Added testing for split_genomic_fasta_to_nascent

Lioscro · Jan 19, 2023 · d48dad1 · d48dad1
1 parent 55cb906
commit d48dad1
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diff --git a/tests/fixtures/fasta/nascent.fa b/tests/fixtures/fasta/nascent.fa
@@ -0,0 +1,8 @@
+>GENE_C gene_id:GENE_C gene_name:GENE_C_NAME chr:2 start:2 end:14 strand:-
+TAATCAGATCCGA
+>GENE_B gene_id:GENE_B gene_name:GENE_B_NAME chr:2 start:1 end:10 strand:+
+ATCGGATCTG
+>GENE_A gene_id:GENE_A gene_name:GENE_A_NAME chr:1 start:1 end:2 strand:+
+CA
+>GENE_D gene_id:GENE_D gene_name:GENE_D_NAME chr:1 start:1 end:2 strand:+
+CA
diff --git a/tests/mixins.py b/tests/mixins.py
@@ -44,6 +44,7 @@ def setUpClass(cls):
         cls.fasta2_path = os.path.join(cls.fasta_dir, 'not_sorted.fa')
         cls.cdna_fasta_path = os.path.join(cls.fasta_dir, 'cdna.fa')
         cls.intron_fasta_path = os.path.join(cls.fasta_dir, 'intron.fa')
+        cls.nascent_fasta_path = os.path.join(cls.fasta_dir, 'nascent.fa')
 
         cls.fastq_dir = os.path.join(cls.fixtures_dir, 'fastq')
         cls.fastq_path = os.path.join(cls.fastq_dir, 'small.fastq')

diff --git a/tests/test_fasta.py b/tests/test_fasta.py
@@ -53,3 +53,13 @@ def test_split_genomic_fasta_to_intron(self):
             self.fasta2_path, path, gene_infos, transcript_infos, flank=1
         )
         self.assertTrue(mixins.files_equal(self.intron_fasta_path, path))
+
+    def test_split_genomic_fasta_to_nascent(self):
+        path = os.path.join(self.temp_dir, 'test.fa')
+        gene_infos, transcript_infos = gtf.genes_and_transcripts_from_gtf(
+            self.gtf_path, use_version=False
+        )
+        fasta.split_genomic_fasta_to_nascent(
+            self.fasta2_path, path, gene_infos
+        )
+        self.assertTrue(mixins.files_equal(self.nascent_fasta_path, path))