Move GFF out of cdot package (only used to build data). #35 - make ta…

…gs genome build specific
SACGF · Mar 6, 2023 · 77f3ab4 · 77f3ab4
1 parent 035bd30
commit 77f3ab4
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Showing 6 changed files with 8 additions and 5 deletions.
diff --git a/cdot/__init__.py b/cdot/__init__.py
@@ -1,4 +1,4 @@
-__version__ = "0.2.13"
+__version__ = "0.2.14"
 
 
 def get_json_schema_version():

diff --git a/cdot/gff/__init__.py → generate_transcript_data/__init__.py b/cdot/gff/__init__.py → generate_transcript_data/__init__.py
diff --git a/generate_transcript_data/cdot_json.py b/generate_transcript_data/cdot_json.py
@@ -13,7 +13,7 @@
 import cdot
 import ijson
 from cdot.pyhgvs.pyhgvs_transcript import PyHGVSTranscriptFactory
-from cdot.gff.gff_parser import GTFParser, GFF3Parser
+from gff_parser import GTFParser, GFF3Parser
 from cdot.json_encoders import SortedSetEncoder
 from pyhgvs import CDNACoord
 

diff --git a/cdot/gff/gff_parser.py → generate_transcript_data/gff_parser.py b/cdot/gff/gff_parser.py → generate_transcript_data/gff_parser.py
@@ -66,7 +66,7 @@ def _finish(self):
             gene_data["url"] = self.url
 
         # At the moment the transcript dict is flat - need to move it into "genome_builds" dict
-        GENOME_BUILD_FIELDS = ["cds_start", "cds_end", "strand", "contig", "exons", "other_chroms"]
+        GENOME_BUILD_FIELDS = ["cds_start", "cds_end", "strand", "contig", "exons", "other_chroms", "tag"]
         for transcript_accession, transcript_data in self.transcript_data_by_accession.items():
             if protein := self.transcript_proteins.get(transcript_accession):
                 transcript_data["protein"] = protein

diff --git a/setup.cfg b/setup.cfg
@@ -26,4 +26,7 @@ install_requires =
 
 [options.packages.find]
 where =
-exclude=tests
+exclude=
+    tests
+    generate_transcript_data
+
diff --git a/tests/test_gff_parsers.py b/tests/test_gff_parsers.py
@@ -2,7 +2,7 @@
 import os
 from inspect import getsourcefile
 import unittest
-from cdot.gff.gff_parser import GTFParser, GFF3Parser
+from generate_transcript_data.gff_parser import GTFParser, GFF3Parser
 
 
 class Test(unittest.TestCase):