Merge pull request #49 from galaxy-genome-annotation/fix-48

should fix the addition of the Shine_Dalgarno_sequence
galaxy-genome-annotation · Feb 1, 2021 · a9d91a7 · a9d91a7
2 parents 446cdac + 63b565d
commit a9d91a7
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Showing 3 changed files with 15 additions and 5 deletions.
diff --git a/README.rst b/README.rst
@@ -85,6 +85,8 @@ Or with the Arrow client:
 History
 -------
 
+- 4.2.10
+    - Bugfix handling Shine-Dalgarno sequences (https://github.com/galaxy-genome-annotation/python-apollo/issues/48)
 - 4.2.9
     - Bugfix to  update_organism when using suppress_output
 - 4.2.8

diff --git a/apollo/util.py b/apollo/util.py
@@ -15,7 +15,11 @@
 noncoding_transcript_types = ['transcript', 'tRNA', 'snRNA', 'snoRNA', 'ncRNA', 'rRNA', 'mRNA', 'miRNA', 'guide_RNA',
                               'RNase_P_RNA', 'telomerase_RNA', 'SRP_RNA', 'lnc_RNA', 'RNase_MRP_RNA', 'scRNA', 'piRNA',
                               'tmRNA', 'enzymatic_RNA']
-single_level_feature_types = ["repeat_region", "terminator", "shine_dalgarno_sequence", "transposable_element"]
+single_level_feature_types = ["repeat_region", "terminator", "transposable_element"]
+
+other_genomic_feature_types = ['exon', 'CDS', 'Shine_Dalgarno_sequence', 'non_canonical_three_prime_splice_site',
+                               'non_canonical_five_prime_splice_site']
+all_feature_types = gene_types + coding_transcript_types + pseudogenes_types + noncoding_transcript_types + single_level_feature_types + other_genomic_feature_types
 
 
 def WAAuth(parser):
@@ -89,7 +93,7 @@ def AssertAdmin(user):
 
 
 def _tnType(feature):
-    if feature.type in ('gene', 'mRNA', 'exon', 'CDS', 'terminator', 'tRNA', 'snRNA', 'snoRNA', 'ncRNA', 'rRNA', 'miRNA', 'repeat_region', 'transposable_element', 'pseudogene', 'transcript'):
+    if feature.type in all_feature_types:
         return feature.type
     else:
         return 'exon'
@@ -102,9 +106,13 @@ def _yieldGeneData(gene, disable_cds_recalculation=False, use_name=False):
         current['children'] = []
         for sf in gene.sub_features:
             if _tnType(sf) in coding_transcript_types:
-                current['children'].append(_yieldCodingTranscriptData(sf, disable_cds_recalculation=disable_cds_recalculation, use_name=use_name))
+                current['children'].append(
+                    _yieldCodingTranscriptData(sf, disable_cds_recalculation=disable_cds_recalculation,
+                                               use_name=use_name))
             elif _tnType(sf) in noncoding_transcript_types:
-                current['children'].append(_yieldNonCodingTranscriptData(sf, disable_cds_recalculation=disable_cds_recalculation, use_name=use_name))
+                current['children'].append(
+                    _yieldNonCodingTranscriptData(sf, disable_cds_recalculation=disable_cds_recalculation,
+                                                  use_name=use_name))
 
     # # TODO: handle comments
     # # TODO: handle dbxrefs

diff --git a/setup.py b/setup.py
@@ -16,7 +16,7 @@
 
 setup(
     name="apollo",
-    version='4.2.9',
+    version='4.2.10',
     description="Apollo API library",
     long_description=readme,
     author="Helena Rasche;Anthony Bretaudeau;Nathan Dunn",