Merge pull request #676 from uclahs-cds/czhu-fix-rmats

fix (moPepGen): rMATs -> rMATS
uclahs-cds · Feb 8, 2023 · ae7bf7e · ae7bf7e
2 parents 675f269 + d5779e8
commit ae7bf7e
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Showing 9 changed files with 18 additions and 18 deletions.
diff --git a/moPepGen/cli/parse_rmats.py b/moPepGen/cli/parse_rmats.py
@@ -21,7 +21,7 @@
 
 def add_rmats_input_arg(parser:argparse.ArgumentParser, name:str, message:str,
         dest:str):
-    """ add input arg for rMATs """
+    """ add input arg for rMATS """
     message += f" Valid formats: {INPUT_FILE_FORMATS}"
     parser.add_argument(
         name,
@@ -48,35 +48,35 @@ def add_subparser_parse_rmats(subparsers:argparse._SubParsersAction):
     add_rmats_input_arg(
         p, '--se',
         message="File path to the SE (skipped exons) junction count file output"
-        " by rMATs. The file name should look like '*_SE.MATS.JC.txt' or "
+        " by rMATS. The file name should look like '*_SE.MATS.JC.txt' or "
         "'*_SE.MATS.JCEC.txt'.",
         dest='skipped_exon'
     )
     add_rmats_input_arg(
         p, '--a5ss',
         message="File path to the A5SS (alternative 5' splicint site) junction"
-        " count file output by rMATs. The file name should look like"
+        " count file output by rMATS. The file name should look like"
         " '_S5SS.MATS.JC.txt' or '*_A5SS.MATS.JCEC.txt'.",
         dest='alternative_5_splicing'
     )
     add_rmats_input_arg(
         p, '--a3ss',
         message="File path to the A3SS (alternative 3' splicint site) junction"
-        " count file output by rMATs. The file name should look like"
+        " count file output by rMATS. The file name should look like"
         " '_S3SS.MATS.JC.txt' or '*_A3SS.MATS.JCEC.txt'.",
         dest='alternative_3_splicing'
     )
     add_rmats_input_arg(
         p, '--mxe',
         message="File path to the MXE (mutually exclusive exons) junction"
-        " count file output by rMATs. The file name should look like"
+        " count file output by rMATS. The file name should look like"
         " '_MXE.MATS.JC.txt' or '*_MXE.MATS.JCEC.txt'.",
         dest='mutually_exclusive_exons'
     )
     add_rmats_input_arg(
         p, '--ri',
         message="File path to the RI (retained intron) junction"
-        " count file output by rMATs. The file name should look like"
+        " count file output by rMATS. The file name should look like"
         " '_RI.MATS.JC.txt' or '*_RI.MATS.JCEC.txt'.",
         dest='retained_intron'
     )

diff --git a/test/files/alternative_splicing/CPCG0486_ENST00000481806.1.gvf b/test/files/alternative_splicing/CPCG0486_ENST00000481806.1.gvf
@@ -4,7 +4,7 @@
 ##reference_index=/data/Index/GRCh38-EBI-GENCODE34
 ##genome_fasta=
 ##annotation_gtf=
-##source=rMATs
+##source=rMATS
 ##CHROM=<Description='{'Description': "'Gene ID'"}'>
 ##INFO=<ID=TRANSCRIPT_ID,Number=1,Type=String,Description="Transcript ID">
 ##INFO=<ID=GENE_SYMBOL,Number=1,Type=String,Description="Gene Symbol">

diff --git a/...comb/CPCG0235_ENST00000525687.5/rMATs.gvf → ...comb/CPCG0235_ENST00000525687.5/rMATS.gvf b/...comb/CPCG0235_ENST00000525687.5/rMATs.gvf → ...comb/CPCG0235_ENST00000525687.5/rMATS.gvf
@@ -4,7 +4,7 @@
 ##reference_index=/data/Index/GRCh38-EBI-GENCODE34
 ##genome_fasta=
 ##annotation_gtf=
-##source=rMATs
+##source=rMATS
 ##CHROM=<Description='{'Description': "'Gene ID'"}'>
 ##INFO=<ID=TRANSCRIPT_ID,Number=1,Type=String,Description="Transcript ID">
 ##INFO=<ID=GENE_SYMBOL,Number=1,Type=String,Description="Gene Symbol">

diff --git a/...comb/CPCG0235_ENST00000590400.1/rMATs.gvf → ...comb/CPCG0235_ENST00000590400.1/rMATS.gvf b/...comb/CPCG0235_ENST00000590400.1/rMATs.gvf → ...comb/CPCG0235_ENST00000590400.1/rMATS.gvf
@@ -4,7 +4,7 @@
 ##reference_index=/data/Index/GRCh38-EBI-GENCODE34
 ##genome_fasta=
 ##annotation_gtf=
-##source=rMATs
+##source=rMATS
 ##CHROM=<Description='{'Description': "'Gene ID'"}'>
 ##INFO=<ID=TRANSCRIPT_ID,Number=1,Type=String,Description="Transcript ID">
 ##INFO=<ID=GENE_SYMBOL,Number=1,Type=String,Description="Gene Symbol">

diff --git a/...comb/CPCG0266_ENST00000381461.6/rMATs.gvf → ...comb/CPCG0266_ENST00000381461.6/rMATS.gvf b/...comb/CPCG0266_ENST00000381461.6/rMATs.gvf → ...comb/CPCG0266_ENST00000381461.6/rMATS.gvf
@@ -4,7 +4,7 @@
 ##reference_index=/data/Index/GRCh38-EBI-GENCODE34
 ##genome_fasta=
 ##annotation_gtf=
-##source=rMATs
+##source=rMATS
 ##CHROM=<Description='{'Description': "'Gene ID'"}'>
 ##INFO=<ID=TRANSCRIPT_ID,Number=1,Type=String,Description="Transcript ID">
 ##INFO=<ID=GENE_SYMBOL,Number=1,Type=String,Description="Gene Symbol">

