Remove forward slash in m/z for txt outputs

computational-metabolomics · Feb 19, 2018 · cde30e3 · cde30e3
1 parent 24b3ff9
commit cde30e3
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Showing 5 changed files with 7 additions and 7 deletions.
diff --git a/dimspy/models/peak_matrix.py b/dimspy/models/peak_matrix.py
@@ -757,7 +757,7 @@ def to_str(self, attr_name='intensity', delimiter='\t', samples_in_rows=True, co
         self.remove_empty_peaks()
 
         mz = self.attr_matrix('mz', flagged_only = not comprehensive)
-        hd = ['m/z'] + map(str, np.average(mz, axis = 0, weights = mz.astype(bool)))
+        hd = ['mz'] + map(str, np.average(mz, axis = 0, weights = mz.astype(bool)))
         dm = [map(str, self.peaklist_ids)] + \
              [map(str, ln) for ln in self.attr_matrix(attr_name, flagged_only = not comprehensive).T]
 

diff --git a/tests/data/MTBLS79_subset/pm_mzml_triplicates.txt b/tests/data/MTBLS79_subset/pm_mzml_triplicates.txt
diff --git a/tests/data/MTBLS79_subset/pm_mzml_triplicates_comprehensive.txt b/tests/data/MTBLS79_subset/pm_mzml_triplicates_comprehensive.txt
diff --git a/tests/data/MTBLS79_subset/pm_mzml_triplicates_comprehensive_T.txt b/tests/data/MTBLS79_subset/pm_mzml_triplicates_comprehensive_T.txt
@@ -1,4 +1,4 @@
-m/z	present	occurrence	purity	rsd_QC	rsd_all	flags	batch04_B02_rep01_301.mzML	batch04_B02_rep02_302.mzML	batch04_B02_rep03_303.mzML	batch04_QC17_rep01_262.mzML	batch04_QC17_rep02_263.mzML	batch04_QC17_rep03_264.mzML	batch04_S01_rep01_247.mzML	batch04_S01_rep02_248.mzML	batch04_S01_rep03_249.mzML
+mz	present	occurrence	purity	rsd_QC	rsd_all	flags	batch04_B02_rep01_301.mzML	batch04_B02_rep02_302.mzML	batch04_B02_rep03_303.mzML	batch04_QC17_rep01_262.mzML	batch04_QC17_rep02_263.mzML	batch04_QC17_rep03_264.mzML	batch04_S01_rep01_247.mzML	batch04_S01_rep02_248.mzML	batch04_S01_rep03_249.mzML
 missing values							2548	2454	2474	2839	2832	2829	2865	2859	2884
 tags_class_label							blank	blank	blank	QC	QC	QC	sample	sample	sample
 tags_untyped															

diff --git a/tests/test_tools.py b/tests/test_tools.py
@@ -218,14 +218,14 @@ def test_hdf5_peak_matrix_to_txt(self):
                                 attr_name="intensity", rsd_tags=(), delimiter="\t", samples_in_rows=True, comprehensive=False)
         with open(to_test_result("pm_mzml_triplicates.txt"), "rU") as test_result:
             ln = test_result.readline().split("\t")[:5]
-            self.assertEqual(ln[0], "m/z")
+            self.assertEqual(ln[0], "mz")
             self.assertTrue(np.allclose(map(float,ln[1:]), [74.0166655257, 74.0198337519, 74.0200238089, 74.0202012645], atol = 1e-10))
 
         hdf5_peak_matrix_to_txt(to_test_data("MTBLS79_mzml_peak_matrix.hdf5"), to_test_result("pm_mzml_triplicates_comprehensive.txt"),
                                 attr_name="intensity", rsd_tags=(Tag("QC", "classLabel"),), delimiter="\t", samples_in_rows=True, comprehensive=True)
         with open(to_test_result("pm_mzml_triplicates_comprehensive.txt"), "rU") as test_result:
             ln = test_result.readline().split("\t")[:8]
-            self.assertEquals(ln[:-2], ['m/z', 'missing values', 'tags_batch', 'tags_replicate', 'tags_injectionOrder', 'tags_classLabel'])
+            self.assertEquals(ln[:-2], ['mz', 'missing values', 'tags_batch', 'tags_replicate', 'tags_injectionOrder', 'tags_classLabel'])
             self.assertTrue(np.isclose(float(ln[-1]), 74.0166655257))
 
         hdf5_peak_matrix_to_txt(to_test_data("MTBLS79_mzml_peak_matrix.hdf5"), to_test_result("pm_mzml_triplicates_snr.txt"),
@@ -239,7 +239,7 @@ def test_hdf5_peak_matrix_to_txt(self):
                                 attr_name="intensity", rsd_tags=(Tag("QC", "classLabel"),), delimiter="\t", samples_in_rows=False, comprehensive=True)
         with open(to_test_result("pm_mzml_triplicates_comprehensive_T.txt"), "rU") as test_result:
             self.assertEquals(test_result.readline().split("\t")[0:5],
-                              ['m/z', 'present', 'occurrence', 'purity', 'rsd_QC'])
+                              ['mz', 'present', 'occurrence', 'purity', 'rsd_QC'])
 
 
     def test_create_sample_list(self):