Output translations to a GFF3 file'  )
-  parser.add_option( '-S', '--seqtype', dest='seqtype', default='pep:splice', help='SEQTYPE:STATUS for fasta ID line'  )
-  parser.add_option( '-P', '--id_prefix', dest='id_prefix', default='', help='prefix for the sequence ID'  )
-  parser.add_option( '-R', '--reference', dest='reference', default=None, help='Genome Reference Name for fasta ID location '  )
-  parser.add_option( '-r', '--refsource', dest='refsource', default=None, help='Source for Genome Reference, e.g. Ensembl, UCSC, or NCBI'  )
-  parser.add_option( '-Q', '--score_name', dest='score_name', default=None, help='include in the fasta ID line score_name:score '  )
-  parser.add_option( '-l', '--leading_bp', dest='leading_bp', type='int', default=None, help='leading number of base pairs to ignore when filtering' )
-  parser.add_option( '-t', '--trailing_bp', dest='trailing_bp', type='int', default=None, help='trailing number of base pairs to ignore when filtering' )
-  parser.add_option( '-U', '--unfiltered', dest='filtering', action='store_false', default=True, help='Do NOT filterout translation with stop codon in the first exon'  )
-  parser.add_option( '-u', '--untrimmed', dest='untrimmed', action='store_true', default=False, help='Do NOT trim from splice site to stop codon'  )
-  parser.add_option( '-L', '--min_length', dest='min_length', type='int', default=None, help='Minimun length (to first stop codon)'  )
-  parser.add_option( '-M', '--max_stop_codons', dest='max_stop_codons', type='int', default=None, help='Filter out translations with more than max_stop_codons'  )
-  parser.add_option( '-d', '--debug', dest='debug', action='store_true', default=False, help='Turn on wrapper debugging to stdout'  )
-  (options, args) = parser.parse_args()
-  # Input files
-  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
-  # Output files
-  bed_fh = None
-  gff_fh = None
-  gff_fa_file = None
-  gff_fa = None
-  outFile = None
-  if options.output == None:
-    #write to stdout
-    outFile = sys.stdout
-    if options.gff:
-      gff_fa_file  = tempfile.NamedTemporaryFile(prefix='gff_fasta_',suffix=".fa",dir=os.getcwd()).name
-      gff_fa = open(gff_fa_file,'w')
-  else:
-    try:
-      outPath = os.path.abspath(options.output)
-      outFile = open(outPath, 'w')
-    except Exception, e:
-      print >> sys.stderr, "failed: %s" % e
-      exit(3)
-    if options.gff:
-      gff_fa_file = outPath
-  if options.bed:
-    bed_fh = open(options.bed,'w')
-    bed_fh.write('track name="%s" description="%s" \n' % ('novel_junctioni_translations','test'))
-  if options.gff:
-    gff_fh = open(options.gff,'w')
-    gff_fh.write("##gff-version 3.2.1\n")
-    if options.reference:
-      gff_fh.write("##genome-build %s %s\n" % (options.refsource if options.refsource else 'unknown', options.reference))
-  leading_bp = 0
-  trailing_bp = 0
-  if options.leading_bp:
-    if options.leading_bp >= 0:
-      leading_bp = options.leading_bp
+    # Parse Command Line
+    parser = optparse.OptionParser()
+    parser.add_option('-i', '--input', dest='input', help='BED file (tophat junctions.bed) with sequence column added')
+    parser.add_option('-o', '--output', dest='output', help='Translations of spliced sequence')
+    parser.add_option('-b', '--bed_format', dest='bed_format', action='store_true', default=False, help='Append translations to bed file instead of fasta')
+    parser.add_option('-D', '--fa_db', dest='fa_db', default=None, help='Prefix DB identifier for fasta ID line, e.g. generic')
+    parser.add_option('-s', '--fa_sep', dest='fa_sep', default='|', help='fasta ID separator defaults to pipe char, e.g. generic|ProtID|description')
+    parser.add_option('-B', '--bed', dest='bed', default=None, help='Output a bed file with added 13th column having translation')
+    parser.add_option('-G', '--gff3', dest='gff', default=None, help='Output translations to a GFF3 file')
+    parser.add_option('-S', '--seqtype', dest='seqtype', default='pep:splice', help='SEQTYPE:STATUS for fasta ID line')
+    parser.add_option('-P', '--id_prefix', dest='id_prefix', default='', help='prefix for the sequence ID')
+    parser.add_option('-R', '--reference', dest='reference', default=None, help='Genome Reference Name for fasta ID location ')
+    parser.add_option('-r', '--refsource', dest='refsource', default=None, help='Source for Genome Reference, e.g. Ensembl, UCSC, or NCBI')
+    parser.add_option('-Q', '--score_name', dest='score_name', default=None, help='include in the fasta ID line score_name:score ')
