# HG changeset patch
# User galaxyp
# Date 1516647542 18000
# Node ID 817e54905a9f8e7e48a3e20d35b0721dc18b9756
# Parent  d615767650a0545af37f69db45e0d5fa21590b74
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed commit 383bb485120a193bcc14f88364e51356d6ede219

diff -r d615767650a0 -r 817e54905a9f bedutil.py
--- a/bedutil.py	Sun Jan 14 14:06:15 2018 -0500
+++ b/bedutil.py	Mon Jan 22 13:59:02 2018 -0500
@@ -12,6 +12,8 @@
 #------------------------------------------------------------------------------
 """
 
+from __future__ import print_function
+
 import sys
 
 from Bio.Seq import reverse_complement, translate
@@ -45,6 +47,17 @@
     return bed_entry
 
 
+def as_int_list(obj):
+    if obj is None:
+        return None
+    if isinstance(obj, list):
+        return [int(x) for x in obj]
+    elif isinstance(obj, str):
+        return [int(x) for x in obj.split(',')]
+    else:  # python2 unicode?
+        return [int(x) for x in str(obj).split(',')]
+
+
 class BedEntry(object):
     def __init__(self, chrom=None, chromStart=None, chromEnd=None,
                  name=None, score=None, strand=None,
@@ -60,18 +73,8 @@
         self.thickEnd = int(thickEnd) if thickEnd else self.chromEnd
         self.itemRgb = str(itemRgb) if itemRgb is not None else r'100,100,100'
         self.blockCount = int(blockCount)
-        if isinstance(blockSizes, str) or isinstance(blockSizes, unicode):
-            self.blockSizes = [int(x) for x in blockSizes.split(',')]
-        elif isinstance(blockSizes, list):
-            self.blockSizes = [int(x) for x in blockSizes]
-        else:
-            self.blockSizes = blockSizes
-        if isinstance(blockStarts, str) or isinstance(blockSizes, unicode):
-            self.blockStarts = [int(x) for x in blockStarts.split(',')]
-        elif isinstance(blockStarts, list):
-            self.blockStarts = [int(x) for x in blockStarts]
-        else:
-            self.blockStarts = blockStarts
+        self.blockSizes = as_int_list(blockSizes)
+        self.blockStarts = as_int_list(blockStarts)
         self.second_name = None
         self.cds_start_status = None
         self.cds_end_status = None
@@ -165,6 +168,11 @@
                 return self.set_cds(min(cds_pos), max(cds_pos) + basepairs)
         return None
 
+    def get_cds_bed(self):
+        cds_pos = [self.cdna_offset_of_pos(self.thickStart),
+                   self.cdna_offset_of_pos(self.thickEnd)]
+        return self.trim(min(cds_pos), max(cds_pos))
+
     def get_cigar(self):
         cigar = ''
         r = range(self.blockCount)
@@ -214,7 +222,7 @@
 
     def pos_of_cdna_offet(self, offset):
         if offset is not None and 0 <= offset < sum(self.blockSizes):
-            r = range(self.blockCount)
+            r = list(range(self.blockCount))
             rev = self.strand == '-'
             if rev:
                 r.reverse()
@@ -233,7 +241,7 @@
     def cdna_offset_of_pos(self, pos):
         if not self.chromStart <= pos < self.chromEnd:
             return -1
-        r = range(self.blockCount)
+        r = list(range(self.blockCount))
         rev = self.strand == '-'
         if rev:
             r.reverse()
@@ -248,19 +256,21 @@
     def apply_variant(self, pos, ref, alt):
         pos = int(pos)
         if not ref or not alt:
-            print >> sys.stderr, "variant requires ref and alt sequences"
+            print("variant requires ref and alt sequences", file=sys.stderr)
             return
         if not self.chromStart <= pos <= self.chromEnd:
-            print >> sys.stderr, "variant not in entry %s: %s %d < %d < %d"\
-                % (self.name, self.strand, self.chromStart, pos, self.chromEnd)
-            print >> sys.stderr, "%s" % str(self)
+            print("variant not in entry %s: %s %d < %d < %d" %
+                  (self.name, self.strand,
+                   self.chromStart, pos, self.chromEnd),
+                  file=sys.stderr)
+            print("%s" % str(self), file=sys.stderr)
             return
         if len(ref) != len(alt):
-            print >> sys.stderr, "variant only works for snp: %s  %s"\
-                % (ref, alt)
+            print("variant only works for snp: %s  %s" % (ref, alt),
+                  file=sys.stderr)
             return
         if not self.seq:
-            print >> sys.stderr, "variant entry %s has no seq" % self.name
+            print("variant entry %s has no seq" % self.name, file=sys.stderr)
             return
         """
         if self.strand  == '-':
@@ -274,27 +284,27 @@
             if offset is not None:
                 bases[offset+i] = alt[i]
             else:
-                print >> sys.stderr,\
-                    "variant offset %s: %s %d < %d < %d"\
-                    % (self.name, self.strand, self.chromStart,
-                       pos+1, self.chromEnd)
-                print >> sys.stderr, "%s" % str(self)
+                print("variant offset %s: %s %d < %d < %d" %
+                      (self.name, self.strand, self.chromStart,
+                       pos+1, self.chromEnd), file=sys.stderr)
+                print("%s" % str(self), file=sys.stderr)
         self.seq = ''.join(bases)
         self.variants.append("g.%d%s>%s" % (pos+1, ref, alt))
 
