Fixed EI-CoreBioinformatics#133. Now implementing the unit-test

lucventurini · Oct 10, 2018 · 6e7b941 · 6e7b941
1 parent e0b50ea
commit 6e7b941
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Showing 4 changed files with 126 additions and 7 deletions.
diff --git a/Mikado/preparation/annotation_parser.py b/Mikado/preparation/annotation_parser.py
@@ -233,12 +233,12 @@ def load_into_storage(shelf_name, exon_lines, min_length, logger, strip_cds=True
                         exons.append(current)
                         current = segment
                     elif segment[0] == current[1] + 1:
-                        current = (current[0], segment[1])
+                        current = (current[0], segment[1], None)
                     else:
                         logger.warning("Overlapping segments found in %s. Discarding it", tid)
                         continue
                 exons.append(current)
-                exon_lines[tid]["features"]["exon"] = exons[:]
+            exon_lines[tid]["features"]["exon"] = exons[:]
         else:
             raise KeyError(exon_lines[tid]["features"])
 
@@ -337,7 +337,7 @@ def load_from_gff(shelf_name,
             # Here we have to add the match feature as an exon, in case it is the only one present
             if row.feature == "match":
                 exon_lines[row.id]["features"][row.feature] = []
-                exon_lines[row.id]["features"][row.feature].append((row.start, row.end))
+                exon_lines[row.id]["features"][row.feature].append((row.start, row.end, row.phase))
 
             exon_lines[row.id]["strand_specific"] = strand_specific
             continue
@@ -392,7 +392,7 @@ def load_from_gff(shelf_name,
 
                     if row.feature not in exon_lines[tid]["features"]:
                         exon_lines[tid]["features"][row.feature] = []
-                    exon_lines[tid]["features"][row.feature].append((row.start, row.end))
+                    exon_lines[tid]["features"][row.feature].append((row.start, row.end, row.phase))
                     new_ids.add(tid)
             else:
                 continue
@@ -499,7 +499,7 @@ def load_from_gtf(shelf_name,
