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feat(IPVC-2276): skip accessions from gff that are not in the tx_info file, log missing acs to file #18

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merged 10 commits into from
Apr 5, 2024
Merged

feat(IPVC-2276): skip accessions from gff that are not in the tx_info file, log missing acs to file #18

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4ecb9b4
feat(IPVC-2276): skip acs missing from seqrepo and save them to a file
sptaylor Apr 2, 2024
dc48fa0
feat(IPVC-2276): update fx name
sptaylor Apr 2, 2024
5b77ba6
feat(IPVC-2276): update fx name
sptaylor Apr 2, 2024
523f06c
style(IPVC-2276): add empty new line
sptaylor Apr 2, 2024
2eea2a0
Merge branch 'main' into IPVC-2276-filter-accessions
sptaylor Apr 2, 2024
50ff903
Revert "feat(IPVC-2276): skip acs missing from seqrepo and save them …
sptaylor Apr 4, 2024
0e15485
refactor(IPVC-2276): pull out open_file into module
sptaylor Apr 4, 2024
18b0443
feat(IPVC-2276): filter exonsets by transcript info file
sptaylor Apr 4, 2024
9327609
feat(IPVC-2276): add exonset filtering to build pipeline
sptaylor Apr 4, 2024
348d942
style(IPVC-2276): add newline
sptaylor Apr 4, 2024
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feat(IPVC-2276): update fx name
  • Loading branch information
@sptaylor
sptaylor committed Apr 2, 2024
commit 5b77ba6fd2196084bf231e2c065a460f7153787e
6 changes: 3 additions & 3 deletions tests/test_ncbi_parse_genomic_gff.py
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@
from sbin.ncbi_parse_genomic_gff import (
get_zero_based_exon_ranges,
GFFRecord,
parse_gff_file,
parse_gff_files,
parse_gff_record,
)

Expand Down Expand Up @@ -160,7 +160,7 @@ def test_parse_gff_record_raises_unparseable_id(self):
def test_parse_gff_file(self):
# Test parsing the entire uncompressed GFF file
expected_result = {"rna-NR_046018.2": self.gff_records}
parsed_result = parse_gff_file([self.temp_gff.name])
parsed_result = parse_gff_files([self.temp_gff.name])
self.assertEqual(parsed_result, expected_result)

def test_parse_gff_file_accepts_gzipped_files(self):
Expand All @@ -171,7 +171,7 @@ def test_parse_gff_file_accepts_gzipped_files(self):

# Test parsing the gzipped GFF file
expected_result = {"rna-NR_046018.2": self.gff_records}
parsed_result = parse_gff_file([self.temp_gff.name + ".gz"])
parsed_result = parse_gff_files([self.temp_gff.name + ".gz"])
self.assertEqual(parsed_result, expected_result)

def test_get_zero_based_exon_ranges(self):
Expand Down