     def get_variant_bed(self, pos, ref, alt):
         pos = int(pos)
         if not ref or not alt:
-            print >> sys.stderr, "variant requires ref and alt sequences"
+            print("variant requires ref and alt sequences", file=sys.stderr)
             return None
         if not self.chromStart <= pos <= self.chromEnd:
-            print >> sys.stderr,\
-                "variant not in entry %s: %s %d < %d < %d"\
-                % (self.name, self.strand, self.chromStart, pos, self.chromEnd)
-            print >> sys.stderr, "%s" % str(self)
+            print("variant not in entry %s: %s %d < %d < %d" %
+                  (self.name, self.strand,
+                   self.chromStart, pos, self.chromEnd),
+                  file=sys.stderr)
+            print("%s" % str(self), file=sys.stderr)
             return None
         if not self.seq:
-            print >> sys.stderr, "variant entry %s has no seq" % self.name
+            print("variant entry %s has no seq" % self.name, file=sys.stderr)
             return None
         tbed = BedEntry(chrom=self.chrom,
                         chromStart=self.chromStart, chromEnd=self.chromEnd,
@@ -330,8 +340,8 @@
         chromStart = self.chromStart
         chromEnd = self.chromEnd
         if debug:
-            print >> sys.stderr, "%s" % (str(self))
-        r = range(self.blockCount)
+            print("%s" % (str(self)), file=sys.stderr)
+        r = list(range(self.blockCount))
         if self.strand == '-':
             r.reverse()
         bStart = 0
@@ -353,10 +363,9 @@
                     chromStart = self.chromStart + self.blockStarts[x] +\
                         self.blockSizes[x] - (tstop - bStart)
             if debug:
-                print >> sys.stderr,\
-                    "%3d %s\t%d\t%d\t%d\t%d\t%d\t%d"\
-                    % (x, self.strand, bStart, bEnd,
-                       tstart, tstop, chromStart, chromEnd)
+                print("%3d %s\t%d\t%d\t%d\t%d\t%d\t%d" %
+                      (x, self.strand, bStart, bEnd,
+                       tstart, tstop, chromStart, chromEnd), file=sys.stderr)
             bStart += self.blockSizes[x]
         return(chromStart, chromEnd)
 
@@ -409,7 +418,7 @@
         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
+            print("splice_sites: %s" % splice_sites, file=sys.stderr)
         junc = splice_sites[0] if len(splice_sites) > 0 else exon_sizes[0]
         if seq:
             for i in range(3):
@@ -419,9 +428,10 @@
                     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)
+                        print("frame: %d\ttstart: %d  tstop: %d  " +
+                              "offset: %d\t%s" %
+                              (i, tstart, tstop, offset, translation),
+                              file=sys.stderr)
                     if not untrimmed:
                         tstart = translation.rfind('*', 0, junc) + 1
                         stop = translation.find('*', junc)
@@ -429,9 +439,10 @@
                     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)
+                        print("frame: %d\ttstart: %d  tstop: %d  " +
+                              "offset: %d\t%s" %
+                              (i, tstart, tstop, offset, trimmed),
+                              file=sys.stderr)
                     if filtering and tstart > ignore:
                         continue
                     # get genomic locations for start and end
@@ -449,9 +460,10 @@
                     translations[i] = (chromStart, chromEnd, trimmed,
                                        tblockCount, tblockSizes, tblockStarts)
                     if debug:
-                        print >> sys.stderr,\
-                            "tblockCount: %d tblockStarts: %s tblockSizes: %s"\
-                            % (tblockCount, tblockStarts, tblockSizes)
+                        print("tblockCount: %d tblockStarts: %s " +
+                              "tblockSizes: %s" %
+                              (tblockCount, tblockStarts, tblockSizes),
+                              file=sys.stderr)
         return translations
 
     def get_seq_id(self, seqtype='unk:unk', reference='', frame=None):
diff -r d615767650a0 -r 817e54905a9f ensembl_rest.py
--- a/ensembl_rest.py	Sun Jan 14 14:06:15 2018 -0500
+++ b/ensembl_rest.py	Mon Jan 22 13:59:02 2018 -0500
@@ -12,6 +12,8 @@
 #------------------------------------------------------------------------------
 """
 