             exon_lines[row.transcript]["attributes"].update(row.attributes)
         if row.feature not in exon_lines[row.transcript]["features"]:
             exon_lines[row.transcript]["features"][row.feature] = []
-        exon_lines[row.transcript]["features"][row.feature].append((row.start, row.end))
+        exon_lines[row.transcript]["features"][row.feature].append((row.start, row.end, row.phase))
         new_ids.add(row.transcript)
     gff_handle.close()
     load_into_storage(shelf_name, exon_lines, logger=logger, min_length=min_length, strip_cds=strip_cds)

diff --git a/Mikado/preparation/checking.py b/Mikado/preparation/checking.py
@@ -70,8 +70,10 @@ def create_transcript(lines,
         transcript_line.parent = lines["parent"]
 
         for feature in lines["features"]:
-            transcript_line.add_exons(lines["features"][feature],
-                                      features=feature)
+            coords = [(_[0], _[1]) for _ in lines["features"][feature]]
+            phases = [_[2] for _ in lines["features"][feature]]
+            transcript_line.add_exons(coords, features=feature, phases=phases)
+
         transcript_object = TranscriptChecker(transcript_line,
                                               fasta_seq,
                                               lenient=lenient,

diff --git a/Mikado/tests/prepare_phase_correctdness.gff b/Mikado/tests/prepare_phase_correctdness.gff
@@ -0,0 +1,4 @@
+test	test	gene	1	6706	1	+	.	ID=test_0245940;Name=test_0245940;
+test	test	mRNA	1	6706	.	+	.	ID=test_0245940.1;Parent=test_0245940;Name=test_0245940.1
+test	test	CDS	1	370	.	+	2	ID=test_0245940..cds1;Parent=test_0245940.1
+test	test	exon	1	370	.	+	.	ID=test_0245940.exon1;Parent=test_0245940.1
diff --git a/Mikado/tests/prepare_phase_correctedness.fa b/Mikado/tests/prepare_phase_correctedness.fa
@@ -0,0 +1,113 @@
+>test
+ATGATGCAGCAGATGCAGTGGGTGATGCAGTGGGTGCAGTGAATGGTGCAGTGAGTGGAG
+AAATGGATGATGCAGTGGATGCTGTGGATGCTGTGGATGCAGTGGATGCAGAGAGTGGTG
+CAGCGAGTGGAGAAATGGATGATGCAGTGGATGCAGTGAATGCTGTGGGTGATGTGGTGG
+ATGACTCAGTGGGTGCTGTGGACACAGTGGTGGATGTAGAAGATGCTGTCTACACAGTGT
+ATGCAGTGATTTATGCAGTGGATGAAGAAGCAGAAGTAGCCCAGAGCTCAGCTTTCCATC
