--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/translate_bed_sequences.py	Mon Jan 25 12:21:21 2016 -0500
@@ -0,0 +1,375 @@
+#!/usr/bin/env python
+"""
+#
+#------------------------------------------------------------------------------
+#                         University of Minnesota
+#         Copyright 2014, Regents of the University of Minnesota
+#------------------------------------------------------------------------------
+# Author:
+#
+#  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 tempfile
+import optparse
+from optparse import OptionParser
+from Bio.Seq import reverse_complement, transcribe, back_transcribe, 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, 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 __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
+    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
+    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)
+
+if __name__ == "__main__" : __main__()
+