fix: update FASTA header format (#182)

GenomicMedLab · Aug 9, 2023 · e502616 · e502616
1 parent 3c9e30b
commit e502616
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Showing 3 changed files with 5 additions and 5 deletions.
diff --git a/cool_seq_tool/app.py b/cool_seq_tool/app.py
@@ -640,12 +640,12 @@ def get_fasta_file(
             aliases = self.seqrepo_access.translate_identifier(
                 sequence_id, ["ensembl", "ga4gh"]
             )
-            header = f">ref|refseq:{sequence_id}|{'|'.join(aliases[0])}"
+            header = f">refseq:{sequence_id}|{'|'.join(aliases[0])}"
         elif sequence_id[:4] in ENSEMBL_PREFIXES:
             aliases = self.seqrepo_access.translate_identifier(
                 sequence_id, ["refseq", "ga4gh"]
             )
-            header = f">emb|ensembl:{sequence_id}|{'|'.join(aliases[0])}"
+            header = f">ensembl:{sequence_id}|{'|'.join(aliases[0])}"
         else:
             aliases = self.seqrepo_access.translate_identifier(
                 sequence_id, ["ensembl", "refseq", "ga4gh"]

diff --git a/cool_seq_tool/version.py b/cool_seq_tool/version.py
@@ -1 +1 @@
-__version__ = "0.1.14-dev0"
+__version__ = "0.1.14-dev1"
diff --git a/tests/unit/test_cool_seq_tool.py b/tests/unit/test_cool_seq_tool.py
@@ -768,7 +768,7 @@ def test_get_fasta_file(test_cool_seq_tool, tmp_path):
     """Test get_fasta_file method"""
     tpm3 = tmp_path / "NM_002529.3.fasta"
     test_cool_seq_tool.get_fasta_file("NM_002529.3", tpm3)
-    tpm3_expected = """>ref|refseq:NM_002529.3|ga4gh:SQ.RSkww1aYmsMiWbNdNnOTnVDAM3ZWp1uA
+    tpm3_expected = """>refseq:NM_002529.3|ga4gh:SQ.RSkww1aYmsMiWbNdNnOTnVDAM3ZWp1uA
 TGCAGCTGGGAGCGCACAGACGGCTGCCCCGCCTGAGCGAGGCGGGCGCCGCCGCGATGC
 TGCGAGGCGGACGGCGCGGGCAGCTTGGCTGGCACAGCTGGGCTGCGGGGCCGGGCAGCC
 TGCTGGCTTGGCTGATACTGGCATCTGCGGGCGCCGCACCCTGCCCCGATGCCTGCTGCC
@@ -818,7 +818,7 @@ def test_get_fasta_file(test_cool_seq_tool, tmp_path):
 
     limk2 = tmp_path / "ENST00000331728.9.fasta"
     test_cool_seq_tool.get_fasta_file("ENST00000331728.9", limk2)
-    limk2_expected = """>emb|ensembl:ENST00000331728.9|refseq:NM_005569.4|ga4gh:SQ.7_mlQyDN-uWH0RlxTQFvFEv6ykd2D-xF
+    limk2_expected = """>ensembl:ENST00000331728.9|refseq:NM_005569.4|ga4gh:SQ.7_mlQyDN-uWH0RlxTQFvFEv6ykd2D-xF
 GTCTTCCCGCGCCTGAGGCGGCGGCGGCAGGAGCTGAGGGGAGTTGTAGGGAACTGAGGG
 GAGCTGCTGTGTCCCCCGCCTCCTCCTCCCCATTTCCGCGCTCCCGGGACCATGTCCGCG
 CTGGCGGGTGAAGATGTCTGGAGGTGTCCAGGCTGTGGGGACCACATTGCTCCAAGCCAG
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		__version__ = "0.1.14-dev0"
		__version__ = "0.1.14-dev1"