Add tests for 2 samples and 1 sample for zpca-tpm (#15)

* Add tests for 2 samples and 1 sample when using zpca-tpm
* Bump version to 0.8.3

.gitignore

@@ -127,3 +127,6 @@ dmypy.json
 
 # Pyre type checker
 .pyre/
+
+test_data/TRANSCRIPT_TPM_2_SAMPLES/
+test_data/TRANSCRIPT_TPM_1_SAMPLE/

scripts/zpca-counts

@@ -135,6 +135,17 @@ def main():
         sys.stdout.write(f"Running PCA {os.linesep}")
 
     n_components = determine_number_of_components(df)
+
+    if n_components == 1:
+        w = open(os.path.join(options.out, "PCA.tsv"), 'w')
+        w.write(f"")
+        w.close()
+        w = open(os.path.join(options.out, "scree.tsv"), 'w')
+        w.write(f"")
+        w.close()
+        sys.stderr.write(f"Too few samples for PCA {os.linesep}")
+        sys.stderr.write(f"Exiting {os.linesep}")
+        sys.exit(0)
 
     scaled_data, pca_data, per_var, labels, = perform_pca(df, n_components)
 

scripts/zpca-tpm

@@ -101,6 +101,17 @@ def main():
 
     n_components = determine_number_of_components(df)
 
+    if n_components == 1:
+        w = open(os.path.join(options.out, "PCA.tsv"), 'w')
+        w.write(f"")
+        w.close()
+        w = open(os.path.join(options.out, "scree.tsv"), 'w')
+        w.write(f"")
+        w.close()
+        sys.stderr.write(f"Too few samples for PCA {os.linesep}")
+        sys.stderr.write(f"Exiting {os.linesep}")
+        sys.exit(0)
+
     scaled_data, pca_data, per_var, labels, = perform_pca(df, n_components)
 
     if options.verbose:

setup.py

@@ -13,7 +13,7 @@
 
 setup(
     name='zpca',
-    version='0.8.2',
+    version='0.8.3',
     description="PCA analysis for genes or transcripts.",
     author="Foivos Gypas",
     author_email='[email protected]',