From 1d1c168cd63e8fab67f48fa905ae5331b3693f28 Mon Sep 17 00:00:00 2001 From: Foivos Gypas Date: Fri, 9 Apr 2021 19:33:52 +0200 Subject: [PATCH] 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 | 3 + scripts/zpca-counts | 11 + scripts/zpca-tpm | 11 + setup.py | 2 +- test_data/transcripts_tpm_1_sample.tsv | 133225 +++++++++++++++ test_data/transcripts_tpm_1_sample_PCA.tsv | 0 test_data/transcripts_tpm_1_sample_scree.tsv | 0 test_data/transcripts_tpm_2_samples.tsv | 133225 +++++++++++++++ test_data/transcripts_tpm_2_samples_PCA.tsv | 3 + test_data/transcripts_tpm_2_samples_scree.tsv | 2 + tests/test.py | 41 +- zpca/zpca.py | 2 - 12 files changed, 266521 insertions(+), 4 deletions(-) create mode 100644 test_data/transcripts_tpm_1_sample.tsv create mode 100644 test_data/transcripts_tpm_1_sample_PCA.tsv create mode 100644 test_data/transcripts_tpm_1_sample_scree.tsv create mode 100644 test_data/transcripts_tpm_2_samples.tsv create mode 100644 test_data/transcripts_tpm_2_samples_PCA.tsv create mode 100644 test_data/transcripts_tpm_2_samples_scree.tsv diff --git a/.gitignore b/.gitignore index b6e4761..6cb124b 100644 --- a/.gitignore +++ b/.gitignore @@ -127,3 +127,6 @@ dmypy.json # Pyre type checker .pyre/ + +test_data/TRANSCRIPT_TPM_2_SAMPLES/ +test_data/TRANSCRIPT_TPM_1_SAMPLE/ diff --git a/scripts/zpca-counts b/scripts/zpca-counts index 5964d6c..80649bb 100755 --- a/scripts/zpca-counts +++ b/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) diff --git a/scripts/zpca-tpm b/scripts/zpca-tpm index d3808d0..8e41c61 100755 --- a/scripts/zpca-tpm +++ b/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: diff --git a/setup.py b/setup.py index ef370ab..e537a7e 100755 --- a/setup.py +++ b/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='fgypas@gmail.com', diff --git a/test_data/transcripts_tpm_1_sample.tsv 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+ENST00000611412 15.688 17.0487 +ENST00000556494 2.20296 0.0 +ENST00000378560 0.251517 0.679901 +ENST00000556157 0.0 1.04485 +ENST00000556792 0.085384 0.161113 +ENST00000393591 0.0 0.0 +ENST00000478308 0.851906 0.809796 +ENST00000370100 0.0 0.0 +ENST00000409934 18.926 17.5214 +ENST00000555981 0.702501 0.457049 +ENST00000518489 0.0 0.0 +ENST00000520078 0.320318 0.273787 +ENST00000553969 2.70927 1.45206 +ENST00000259631 0.0 0.0 +ENST00000545043 0.0 0.0 +ENST00000564224 0.087951 0.111831 +ENST00000577222 0.0 0.043118 +ENST00000416454 0.831226 0.0 diff --git a/test_data/transcripts_tpm_2_samples_PCA.tsv b/test_data/transcripts_tpm_2_samples_PCA.tsv new file mode 100644 index 0000000..3afce9c --- /dev/null +++ b/test_data/transcripts_tpm_2_samples_PCA.tsv @@ -0,0 +1,3 @@ + PC1 PC2 +cond1_rep1 -78.88870415886339 9.079282464741212e-14 +cond2_rep1 78.88870415886339 -9.079282464741212e-14 diff --git a/test_data/transcripts_tpm_2_samples_scree.tsv b/test_data/transcripts_tpm_2_samples_scree.tsv new file mode 100644 index 0000000..46da2eb --- /dev/null +++ b/test_data/transcripts_tpm_2_samples_scree.tsv @@ -0,0 +1,2 @@ + PC1 PC2 +Percentage of Explained Variance 100.0 0.0 diff --git a/tests/test.py b/tests/test.py index 9368769..4cbe5ce 100644 --- a/tests/test.py +++ b/tests/test.py @@ -12,6 +12,14 @@ TRANSCRIPT_TPM = "test_data/transcripts_tpm.tsv" TRANSCRIPT_LENGTH = "test_data/transcripts_length.tsv" +TRANSCRIPT_TPM_2_SAMPLES = "test_data/transcripts_tpm_2_samples.tsv" +TRANSCRIPT_TPM_2_SAMPLES_PCA = "test_data/transcripts_tpm_2_samples_PCA.tsv" +TRANSCRIPT_TPM_2_SAMPLES_scree = "test_data/transcripts_tpm_2_samples_scree.tsv" + +TRANSCRIPT_TPM_1_SAMPLE = "test_data/transcripts_tpm_1_sample.tsv" +TRANSCRIPT_TPM_1_SAMPLE_PCA = "test_data/transcripts_tpm_1_sample_PCA.tsv" +TRANSCRIPT_TPM_1_SAMPLE_scree = "test_data/transcripts_tpm_1_sample_scree.tsv" + def test_counts2tpm(): counts = pd.read_csv( @@ -87,4 +95,35 @@ def test_zpca_counts_path(script_runner): def test_zpca_tpm_path(script_runner): ret = script_runner.run('zpca-tpm', '--help') - assert ret.success \ No newline at end of file + assert ret.success + +def test_zpca_tpm_2_samples(script_runner): + script_runner.run('zpca-tpm', + '--tpm', + TRANSCRIPT_TPM_2_SAMPLES, + '--out', + 'test_data/TRANSCRIPT_TPM_2_SAMPLES', + '--verbose') + pca_out = pd.read_csv("test_data/TRANSCRIPT_TPM_2_SAMPLES/PCA.tsv", header=0, sep="\t", index_col=0) + pca_control = pd.read_csv(TRANSCRIPT_TPM_2_SAMPLES_PCA, header=0, sep="\t", index_col=0) + + assert pca_out.shape == pca_control.shape + + scree_out = pd.read_csv("test_data/TRANSCRIPT_TPM_2_SAMPLES/scree.tsv", header=0, sep="\t", index_col=0) + scree_control = pd.read_csv(TRANSCRIPT_TPM_2_SAMPLES_scree, header=0, sep="\t", index_col=0) + + assert scree_out.shape == scree_control.shape + +def test_zpca_tpm_1_sample(script_runner): + ret = script_runner.run('zpca-tpm', + '--tpm', + TRANSCRIPT_TPM_1_SAMPLE, + '--out', + 'test_data/TRANSCRIPT_TPM_1_SAMPLE', + '--verbose') + filesize_pca = os.path.getsize("test_data/TRANSCRIPT_TPM_1_SAMPLE/PCA.tsv") + filesize_scree = os.path.getsize("test_data/TRANSCRIPT_TPM_1_SAMPLE/scree.tsv") + + assert filesize_pca == 0 + assert filesize_scree == 0 + \ No newline at end of file diff --git a/zpca/zpca.py b/zpca/zpca.py index aa80300..31e79cc 100644 --- a/zpca/zpca.py +++ b/zpca/zpca.py @@ -15,8 +15,6 @@ def determine_number_of_components(df): samples = list(df.shape)[1] if samples == 1: n_components = 1 - sys.stderr.write(f"Too few samples for PCA {os.linesep}") - sys.exit(0) elif samples == 2: n_components = 2 else: