Merge branch 'master' into ct-add-bwa-depletion

Dockerfile

@@ -1,4 +1,4 @@
-FROM quay.io/broadinstitute/viral-baseimage:0.1.6
+FROM quay.io/broadinstitute/viral-baseimage:0.1.7
 
 LABEL maintainer "viral-ngs@broadinstitute.org"
 

test/input/TestOrderAndOrient/expected.lasv.ambig.fasta

@@ -0,0 +1,119 @@
+>KM821998.1|LASV-ISTH2376-S-NG-2012H_contigs_ordered_and_oriented
+ACTCGGACTCTCTCTGATTCTGAAGGTAATGAAACACCAGGTGGGTATTGTCTAACAAGA
+TGGATGCTGATTGAGGCCGAGTTGAAGTGCTTTGGGAACACAGCAGTTGCAAAATGCAAT
+GAGAAACATGATGAAGAGTTTTGTGACATGTTAAGATTGTTTGACTTTAACAAACAAGCC
+ATAAGCAGGCTGAAGACAGAAGCACAAATGAGTATCCAACTGATAAACAAAGCAGTGAAC
+GCACTGATCAATGACCAGCTGATTATGAAGAATCATTTGAGAGATATCATGGGAATTCCT
+TACTGCAATTACAGCAAGTACTGGTATCTGAATCACACTGTAACAGGGAAGACATCATTG
+CCAAGGTGCTGGCTTGTATCAAATGGTTCCTACCTAAATGAAACACACTTTTCTGATGAT
+ATTGAACAACAAGCAGACAACATGATAACAGAAATGTTGCAAAAGGAGTACATAGACAGG
+CAAGGGAAGACACCCTTGGGGTTAGTGGATCTTTTTGTCTTCAGCACCAGCTTTTACCTC
+ATTAGCATCTTCCTCCACCTGGTTAAAATCCCAACCCACAGACATGTCATAGGAAAACCC
+TGCCCCAAACCACACAGACTCAACCATATGGGCATATGCTCATGTGGTTTATACAAACAT
+CCTGGTGTACCAGTCAAGTGGAAAAGATAAGAGATAGACCCACCCATGGGCCCCCGTGAC
+CCACCGCCGAAAGGCGGTGGGTCACGGGGGCGTCCATTTACAGGACGACCTTGGGGCTTG
+AGGTTCTAAACACCATGTCCCTGGGGAGAACTGCCCTCAAAACTGGTATATTGAGTCCTC
+CTGACACAGCTGCATCATACATTATGCAATCCATTAGAGCACAGTGCGGGGTGATTTCCT
+CTTTGCCTCCTCTTTTCTTCTTTTCGACAACCACTCCAGTATGCATATGGCATAGATCTT
+TGCACTGATCCCAAACAGCATTTTCAAATCTCCTAGAGTCAACCTTGCTCAGTGCAATGT
+CAATAAGCTTTATGTCCTTTCTTCCTTGGGAGTCCAAGAGTTTCTTGATATCATCTGAAC
+CTTGACAGGTCAGTACCATATTGCGAGGGAGGGCTTCAATGACTGCGCTGGTCAAACCAG
+GCTGAGCAGGGAAGAGATCTGCCACATCAATCCCATGAGAGTATTTGGCATCCTGCTTGA
+ACTGTTTTAGGTCTGTTGGTTCTCTGAAGAAGTGTATGTAACAGCCTGACATAGGTTGGT
+AAAGAGCTATTTCCACAGGGTCTTCTGGACGACCTTCGATGTCTATCCAGGTTTTGGCGC
+TTGGGTCAAGCTGCATCATTGAGTCTTTGAGTGTCATTAATTGAGAATAGGTCAGCCCTG
+TTGGAAACCCTGCTGACTGTAAAGACTTGTTAGACCCAGCAATGCCCACTTTTTGCGGTT
+TTCCATCTGACTCGAGATCCACAGTAGTGTTCTCCCAAGCTCTACCCACAATAGAAGTCC
+TTGAAGCTATGTAGGGCCAGCCGTCACCGGAGAGACAGATCTTGTAAAGTATATTCTCAT
+AAGGGTTCCTCTCACCAGGTGTATCTGAAACAAACATTCCCAAAGATCTTTTTACTTTTA
+AAATAGACTTCAAGATGCCATCCATTGTCTGAGGTGTAACCTTGATGGTCTCCAACATGT
+TCCCCCCATCAAGCATACAAGCTCCGGCTTTCACTGCAGCTCCTAAGCTGAAGTTGTAAC
+CAGAAATGTTCAAGGAGCTCTTCTTAGTGTCCACCATATTCAGTATAGGGTGGCTTTGGG
+AAAGTCTGTCCAGGTCGGAGCTATTCGGGTACTTAGCTGTGTATATCAGGCCCAGGTCTG
+TTAGTGCTAAGACGGCATCATTCAAATCAACTTGACCTTGTTTGGTGAGACATGCTAATG
+TCAGACTAGGCATGGTGCCGAACTGGTTGTTCAAAAGGTCCGGATTCTTGACATCCCACA
+CTCTAACGACTCCGTCTCTTCCAGGTTGGGTGCCCTGAGCCCCACCAACCATACCTATCA
+TGTTCAGCAATGCCCTTCTCTGCTCAAGCTGCTGTGTACTCAAATTCCCCATATAAACAC
+CTGAGCTTAGTGGCCTTTCTGTTCTAATGACCTTCGACTTTAGTTTTTCTAAGTCAGCTG
+CCAGTGTCAGCAGATCATCTGAGGTCAAGGTCCCAACTCTCAAGATACTCTTTTGTTGTG
+TCGATTTGAGTTCTACAAGATTGTTGACAGCCTGATTCAAATCTCTGAGACGTTTTAAGT
+CACTATCATCCCTTTTTTGTTTACGCATTAAGCGCTGCACATTGCTGACTTCAGAAAAAT
+CAAGACCATGAAGGAGAGCCTGAGCATCCTTAACAACTTGTAGTTTTATATTGGAGCAAT
+AACCTGAAAGCTCCCTCCTCAATGACTGTGTCCAGAGAAATGACTTCACTTCCTTAGAAG
+CACTCATCTTGGTCTGGACACTCGGGGACTTACTGGTTGAAAGTATCACTCAGTGAGTC
+>KM821997.1|LASV-ISTH2376-L-NG-2012H_contigs_ordered_and_oriented
+TTATTGAACAATATCCTAAGCATTGACCTCATCTTTTTACATGCATCAGGAATCAGCCTC
+TCAATTTGCCTCATTATTCTATAACTACGATTCCCATCCACCCAATCTCTTACATCAGTC
+TCACAGTTCAAAAGGAATGGATCAATAGGATACTTAGCATAACATAACAAACTCAAAGTC
+CTCTTCTGAATTTGATTACACAGATCGACTGGGACACCATTAGCCACAGATTGATCAATT
+ATGGTGTCAATTGTTTCTGCCAATTGATGGGGTTCTTTGCACTTTATGTTATGTAAAGCC
+GCAGCAACAAATTTTGTTAGCAGAGGTACTTCGTCACCCCAGACATAGAACCTTGATTTG
+AACTCTGCGACAAACCTGCCAATTGCACTCTTTGGACTCACAAACTTATTTAGCTGATCA
+CTCATGTAGTAATGAAATTCTAACAATGTTTTGAATTCCTCTGTATCTCTTGAGAGTAAC
+TCTGTTAGGTTCTGATCAAATAAAGATATCTGATCGTCACTGGACGTGTAAGCATCAATT
+TGTCCTCCAGATACACACTTCACTGCAAAATTTATAAATCTTTCAGAAATCAATGCATAA
+AAGTCTGAGGTGTTGTGCAGGATACCCTGTCCCATATCAAGGATTGAACTAATGTGTGAA
+GGGACTATCCCAATTTGAAAGTTGGAATTAAAGAAGTCCTCAGTCATTGATTGTGTTGTC
+TTCTTCTTTAATCCAAGTTGGGATTTGATGTATGACTTCATCATTGCTGATACAACATTA
+AATGGGATCTCAACCATTTTGTGCATATGCCATGTTAATAATGTTGATAGGTAATCTTTA
+CCTTTTAAATCAGCTTGTAAATCATCAGAAAGTAAGATTAGGTTTTGAATTATTGTTAGA
+AATAAGAAAGGACACATCATAGGGCCCCACTTACTGTGGTCCATACTGTATGATACATGT
+GCCGATGAGACATTTAGCTTCATTGACAAAATGGCATTGTCAAACTCCTTCTCATTATTT
+AGACAGCTGCCTGCTAATTGTGATGTGAGCGCTTCAAAGTAATCCTCAATAAGCCTTGTG
+AACATCTTTGTCCTTAAATCTCCGATGTACAACTCTCTATTGCCTCCCACTTGTTCCTTG
+TAAGATAAAGAGAATTTTAGTCTACCAGTGTCAGGGCCAGTTGAATTATAAGACTGAGGT
+GATTCTTGACTGTAAAAACACAGGTTTTTCAACATTGCTGTAGTACAGTTAGTTAGGGAC
+AAGGCCTTGCTAAGTGCCTCAGAATTACTCTCACGCTCACTTATCCTGACATCATCAGCC
+AGTCTTCCTGTATCAAATTTAAAGTTCAGACACTTACTCTTATAATGGGAGTACCTTCCC
+ATCAGCTTGTTCCCATTCATCACTAACAAAATTGATTTGAAGCACTGGAAATATTCTTGG
+TCCAAAAAAGTCCTAGTCACTACTGCTTTTGTCAGCTCACTAATAGGACATGAATTCATC
+GGCCCTACATAAAAATACTTACTTCTCAAAGTAGCATCATTGTAGATATTCTCACAAATT
+TTGATGTATTGATCCTCAGACAGGATTTCTCGATCAAAATCTTCTATCATATGGTTCGAA
+AGTTCACATTTTATCAACCTTATTAAGAGTTTTTCTTCCACCACTTTGTCAAGATCAGAT
+ATTGAGGGAGCATTGCAGTCTGCCTGCTGCTGTCTCTCTGGTTGCTCTCTATATTGACTG
+ACAATATTGTCAACAGTACACCTCAGTTGATCAAAGTATTCTGATGCTCCTCCATCCAAT
+AGTATCTCATCTAGATCAGCATTGTTGGTGTCACCACCCCTTCCTTTGGACCCCAGAACA
+AGATTACTCATTGCTTGCTGTATCTTGTAATCATAATCCTGCTTATTGAGTAAGAATTTA
+CCTTTACGTGCAAATACTTCAGTTAACTGTGTGACAGCCAAAGCTGTAAGCTTGTTGAAG
+TCATAATCTAGAACACGGGACCCATCTGTATACTTATTCACAACGACACTCTTATTACTG
+GCCAAGTCCAAAGCTGTCGCACAGCCGCTTGTAATAAGAGGGTCTCGCAGTGTCTTCTTT
+ACTTCCTTTTCTTTAAACAATGAACCATTATTAAAACTAGACACTAGGAGTGAAATAAAT
+TTCTTGGAAACACCAGGCTTTTTATACCTAACCTTTTCCGCATCTGCACAACATTCTTTG
+CCTAGAAACTTTCTTGCATTATAAACCATTTCAGCAAGCTCTTCCTCCAATGCATCATCT
+TTCGGGTTCACACTTACATGCCCAAATTCCAATTTAGGCTCAAGGAATTTTTCAAAGCAT
+TTTATCTGGTCAGTCAGTCTGTCAGGTGTTTCTTTTGTAATGAAATGACACATATAAGAG
+ATATTTAAAACAAACTTAAATCTATTGGTCATCATACTGACTACTTCTTCAGACAGAATT
+ATTTTTAGTAGGTGACGAACAAGTTTGTAGAGCAGATATTCAACTTCTGTGATTAAATCC
+TCCCTGATCTTCTCAATCAAATCCTTGTGATAAAAATCGGATACAAAGGCCATTACAAAA
+TACCTAATGTTTTGTAAAAACTTCTGACACCTTTTACTAGGATGTGTTAGTATCAAAACC
+AAAATCATCTTGGTTAACAATTTTATAGTAATCAATTGTTCAGATAGCTCTGTGCACTCT
+TCTATCCAGCTGACCATAACATCGACTACTTTCTGTAACACATCACTGGAGAATACTGAA
+GGGAAAAACCGTTTGGGATCAGCATAAAAGGAGCAAACCTCTCCAACTACATTGTTGTTA
+ATAGCATAACACTTTGAGCATTCACCTGTCTTTTGATATAGTAGTTTGAATCCCATCCTA
+CTGATGAAGAACTCTTGGCAATAGGCCTCTTTGCACCTTACAACCTGGTATCTAGAGGGT
+CCAAATTCATTTTGTCTTAGTTTCACTGTGGAAGACGTTTTCATTGAGTTGATCAGAGCC
+AGGCTCAATGATGATAGTCTTTCTAAGTCTGTCACATCTAGAATGTCAATAACACCAAGA
+GTATAAGGGAACATGTCTTCCTTAGTTTTCTGGTAACTTATAGTGGGCGTGATACCGGAG
+ATCTCAATGTCCATGATGGCATCATAAACATCACAATCAAGGATCTTGAGATCAATTCCA
+TAAGAGTTGGTTTCTATGCCAACCTCCCTCAAAGCATTAGTGGCCCGAGTTAAAACTCTG
+TTAATGATGGCAAGGAGCTCACAATTTCGTTCTTCTTTGAGTGATAGAACACCTGCATTC
+CTGTCTTTAGCTCTCTTCCTACTGTCTATCCACCGTTTNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NNNNNNNNNTCAGTTTTAACAAATTGACTTTCTATGTTCCCTTGCCTTAGTTTGTTCCTA
+AAGATTTGATACTCCTCTTCAATTAAACTCTTGACTTCATGAGAGGTGAGCTTGTTATTA
+ATGCCCTGATGACAACAAGAAATTATTTCCTCAAAGTGTTTTGCACGCTTGTCAGTTAGA
+ACATTAATGCTTTCAATCCCGGAGAGCCTCCCAGACGTTAAGGCTAAAGATTCACAAAGT
+CTTGAATACTCAGATTCTTCGAACAATGCATTACTTTCTTGTGAGTATTTTAATAAAGTG
+AACAAGGTGTCCCTGAGTTTGTCATTCACCCAATCAGGTATCTGCTCATTGTAAAAAGTT
+GTCCTACCGTCTATGAGAGGGATAAGATTGATGCCAACGGATTCCAAGTCATTCTTTAAT
+TGTTCTAGCTTCTTGTGATCTTCTAAATACTTCTGTTCAAAATTGGCAGGGGATGATCTG
+ACAAAGCACTCAAGTAAGATAAGTACATTACCAGTAAGTTTGTAGCCGTCAGGCACCACA
+AAGCATAAAGCTGGAGTGAGAATCCCATGATCGCTCAGAATGGATTCAACCGTTTTGTCT
+TCAGTGTTATGTTCACATCCATTGGCTTTGCAAGAGTCAATCTCAATGCAAAGAGATAGT
+AGTTTCAATCCCTCCATGAGAAGCATTCTGGGTTCGGTTTGGACCAAAAAGGCTAGCTTT
+TGTCTCGATAGCTTCTCAT