+AATGGCACTTACAGCGGCCACCACATGCCACCATGACCCTCATGCCCTTTATTCCAGAAG
+CTTCATGGAGGTAGGTTTGGGGACAGTGTGGGCATGGCTAGAGAGATGAAAGAATAGACT
+AAAGTCCTGAAGTCACCTCATTACACACTGTGCACCCTCCAGGGGTCTGTCACCAAGAAG
+TGCTGGGCCTCTGGAGACAGACAAGATGAGACCCTCAAAGCAGAGTCTGAGCTTGGGTGA
+GGAAAGACTAGGCCAGATGTGCACGCTAAAAATATCCACATTCCGTAGACTCCAGTAAGA
+AGGGCTAGCTACTCTGGCTGTGGCACCGGAAGCTTGCCTGGAGCAGCCTTGACCTTCACA
+AGCCCCGCTCCCACCCCAGCCTCCCATGATCACCCCAGTCAGTGATGGGCAGCCTGGGTA
+CCAGGATGTCAAAGAAACTTCCCTTGGGTGGTGAGATGGCGCAGCAGGCAAAGGTGCTTG
+CCAACAAGCCTGCAGACTTGAGTTCGATTCCCAAAGCCCCCATAGTAGAAAGAGAGAATC
+CATGCCCACAAATTGTCTCATGACATTCACACATTCTTAGTGTCACACATGCGCACACAC
+ACATACACGCAATAAGTAAATAAATACTATTATAAAAATAAGCTTCTCTCAGGCCCCCAA
+ATATATCCCTCCTCACCAGCCAAATGAATTCCAGATGGATTAAATTCAAACATTAAAGTC
+ATAAAAAGCCCAAGAAAGGAGTAGAATATCATTAAACACGTATAGAAGCCTGGAGAGAAA
+AAAGACAAATATAAAACCTGCAGCCATAAAAAAAAAAAAAAAAGGACAAGCAGATCCAAC
+TGTACAAAAATTAAAGTCTCTATGTAGTAAAAAAAAAAAAAATTAAAAACATAAACTATA
+TAAACTGGAAAGAATATCTGGAGCCAGCCTTCTTGGTGTTCAGAAAGTTCATTTATCTAT
+CCTCATGAAAAAGACAGGGTTCAAACAAAGAAACTGCATAACACACACACGTACACACAT
+ACCCACAGAGACACACACATATATATGCAAACAAAACAAAACAAAACACAGAAACAGTCC
+TAAAACAAACATCCCCGGCCAATGAACACACACACACACACACACACCTGTGGCTGATGT
+GAAGTGAGTGAGTCAAGTGAGCAAAGATGAATCAGGCTGGTGATGCCCAGAGACAGGGAG
+CTGGGGTTCATGCATGCCTAGGGAAGGCCGGATCTGCATAGCTGCTCGGAGTGAGGCCGG
+GGGATACCTGTTGGAACCCAATGTACAATACCCCTCATCCAGTGGGTCCAATTCGCAGCA
+TCTGTTCTGTGCACACATCTGCCACATGCTCTGAGACATACACTCAAGGGCAGGTCAACA
+TGCTCTAGTATTTGTGTGAAGACGATGGGGCAGGTGGTGACGGAGCTATGATTAAGTACC
+CAAGCTTGTGAAAGAATTAGGAAGTGCCTTGGAGAGACCTTTAAGGTGTGCAGATCTGCA
+GAACAGGATGATCTGAAGGTTTGGTATCATCTCAGCTTGGGAGATAGAGGCAGGAGGATG
+ACCAGAAAACTCCTGGCCAGCTTAGACTATTGAATAAAGACCCAGTCTCAAAACATTAGT
+CAGGAATGGTGATACGTGTCTATAATCTTAACACGTGAGAGGGGACAATAGGAGGACCAG
+CTGTTCAAGAAAGATCAGTGACTACAAAGAGAGTTCAAGGGCAGCCTGGGTCACATAAGA
+CCCTGCCTCAAAAAGTGCCTGAGGGCTGTAGAGATGGCTCAGTGATTAAGAGCACTGGCT
+GCTCCTTCAGAGAATCTGGGTTCAATTCCCAGCACCCACATGACAGCTTAGAAATGTCTA
+TAACTCCCGATCCAAGGGATCTGACACCTTCACACATATGCAGTCAACACACCAATGCAC
+ATACAAGTAAAACTATTTTTTTTAAGTAAAGAAGGAAAAGAATTAATATCCTCCAGTTGC
+TCCAGATATTATTTTTAAAAACAAACAAAACAGCCAGGGACTGTGGAGACCAAGGTGGAG
+GACTGGTATGAGCTTGGGGCCAGCCTGTAATACATAGTCTGAGGCTAGCCTGGACCACAT
+AGTGTGACCTGTCTCAGAATCCAGGGACTGTGGATGTAGGTCAGTGTAGAACACTTGCCT