+from __future__ import print_function
+from __future__ import unicode_literals
 
 import sys
 
@@ -28,10 +30,10 @@
 
 def ensembl_rest(ext, headers):
     if debug:
-        print >> sys.stderr, "%s" % ext
+        print("%s" % ext, file=sys.stderr)
     r = requests.get(server+ext, headers=headers)
     if r.status_code == 429:
-        print >> sys.stderr, "response headers: %s\n" % r.headers
+        print("response headers: %s\n" % r.headers, file=sys.stderr)
         if 'Retry-After' in r.headers:
             sleep(r.headers['Retry-After'])
             r = requests.get(server+ext, headers=headers)
@@ -47,12 +49,11 @@
     r = ensembl_rest(ext, req_header)
     for species in r.json()['species']:
         results[species['name']] = species
-        print >> sys.stdout,\
-            "%s\t%s\t%s\t%s\t%s"\
-            % (species['name'], species['common_name'],
+        print("%s\t%s\t%s\t%s\t%s" %
+              (species['name'], species['common_name'],
                species['display_name'],
                species['strain'],
-               species['taxon_id'])
+               species['taxon_id']), file=sys.stdout)
     return results
 
 
@@ -86,7 +87,7 @@
     bed = []
     param = params if params else ''
     req_header = {"Content-Type": "text/x-bed"}
-    regions = range(start, length, max_region)
+    regions = list(range(start, length, max_region))
     if not regions or regions[-1] < length:
         regions.append(length)
     for end in regions[1:]:
diff -r d615767650a0 -r 817e54905a9f translate_bed.py
--- a/translate_bed.py	Sun Jan 14 14:06:15 2018 -0500
+++ b/translate_bed.py	Mon Jan 22 13:59:02 2018 -0500
@@ -12,6 +12,8 @@
 #------------------------------------------------------------------------------
 """
 
+from __future__ import print_function
+
 import argparse
 import re
 import sys
@@ -122,7 +124,7 @@
                             selected_regions[chrom] = []
                         selected_regions[chrom].append([start, end, strand])
         if args.debug:
-            print >> sys.stderr, "selected_regions: %s" % selected_regions
+            print("selected_regions: %s" % selected_regions, file=sys.stderr)
 
     def filter_by_regions(bed):
         if not selected_regions:
@@ -158,18 +160,21 @@
 
     def get_sequence(chrom, start, end):
         if twobit:
-            if chrom in twobit:
+            if chrom in twobit and 0 <= start < end < len(twobit[chrom]):
                 return twobit[chrom][start:end]
             contig = chrom[3:] if chrom.startswith('chr') else 'chr%s' % chrom
-            if contig in twobit:
+            if contig in twobit and 0 <= start < end < len(twobit[contig]):
                 return twobit[contig][start:end]
         return None
 
-    def write_translation(tbed, prot):
+    def write_translation(tbed, accession, peptide):
         if args.id_prefix:
             tbed.name = "%s%s" % (args.id_prefix, tbed.name)
+        probed = "%s\t%s\t%s\t%s%s" % (accession, peptide,
+                                       'unique', args.reference,
+                                       '\t.' * 9)
         if bed_wtr:
-            bed_wtr.write("%s\t%s\n" % (str(tbed), prot))
+            bed_wtr.write("%s\t%s\n" % (str(tbed), probed))
             bed_wtr.flush()
         location = "chromosome:%s:%s:%s:%s:%s"\
             % (args.reference, tbed.chrom,
@@ -178,7 +183,7 @@
         fa_db = '%s%s' % (args.fa_db, args.fa_sep) if args.fa_db else ''
         fa_id = ">%s%s%s\n" % (fa_db, tbed.name, fa_desc)
         fa_wtr.write(fa_id)
-        fa_wtr.write(prot)
+        fa_wtr.write(peptide)
         fa_wtr.write("\n")
         fa_wtr.flush()
 