test/unit/test_assembly.py

@@ -373,6 +373,24 @@ def test_multi_overlap(self):
             str(Bio.SeqIO.read(outFasta, 'fasta').seq),
             str(Bio.SeqIO.read(expected, 'fasta').seq))
 
+    def test_ambig_align(self):
+        inDir = util.file.get_test_input_path(self)
+        contigs_gz = os.path.join(inDir, 'contigs.lasv.ambig.fasta.gz')
+        contigs = util.file.mkstempfname('.fasta')
+        with util.file.open_or_gzopen(contigs_gz, 'rb') as f_in:
+            with open(contigs, 'wb') as f_out:
+                shutil.copyfileobj(f_in, f_out)
+        expected = os.path.join(inDir, 'expected.lasv.ambig.fasta')
+        outFasta = util.file.mkstempfname('.fasta')
+        assembly.order_and_orient(
+            contigs,
+            os.path.join(inDir, 'ref.lasv.ISTH2376.fasta'),
+            outFasta)
+        def get_seqs(fasta):
+            return [str(s.seq) for s in Bio.SeqIO.parse(fasta, 'fasta')]
+        self.assertEqual(get_seqs(outFasta), get_seqs(expected))
+
+
 class TestGap2Seq(TestCaseWithTmp):
     '''Test gap-filling tool Gap2Seq'''
 

tools/mummer.py

@@ -284,10 +284,14 @@ def scaffold_contigs_custom(self, refFasta, contigsFasta, outFasta,
                 seq = []
                 for _, left, right, n_features, features in fs.get_intervals(c):
                     # get all proposed sequences for this specific region
-                    alt_seqs = list(
-                            alnReaders[(c, f[-1][0])].retrieve_alt_by_ref(left, right, aln_start=f[1], aln_stop=f[2])
-                            for f in features
-                        )
+                    alt_seqs = []
+                    for f in features:
+                        try:
+                            alt_seqs.append(alnReaders[(c, f[-1][0])].retrieve_alt_by_ref(left, right, aln_start=f[1], aln_stop=f[2]))
+                        except AmbiguousAlignmentException:
+                            log.warn("dropping ambiguous alignment to ref seq {} at [{},{}]".format(c, f[1], f[2]))
+                            pass
+
                     # pick the "right" one and glue together into a chromosome
                     ranked_unique_seqs = contig_chooser(alt_seqs, right-left+1, "%s:%d-%d" % (c, left, right))
                     seq.append(ranked_unique_seqs[0])

travis/install-wdl.sh

@@ -18,7 +18,7 @@ cached_fetch_jar_from_github () {
 
 cached_fetch_jar_from_github broadinstitute wdltool 0.14
 cached_fetch_jar_from_github broadinstitute cromwell 29
-cached_fetch_jar_from_github dnanexus dxWDL 0.57
+cached_fetch_jar_from_github dnanexus dxWDL 0.58.1
 
 TGZ=dx-toolkit-v0.240.1-ubuntu-14.04-amd64.tar.gz
 if [ ! -f $CACHE_DIR/$TGZ ]; then