+GGTACCCTGAGAGCCTGGGTTTCATTGCCAGCACTGCAGAGATCTGAGCATCCTCAGGAG
+TTATCGCTTCTTCTGCCGTGGGATGTGCACGCCCAGTCCTCCCTGGAGTCTGGCTCTATC
+CACTGGTGCCTGGCAGACAGCACAGGAAGCTGATGGGTGGTCCTGGCTCCAGACTTCAGT
+CCCACACAGTGTATTTCTCCCATCCATCTCCCATTGGTAACAGAATCGATATCCATTTAA
+CCCCTCCCCGCTTGCTGGCCTCCCACTGCTTACAGGAAACTGTCCCTACTCTGTAACACA
+CAGCATTAAAGGTCCTTGGCAGCCTGCTCCTCCCTTACCCACCAACTTCATCTGCCTACT
+TTCAAACCAATCAGGTGCTTGGGAGAGCTAAAACCAGCAGGCCTGGGGACAGCGGTCCTC
+CACCTGTTAGCCCGTGACCGTGGCCAACTCAGTCTCTCCCGGCTACATCTGAGATCTTCA
+TCTGTAAAAGTGAGCTAATGCCATCTGGATGCTGGAGGAGGGGGACAGTGAGGCAGTGCA
+TGTGTAGAAACCGCATGTCACACATCGTAGGGCATGTAGCGCAGAGGACACTCTTGGCGT
+CCCTTTGTTCCGGTCTTTGTGAAGGCCCTTCCTCCTGTCTCCTCATCTTCTGGCCAGGAA
+ACTCCTTGTAAACTCGTCCCTGACCACCCACACTGTGGTCCCCGGAATGTAAATTCATTT
+GCTTGTGATGACAGCCAGCACTGGCGATGAGTATGGTCCGTGTCGACCGGCTTCTGGTGG
+TCCCCAGCGGATGAGTCACGGCTTCCGTACCACTTGGCATCAACTCGGACAGAGTGTAGG
+CGTGAGCTCAGCGGATGCTAAGTGCTTGTTTTGCACATCTGTGGGTGTGCCATTTGTCGG
+TTTTGTTTGGGGTGGTTTGGTTTCTTGAGACAAAAGTATCTCACTAGGTAGCTCAGGATA
+GTCTCGAACCTGTGGTCCCCCTGACTCTGTTTCCAAGTGCTGGATTTACAGATAGGTGCC
+ACCACATCCAACCTACAGTACTTTTGGTTGCTGCCCAGCCTGGCCTTAAACTCTCTATGT
+GGCTTTGAACTCTTGGTCTTGCTGCCTTGTCCTCTCGCACGCTGAGATCACAGGCATGCA
+TGCTCAACTAGTATTCATTTTTTTTTGAGTGAATATATTTACCCACCTAACCTCAGTAAG
+CCCCTGAGCACCCACTTTATTATCTATCTGCCTTATAAGAAGACTGCATGGGAAAAATGA
+AAGAGGATCACAGAGTGTGCATGCACACAGGGCTGCCTCTGTGCTCACCCGCTGTGTTTT
+TATCCAAGTTGCACAGATCTTCGCTCACGATTTTCCGCAGTGTTCTGCCATTTCTTTTAC
+ACCCAAGCCCTCAGCTCATTGCACACCTGTGCATGTAAACAGTTAGATGCAATGTAACCC
+TTGGGTGCAATAACCACACCTTCTCTTTCAAATGGAATGTTTATGAACAGAGAGGCAAGG
+AGAGCAGCGTTCTGCCTCCAATTACAGATGCATAGGCCTCCAAAAACAGCATCCTTACGC
+TCTTCCGGTCCACAAGCCGGAAAATGTCCGAACAGATGCTTCCAAACTGTGAGGGAAAAA
+AAAATAAACAAGCACACAAATGGCTGCCTGGCTGGTCCCTGGAGGCCGGAGTCAGGCTGG
+AATACAAGTTATAGGCGGTGAGAACCTTGGAATGGAAATCCTACTTGAAGACTCAAGGGA
+TGAGGAGGAAACTGCATCCATTTGGCGGCTCCTTTGCACCTAATGCTCTGCTGAGGTCTT
+TAGCAGCCAGTTTCATTTCACTTTGTTTTTAATTATTTCAAATGTATACTTATTTGTGGG
+GGTGATGGGCAGGGTTCATGTCAGGGCACTTATGTGGAGATTGGAAGGAAATGTGGGAAT
+CCTATTCTCTGCTTCCACCTCGAGGGCCCCCAGGGACTGAAATCAAGTCATCAGGATTGG
+CAGTAAGCGCCTTTAGCTGATGAGGCCATCAGGCCTGGCTTTAATATCTATTCTGTGAGA
+TGGGACGAGAAGGAAAGTAAGGTGGGTGGGGTGCACAGATATGGCCAGAATTCGGTGCCC