diff --git a/...comb/CPCG0333_ENST00000452737.5/rMATs.gvf → ...comb/CPCG0333_ENST00000452737.5/rMATS.gvf b/...comb/CPCG0333_ENST00000452737.5/rMATs.gvf → ...comb/CPCG0333_ENST00000452737.5/rMATS.gvf
@@ -4,7 +4,7 @@
 ##reference_index=/data/Index/GRCh38-EBI-GENCODE34
 ##genome_fasta=
 ##annotation_gtf=
-##source=rMATs
+##source=rMATS
 ##CHROM=<Description='{'Description': "'Gene ID'"}'>
 ##INFO=<ID=TRANSCRIPT_ID,Number=1,Type=String,Description="Transcript ID">
 ##INFO=<ID=GENE_SYMBOL,Number=1,Type=String,Description="Gene Symbol">

diff --git a/...comb/CPCG0462_ENST00000483923.5/rMATs.gvf → ...comb/CPCG0462_ENST00000483923.5/rMATS.gvf b/...comb/CPCG0462_ENST00000483923.5/rMATs.gvf → ...comb/CPCG0462_ENST00000483923.5/rMATS.gvf
@@ -4,7 +4,7 @@
 ##reference_index=/data/Index/GRCh38-EBI-GENCODE34
 ##genome_fasta=
 ##annotation_gtf=
-##source=rMATs
+##source=rMATS
 ##CHROM=<Description='{'Description': "'Gene ID'"}'>
 ##INFO=<ID=TRANSCRIPT_ID,Number=1,Type=String,Description="Transcript ID">
 ##INFO=<ID=GENE_SYMBOL,Number=1,Type=String,Description="Gene Symbol">

diff --git a/test/integration/test_call_variant_peptides.py b/test/integration/test_call_variant_peptides.py
@@ -484,7 +484,7 @@ def test_call_variant_peptide_case25(self):
     def test_call_variant_peptide_case26(self):
         """ Test case reported in #357 with two alternative splicing events. """
         gvf = [
-            self.data_dir/'comb/CPCG0266_ENST00000381461.6/rMATs.gvf',
+            self.data_dir/'comb/CPCG0266_ENST00000381461.6/rMATS.gvf',
             self.data_dir/'comb/CPCG0266_ENST00000381461.6/gsnp.gvf'
         ]
         expected = self.data_dir/'comb/CPCG0266_ENST00000381461.6_expected.txt'
@@ -495,7 +495,7 @@ def test_call_variant_peptide_case27(self):
         """ Test case reported in #360 with one alternative splicing and an
         indel. """
         gvf = [
-            self.data_dir/'comb/CPCG0235_ENST00000525687.5/rMATs.gvf',
+            self.data_dir/'comb/CPCG0235_ENST00000525687.5/rMATS.gvf',
             self.data_dir/'comb/CPCG0235_ENST00000525687.5/gindel.gvf'
         ]
         expected = self.data_dir/'comb/CPCG0235_ENST00000525687.5_expected.txt'
@@ -508,7 +508,7 @@ def test_call_variant_peptide_case28(self):
         collapsing end nodes, the one with lower subgraph level should be kept.
         """
         gvf = [
-            self.data_dir/'comb/CPCG0235_ENST00000590400.1/rMATs.gvf',
+            self.data_dir/'comb/CPCG0235_ENST00000590400.1/rMATS.gvf',
             self.data_dir/'comb/CPCG0235_ENST00000590400.1/gsnp.gvf',
             self.data_dir/'comb/CPCG0235_ENST00000590400.1/gindel.gvf'
         ]
@@ -522,7 +522,7 @@ def test_call_variant_peptide_case29(self):
         aligning nodes in TVG, it failed to limit inside the same subgraph.
         """
         gvf = [
-            self.data_dir/'comb/CPCG0333_ENST00000452737.5/rMATs.gvf',
+            self.data_dir/'comb/CPCG0333_ENST00000452737.5/rMATS.gvf',
             self.data_dir/'comb/CPCG0333_ENST00000452737.5/gsnp.gvf',
             self.data_dir/'comb/CPCG0333_ENST00000452737.5/gindel.gvf'
         ]
@@ -536,7 +536,7 @@ def test_call_variant_peptide_case30(self):
         aligning nodes in TVG, it failed to limit inside the same subgraph.
         """
         gvf = [
-            self.data_dir/'comb/CPCG0462_ENST00000483923.5/rMATs.gvf',
+            self.data_dir/'comb/CPCG0462_ENST00000483923.5/rMATS.gvf',
             self.data_dir/'comb/CPCG0462_ENST00000483923.5/gsnp.gvf'
         ]
         expected = self.data_dir/'comb/CPCG0462_ENST00000483923.5_expected.txt'

diff --git a/test/integration/test_parse_rmats.py b/test/integration/test_parse_rmats.py
@@ -43,7 +43,7 @@ def test_parse_rmats_cli(self):
             -o {self.work_dir}/reditools.gvf \\
             -g {self.data_dir}/genome.fasta \\
             -a {self.data_dir}/annotation.gtf \\
-            --source rMATs
+            --source rMATS
         """
         res = sp.run(cmd, shell=True, check=False, capture_output=True)
         try: