Fix fasta network error v0.3.8

flatironinstitute · Mar 19, 2022 · cc52350 · cc52350
1 parent c1ab322
commit cc52350
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Showing 4 changed files with 53 additions and 2 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,4 +1,8 @@
-### Version 0.3.6
+### Version 0.3.8
+
+* Fixed bug when saving motif locations with `network_from_motifs_fasta`
+
+### Version 0.3.7
 
 * Improved memory usage for `network_from_motifs_fasta` when a large number of sequences or TFs are used
 

diff --git a/inferelator_prior/network_from_motifs_fasta.py b/inferelator_prior/network_from_motifs_fasta.py
@@ -106,6 +106,12 @@ def build_motif_prior_from_fasta(motif_file, promoter_fasta_file, scanner_type='
     if gene_constraint_list is not None:
         genes = select_genes(genes, gene_constraint_list)
 
+    if save_locs and output_prefix is not None:
+        save_locs = output_prefix + "_tf_binding_locs.tsv"
+
+    if save_locs_filtered and output_prefix is not None:
+        save_locs_filtered = output_prefix + "_tf_binding_locs_filtered.tsv"
+
     return scan_and_build_by_tf(promoter_fasta_file, None, genes, None, output_prefix, motif_information,
                                 debug=debug, motif_ic=motif_ic, tandem=tandem, scanner_thresh=scanner_thresh,
                                 save_locs=save_locs, save_locs_filtered=save_locs_filtered, num_cores=num_cores,

diff --git a/inferelator_prior/tests/test_network_maker.py b/inferelator_prior/tests/test_network_maker.py
@@ -240,3 +240,44 @@ def test_file_output(self):
         self.assertTrue(os.path.exists(temp_path_prefix + "g_edge_matrix.tsv.gz"))
         self.assertTrue(os.path.exists(temp_path_prefix + "g_tf_binding_locs.tsv"))
         self.assertTrue(os.path.exists(temp_path_prefix + "g_tf_binding_locs_filtered.tsv"))
+
+
+    def test_file_output_fasta(self):
+        cut, raw, _ = build_motif_prior_from_fasta(os.path.join(artifact_path, "test_ecori.meme"),
+                                                   os.path.join(artifact_path, "test_motif_search.fasta"),
+                                                   output_prefix=temp_path_prefix)
+
+        self.assertTrue(os.path.exists(temp_path_prefix + "_unfiltered_matrix.tsv.gz"))
+        self.assertTrue(os.path.exists(temp_path_prefix + "_edge_matrix.tsv.gz"))
+        self.assertFalse(os.path.exists(temp_path_prefix + "_tf_binding_locs.tsv"))
+        self.assertFalse(os.path.exists(temp_path_prefix + "_tf_binding_locs_filtered.tsv"))
+
+        cut, raw, _ = build_motif_prior_from_fasta(os.path.join(artifact_path, "test_ecori.meme"),
+                                                   os.path.join(artifact_path, "test_motif_search.fasta"),
+                            output_prefix=temp_path_prefix + "c",
+                            save_locs=True)
+
+        self.assertTrue(os.path.exists(temp_path_prefix + "c_unfiltered_matrix.tsv.gz"))
+        self.assertTrue(os.path.exists(temp_path_prefix + "c_edge_matrix.tsv.gz"))
+        self.assertTrue(os.path.exists(temp_path_prefix + "c_tf_binding_locs.tsv"))
+
+        cut, raw, _ = build_motif_prior_from_fasta(os.path.join(artifact_path, "test_ecori.meme"),
+                                                   os.path.join(artifact_path, "test_motif_search.fasta"),
+                            output_prefix=temp_path_prefix + "d",
+                            save_locs_filtered=True)
+
+        self.assertTrue(os.path.exists(temp_path_prefix + "d_unfiltered_matrix.tsv.gz"))
+        self.assertTrue(os.path.exists(temp_path_prefix + "d_edge_matrix.tsv.gz"))
+        self.assertFalse(os.path.exists(temp_path_prefix + "d_tf_binding_locs.tsv"))
+        self.assertTrue(os.path.exists(temp_path_prefix + "d_tf_binding_locs_filtered.tsv"))
+
+        cut, raw, _ = build_motif_prior_from_fasta(os.path.join(artifact_path, "test_ecori.meme"),
+                                                   os.path.join(artifact_path, "test_motif_search.fasta"),
+                            output_prefix=temp_path_prefix + "f",
+                            save_locs_filtered=True,
+                            save_locs=True)
+
+        self.assertTrue(os.path.exists(temp_path_prefix + "f_unfiltered_matrix.tsv.gz"))
+        self.assertTrue(os.path.exists(temp_path_prefix + "f_edge_matrix.tsv.gz"))
+        self.assertTrue(os.path.exists(temp_path_prefix + "f_tf_binding_locs.tsv"))
+        self.assertTrue(os.path.exists(temp_path_prefix + "f_tf_binding_locs_filtered.tsv"))
diff --git a/setup.py b/setup.py
@@ -3,7 +3,7 @@
 
 install_requires = ["numpy", "pandas>=1.0", "HTSeq", "pybedtools", "scipy", "pathos", "sklearn", "tqdm"]
 tests_require = ["coverage", "nose", "pysam"]
-version = "0.3.7"
+version = "0.3.8"
 
 # Description from README.md
 base_dir = os.path.dirname(os.path.abspath(__file__))