+CTCTAGACTCCGTATTCAGCTTTTACACTATGCCGTGGAATGCTGCTGGGAGGCTGACAT
+GGCTTCTTCTTTGCAAGAGACAGCCACACACCCTTGGATGCCCGTGAGCTTCTGGATGGT
+TGAAAACCACTCACTCCTCTCCTCTCCCCAGGCAGGAAGATGTCTGTTCCTAGAGAAGTC
+CAGAACTCACACAGCGGGAGAAAGGTTATACTGCCCCTTGTGTTGGGAGGACCAGCACAC
+ACCTGCAACTCTACAGGAGTGCTGGGACCCCCATCTCTCTTCGTGCCTAGGCTGGACCCA
+GGCTCTGACTTCTCACCAACGGAGACACCGGTGTCATTCACTCAGCTCCCATCCCGAGTT
+CTAGAATGGTGCATGGCCCAGCGATCACAGTGCATAAGATGGGCCTGTGTGTAGACTTGC
+CTCCCAAGATGCCGGGCAAGCCACCCGCACTCCACACCCGCGTTTTGTTCTTTTTAAAAG
+ACGTGTCTATTGATTGCAGTGAACCTCTATGATCCTCAACACATCTGTACCGAGAGTGTT
+CCCAGGCAAGCCAACGCTGTCCTCACCTTGGTTTGATAGACGTTAAGACCCTCCCACATC
+AGCAGAACGCAGGAACGCCACAGTCTGAGTACAGGGGAGTGGTGGGGCTAGACAGTGATG
+GAGAAAAATCAGAGTCTCCATGTAACTGATGGAAGACGATGTGTTGTCGAATCCGATGAA
+AGATTTTTCTAGTCTTTGTTTTGCCAGAGAGGCCTTATATACATTTCCTTTAACAGGCTT
+CCCTGACAGGAAGTCATTTCCAAAGACTCTGCAGCCTGAAGCTTCTTGGGGATTTCTTTT
+CCTCTGGCCGACCTCAGTTTCTCCTATCTGTAAAATGGAGCCATTCGTAAAGAGTCAAAG
+GTACTCTAAGGCTCCTGAGGCTTCCAGGACCCTAGATTTGGAGCACTCCAGCCAACAGCT
+CAGGTCACCTTTTAAAGTGCTACACTGTTAACAAGTCCTGCCTCTTCACGTTACAGACCG
+CTTGCCTGTGACAGAAATTGGGGTGGTCACCTGTCAGGATCCTCTGCCCAAGTGGTCCTA
+CACCCTCACTTATAGCTAGTTATCAATGAAGGGTGTGTGTGTGTGTGTGTGTGTGTGCAG
+GCACACACTTGATCAAAGAACAGGCCTCCCTCAGGTTTTTTTTTTTCTTCAATATGCAAG
+CTGTCACAGATCTCAAGGCAAGATATTATTTCTGATAAATAGAGGCAGACAATAGATGAT
+TTCTATATTAATATCACTAAAGAAAAAGTGCCCCTCTCCTGCAACTCACGGGAGACAGAG
+GAGCCAGTGTATAGAGTTAGGCTACAGACACCGAACAGAGACTCTGGCACTGTGACAGTT
+GGAGCACCGCCCCCCACCCCCACCTTGCACTGCACTCCCCCCTCCCCTCCCCTCTCCTCC
+TTCACCTCACCCAGTTCGGAGAAAGAGGGTCTGCATTTTCCTCCTGCTGATGGTGGTTGA
+TTAGCAGTCAGGTGGAGCGATGCTCCGGGGACAGCACAACAGATTAATTAAATCACTCTG
+GCTGGCTAAGTGGTGACACTGTGATTTATAGCGCCGCTCACTCAACCAGACAGCAGGCTT
+TTCTTGCATGCTGAAGGAAGGAGGGCCCGAGCTGGACCCCGGGTACAGACCTCAGGGGGC
+GCTATGAACTTTCAGGATGAGCATTTTTACCCTTAAGGCAGAGGGCCCCCTGCTGGGAGA
+CTCACAAGGGAGAGGAAGCAGAGGGAGTGCCAGGCCGCTGTGCAGTGGTGTGTCTCTGCA
+GAAGAGAAGCCTCAAAAAAGATTCGGCTGTGGCTCACCCTGAAGAAACAGCCCCCTGCCA
+GTCTCAGCCTGGTGACTCCGGGCCTTTGTCCCTGTTTTCCAGGACGGCATTGTCCCCTCA
+GCGAGATGCCCTACTGTTCCTCTTAGATGTTCCGTGGGCGGCTGCCTCCACTTCCCTGAG
+GAACTAGGTCACACAGGCTAGTGTGACAACGGGGGCTAGTCTAACACATTTAGCAAGTGC
+CGGCTCTGTGATATCCTGTGTGGGAGCGGGGAGCTAGCTCATTTCTACACCATTCCAGAA
+CACACACACACACACACACACACACACACACACACACACACACACA