+    parser.add_option('-l', '--leading_bp', dest='leading_bp', type='int', default=None, help='leading number of base pairs to ignore when filtering')
+    parser.add_option('-t', '--trailing_bp', dest='trailing_bp', type='int', default=None, help='trailing number of base pairs to ignore when filtering')
+    parser.add_option('-U', '--unfiltered', dest='filtering', action='store_false', default=True, help='Do NOT filterout translation with stop codon in the first exon')
+    parser.add_option('-u', '--untrimmed', dest='untrimmed', action='store_true', default=False, help='Do NOT trim from splice site to stop codon')
+    parser.add_option('-L', '--min_length', dest='min_length', type='int', default=None, help='Minimun length (to first stop codon)')
+    parser.add_option('-M', '--max_stop_codons', dest='max_stop_codons', type='int', default=None, help='Filter out translations with more than max_stop_codons')
+    parser.add_option('-d', '--debug', dest='debug', action='store_true', default=False, help='Turn on wrapper debugging to stdout')
+    (options, args) = parser.parse_args()
+    # Input files
+    if options.input is not None:
+        try:
+            inputPath = os.path.abspath(options.input)
+            inputFile = open(inputPath, 'r')
+        except Exception as e:
+            sys.stderr.write("failed: %s\n" % e)
+            exit(2)
     else:
-      print >> sys.stderr, "failed: leading_bp must be positive"
-      exit(5)
-  if options.trailing_bp:
-    if  options.trailing_bp >= 0:
-      trailing_bp = options.trailing_bp
+        inputFile = sys.stdin
+    # Output files
+    bed_fh = None
+    gff_fh = None
+    gff_fa_file = None
+    gff_fa = None
+    outFile = None
+    if options.output is None:
+        # write to stdout
+        outFile = sys.stdout
+        if options.gff:
+            gff_fa_file = tempfile.NamedTemporaryFile(prefix='gff_fasta_', suffix=".fa", dir=os.getcwd()).name
+            gff_fa = open(gff_fa_file, 'w')
     else:
-      print >> sys.stderr, "failed: trailing_bp must be positive"
-      exit(5)
-  # Scan bed file 
-  try:
-    for i, line in enumerate( inputFile ):
-      if line.startswith('track'):
-        if outFile and options.bed_format:
-          outFile.write(line)
-        continue
-      entry = BedEntry(line)
-      strand = 1 if entry.strand == '+' else -1
-      translations = entry.get_translations()
-      if options.debug:
-        exon_seqs = entry.get_exon_seqs()
-        exon_sizes = [len(seq) for seq in exon_seqs]
-        splice_sites = [sum(exon_sizes[:x]) / 3 for x in range(1,len(exon_sizes))]
-        print >> sys.stderr, entry.name
-        print >> sys.stderr, line.rstrip('\r\n')
-        print >> sys.stderr, "exons:  %s" % exon_seqs
-        print >> sys.stderr, "%s" % splice_sites
-        for i,translation in enumerate(translations):
-          print >> sys.stderr, "frame %d:  %s" % (i+1,translation)
-          print >> sys.stderr, "splice:   %s" % (''.join(['^' if (((j*3)+i)/3) in splice_sites else '-' for j in range(len(translation))]))
-        print >> sys.stderr, ""
-      if options.bed_format:
-        tx_entry  = "%s\t%s\n" % (line.rstrip('\r\n'),'\t'.join(translations))
-        outFile.write(tx_entry)
-      else:
-        translations = entry.get_filterd_translations(untrimmed=options.untrimmed,filtering=options.filtering,ignore_left_bp=leading_bp,ignore_right_bp=trailing_bp,debug=options.debug)
-        for i,tx in enumerate(translations):
-          if tx:
-            (chromStart,chromEnd,translation,blockCount,blockSizes,blockStarts) = tx
-            if options.min_length != None and len(translation) < options.min_length:
-              continue
-            if options.max_stop_codons != None and translation.count('*') > options.max_stop_codons:
-              continue
-            frame_name = '_%s' % (i + 1)
-            pep_id = "%s%s%s" % (options.id_prefix,entry.name,frame_name)
-            if bed_fh:
-              bed_fh.write('%s\t%d\t%d\t%s\t%d\t%s\t%d\t%d\t%s\t%d\t%s\t%s\t%s\n' % (str(entry.chrom),chromStart,chromEnd,pep_id,entry.score,entry.strand,chromStart,chromEnd,entry.itemRgb,blockCount,','.join([str(x) for x in blockSizes]),','.join([str(x) for x in blockStarts]),translation))
-            location = "chromosome:%s:%s:%s:%s:%s" % (options.reference,entry.chrom,chromStart,chromEnd,strand)
-            score = " %s:%s" % (options.score_name,entry.score) if options.score_name else ''
-            seq_description = "%s %s%s" % (options.seqtype, location, score)
-            seq_id = "%s " % pep_id
-            if options.fa_db:
-              seq_id = "%s%s%s%s" % (options.fa_db,options.fa_sep,pep_id,options.fa_sep)
-            fa_id = "%s%s" % (seq_id,seq_description)
-            fa_entry = ">%s\n%s\n" % (fa_id,translation)
-            outFile.write(fa_entry)
-            if gff_fh:
-              if gff_fa:
-                gff_fa.write(fa_entry)
-              gff_fh.write("##sequence-region %s %d %d\n" % (entry.chrom,chromStart + 1,chromEnd - 1))
-              gff_fh.write("%s\t%s\t%s\t%s\t%s\t%s\t%s\t%d\tID=%s\n" % (entry.chrom,'splice_junc','gene',chromStart + 1,chromEnd - 1,entry.score,entry.strand,0,pep_id))
-              for x in range(blockCount):
-                start = chromStart+blockStarts[x] + 1
-                end = start + blockSizes[x] - 1
-                phase = (3 - sum(blockSizes[:x]) % 3) % 3
-                gff_fh.write("%s\t%s\t%s\t%s\t%s\t%s\t%s\t%d\tParent=%s;ID=%s_%d\n" % (entry.chrom,'splice_junc','CDS',start,end,entry.score,entry.strand,phase,pep_id,pep_id,x))
-              """
-              ##gff-version 3
-              ##sequence-region 19 1 287484
-              19      MassSpec        peptide 282299  287484  10.0    -       0       ID=TEARLSFYSGHSSFGMYCMVFLALYVQ
-              19      MassSpec        CDS     287474  287484  .       -       0       Parent=TEARLSFYSGHSSFGMYCMVFLALYVQ;transcript_id=ENST00000269812
-              19      MassSpec        CDS     282752  282809  .       -       1       Parent=TEARLSFYSGHSSFGMYCMVFLALYVQ;transcript_id=ENST00000269812
-              19      MassSpec        CDS     282299  282310  .       -       0       Parent=TEARLSFYSGHSSFGMYCMVFLALYVQ;transcript_id=ENST00000269812
-              """
-    if bed_fh:
-      bed_fh.close()
-    if gff_fh:
-      if gff_fa:
-        gff_fa.close()
-      else:
-        outFile.close()
-      gff_fa = open(gff_fa_file,'r')
-      gff_fh.write("##FASTA\n")
-      for i, line in enumerate(gff_fa):
-        gff_fh.write(line)
-      gff_fh.close() 
-  except Exception, e:
-    print >> sys.stderr, "failed: Error reading %s - %s" % (options.input if options.input else 'stdin',e)
+        try:
+            outPath = os.path.abspath(options.output)
+            outFile = open(outPath, 'w')
+        except Exception as e:
+            sys.stderr.write("failed: %s\n" % e)
+            exit(3)
+        if options.gff:
+            gff_fa_file = outPath
+    if options.bed:
+        bed_fh = open(options.bed, 'w')
+        bed_fh.write('track name="%s" description="%s" \n' % ('novel_junctioni_translations', 'test'))
+    if options.gff:
+        gff_fh = open(options.gff, 'w')
+        gff_fh.write("##gff-version 3.2.1\n")
+        if options.reference:
+            gff_fh.write("##genome-build %s %s\n" % (options.refsource if options.refsource else 'unknown', options.reference))
+    leading_bp = 0
+    trailing_bp = 0
+    if options.leading_bp:
+        if options.leading_bp >= 0:
+            leading_bp = options.leading_bp
+        else:
+            sys.stderr.write("failed: leading_bp must be positive\n")
+            exit(5)
+    if options.trailing_bp:
+        if options.trailing_bp >= 0:
+            trailing_bp = options.trailing_bp
+        else:
+            sys.stderr.write("failed: trailing_bp must be positive\n")
+            exit(5)
+    # Scan bed file
+    try:
+        for i, line in enumerate(inputFile):
+            if line.startswith('track'):
+                if outFile and options.bed_format:
+                    outFile.write(line)
+                continue
+            entry = BedEntry(line)
+            strand = 1 if entry.strand == '+' else -1
+            translations = entry.get_translations()
+            if options.debug:
+                exon_seqs = entry.get_exon_seqs()
+                exon_sizes = [len(seq) for seq in exon_seqs]
+                splice_sites = [int(sum(exon_sizes[:x]) / 3) for x in range(1, len(exon_sizes))]
+                sys.stderr.write("%s\n" % entry.name)
+                sys.stderr.write("%s\n" % line.rstrip('\r\n'))
+                sys.stderr.write("exons:  %s\n" % exon_seqs)
+                sys.stderr.write("%s\n" % splice_sites)
+                for i, translation in enumerate(translations):
+                    sys.stderr.write("frame %d:  %s\n" % (i + 1, translation))