@@ -199,8 +204,8 @@
                     cds = bed.get_cds()
                     if cds:
                         if args.debug:
-                            print >> sys.stderr, "cdna:%s" % str(cdna)
-                            print >> sys.stderr, "cds: %s" % str(cds)
+                            print("cdna:%s" % str(cdna), file=sys.stderr)
+                            print("cds: %s" % str(cds), file=sys.stderr)
                         if len(cds) % 3 != 0:
                             cds = cds[:-(len(cds) % 3)]
                         refprot = translate(cds) if cds else None
@@ -208,6 +213,7 @@
                     refprot = None
                 if args.cds:
                     if refprot:
+                        tbed = bed.get_cds_bed()
                         if args.start_codon:
                             m = refprot.find('M')
                             if m < 0:
@@ -220,15 +226,16 @@
                             bed.trim_cds((stop - len(refprot)) * 3)
                             refprot = refprot[:stop]
                         if len(refprot) >= args.min_length:
-                            write_translation(bed, refprot)
+                            write_translation(tbed, bed.name, refprot)
                             return 1
                     return 0
             if args.debug:
-                print >> sys.stderr, "%s\n" % (str(bed))
-                print >> sys.stderr, "CDS: %s %d %d"\
-                    % (bed.strand, bed.cdna_offset_of_pos(bed.thickStart),
-                       bed.cdna_offset_of_pos(bed.thickEnd))
-                print >> sys.stderr, "refprot: %s" % str(refprot)
+                print("%s\n" % (str(bed)), file=sys.stderr)
+                print("CDS: %s %d %d" %
+                      (bed.strand, bed.cdna_offset_of_pos(bed.thickStart),
+                       bed.cdna_offset_of_pos(bed.thickEnd)),
+                      file=sys.stderr)
+                print("refprot: %s" % str(refprot), file=sys.stderr)
             for offset in range(3):
                 seqend = cdna_len - (cdna_len - offset) % 3
                 aaseq = translate(cdna[offset:seqend])
@@ -251,8 +258,8 @@
                                 break
                     is_cds = refprot and prot in refprot
                     if args.debug:
-                        print >> sys.stderr, "is_cds: %s %s"\
-                            % (str(is_cds), str(prot))
+                        print("is_cds: %s %s" % (str(is_cds), str(prot)),
+                              file=sys.stderr)
                     if len(prot) < args.min_length:
                         pass
                     elif not args.all and is_cds:
@@ -265,7 +272,7 @@
                         if args.all or unique_prot(tbed, prot):
                             translate_count += 1
                             tbed.name = prot_acc
-                            write_translation(tbed, prot)
+                            write_translation(tbed, bed.name, prot)
                     aa_start = aa_end + 1
         return translate_count
 
@@ -284,13 +291,12 @@
                 if filter_by_regions(bed):
                     translation_count += translate_bed(bed)
             except Exception as e:
-                print >> sys.stderr, "BED format Error: line %d: %s\n%s"\
-                    % (bedline, e)
+                print("BED format Error: line %d: %s\n%s"
+                      % (i, bedline, e), file=sys.stderr)
                 break
         if args.debug or args.verbose:
-            print >> sys.stderr,\
-                "transcripts: %d\ttranslations: %d"\
-                % (transcript_count, translation_count)
+            print("transcripts: %d\ttranslations: %d"
+                  % (transcript_count, translation_count), file=sys.stderr)
 
 
 if __name__ == "__main__":
diff -r d615767650a0 -r 817e54905a9f translate_bed.xml
--- a/translate_bed.xml	Sun Jan 14 14:06:15 2018 -0500
+++ b/translate_bed.xml	Mon Jan 22 13:59:02 2018 -0500
@@ -126,13 +126,14 @@
         </section>
     </inputs>
     <outputs>
-        <data name="translation_bed" format="bed">
+        <!-- update translation_bed format to "probed" when datatype is available -->
+        <data name="translation_bed" format="bed" label="Translate ${translations.translate} on ${on_string} ${input.name}.proBed">
             <actions>
                 <action name="column_names" type="metadata" 
-                 default="chrom,chromStart,chromEnd,name,score,strand,thickStart,thickEnd,itemRgb,blockCount,blockSizes,blockStarts,peptideSequence"/>
+                 default="chrom,chromStart,chromEnd,name,score,strand,thickStart,thickEnd,itemRgb,blockCount,blockSizes,blockStarts,proteinAccession,peptideSequence,uniqueness,genomeReferenceVersion,psmScore,fdr,modifications,charge,expMassToCharge,calcMassToCharge,psmRank,datasetID,uri"/>
             </actions>
         </data>
-        <data name="translation_fasta" format="fasta"/>
+        <data name="translation_fasta" format="fasta" label="Translate ${translations.translate} on ${on_string} ${input.name}.fasta"/>
     </outputs>
     <tests>
         <test>
@@ -194,13 +195,13 @@
             <param name="id_prefix" value="test_"/>
             <output name="translation_bed">
                 <assert_contents>
-                    <has_text text="generic|test_ENST00000641515" />
+                    <has_text text="test_ENST00000641515" />
                     <has_text text="ELPHTLPQFIFQQLVCYILEYRYKVIMLSKYSFANS" />
                 </assert_contents>
             </output>
             <output name="translation_fasta">
                 <assert_contents>
-                    <has_text text="test_ENST00000641515" />
+                    <has_text text="generic|test_ENST00000641515" />
                     <has_text text="ELPHTLPQFIFQQLVCYILEYRYKVIMLSKYSFANS" />
                 </assert_contents>
             </output>