+                    sys.stderr.write("splice:   %s\n" % (''.join(['^' if int(((j * 3) + i) / 3) in splice_sites else '-' for j in range(len(translation))])))
+                sys.stderr.write("\n")
+            if options.bed_format:
+                tx_entry = "%s\t%s\n" % (line.rstrip('\r\n'), '\t'.join(translations))
+                outFile.write(tx_entry)
+            else:
+                translations = entry.get_filterd_translations(untrimmed=options.untrimmed, filtering=options.filtering, ignore_left_bp=leading_bp, ignore_right_bp=trailing_bp, debug=options.debug)
+                for i, tx in enumerate(translations):
+                    if tx:
+                        (chromStart, chromEnd, translation, blockCount, blockSizes, blockStarts) = tx
+                        if options.min_length is not None and len(translation) < options.min_length:
+                            continue
+                        if options.max_stop_codons is not None and translation.count('*') > options.max_stop_codons:
+                            continue
+                        frame_name = '_%s' % (i + 1)
+                        pep_id = "%s%s%s" % (options.id_prefix, entry.name, frame_name)
+                        if bed_fh:
+                            bed_fh.write('%s\t%d\t%d\t%s\t%d\t%s\t%d\t%d\t%s\t%d\t%s\t%s\t%s\n' % (str(entry.chrom), chromStart, chromEnd, pep_id, entry.score, entry.strand, chromStart, chromEnd, entry.itemRgb, blockCount, ','.join([str(x) for x in blockSizes]), ','.join([str(x) for x in blockStarts]), translation))
+                        location = "chromosome:%s:%s:%s:%s:%s" % (options.reference, entry.chrom, chromStart, chromEnd, strand)
+                        score = " %s:%s" % (options.score_name, entry.score) if options.score_name else ''
+                        seq_description = "%s %s%s" % (options.seqtype, location, score)
+                        seq_id = "%s " % pep_id
+                        if options.fa_db:
+                            seq_id = "%s%s%s%s" % (options.fa_db, options.fa_sep, pep_id, options.fa_sep)
+                        fa_id = "%s%s" % (seq_id, seq_description)
+                        fa_entry = ">%s\n%s\n" % (fa_id, translation)
+                        outFile.write(fa_entry)
+                        if gff_fh:
+                            if gff_fa:
+                                gff_fa.write(fa_entry)
+                            gff_fh.write("##sequence-region %s %d %d\n" % (entry.chrom, chromStart + 1, chromEnd - 1))
+                            gff_fh.write("%s\t%s\t%s\t%s\t%s\t%s\t%s\t%d\tID=%s\n" % (entry.chrom, 'splice_junc', 'gene', chromStart + 1, chromEnd - 1, entry.score, entry.strand, 0, pep_id))
+                            for x in range(blockCount):
+                                start = chromStart + blockStarts[x] + 1
+                                end = start + blockSizes[x] - 1
+                                phase = (3 - sum(blockSizes[:x]) % 3) % 3
+                                gff_fh.write("%s\t%s\t%s\t%s\t%s\t%s\t%s\t%d\tParent=%s;ID=%s_%d\n" % (entry.chrom, 'splice_junc', 'CDS', start, end, entry.score, entry.strand, phase, pep_id, pep_id, x))
+                            # ##gff-version 3
+                            # ##sequence-region 19 1 287484
+                            # 19      MassSpec        peptide 282299  287484  10.0    -       0       ID=TEARLSFYSGHSSFGMYCMVFLALYVQ
+                            # 19      MassSpec        CDS     287474  287484  .       -       0       Parent=TEARLSFYSGHSSFGMYCMVFLALYVQ;transcript_id=ENST00000269812
+                            # 19      MassSpec        CDS     282752  282809  .       -       1       Parent=TEARLSFYSGHSSFGMYCMVFLALYVQ;transcript_id=ENST00000269812
+                            # 19      MassSpec        CDS     282299  282310  .       -       0       Parent=TEARLSFYSGHSSFGMYCMVFLALYVQ;transcript_id=ENST00000269812
+        if bed_fh:
+            bed_fh.close()
+        if gff_fh:
+            if gff_fa:
+                gff_fa.close()
+            else:
+                outFile.close()
+            gff_fa = open(gff_fa_file, 'r')
+            gff_fh.write("##FASTA\n")
+            for i, line in enumerate(gff_fa):
+                gff_fh.write(line)
+            gff_fh.close()
+    except Exception as e:
+        sys.stderr.write("failed: Error reading %s - %s\n" % (options.input if options.input else 'stdin', e))
+        raise
+        exit(1)
 
-if __name__ == "__main__" : __main__()
 
+if __name__ == "__main__":
+    __main__()