diff mztab_reader.py @ 0:84e4b5d4b7ad draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics commit 49b21b01937067ffc7cf088e615d68177644640b"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mztab_reader.py	Fri Jan 15 15:58:54 2021 +0000
@@ -0,0 +1,69 @@
+#!/usr/bin/env python
+
+import argparse
+import os
+
+import pandas as pd
+from pyteomics.mztab import MzTab
+
+
+def read_mztab(input_path, output_path):
+    """
+    Read mztab file
+    """
+    mztab = MzTab(input_path)
+    if mztab.variant == 'P':
+        return read_mztab_p(mztab, output_path)
+    elif mztab.variant == 'M':
+        return read_mztab_m(mztab, output_path)
+
+
+def read_mztab_p(mztab, output_path):
+    """
+    Processing mztab "P"
+    """
+    mtd = pd.DataFrame.from_dict(mztab.metadata, orient='index')
+    mtd.to_csv(os.path.join(output_path, "mtd.tsv"), sep="\t")
+    prt = mztab.protein_table
+    prt.to_csv(os.path.join(output_path, "prt.tsv"), sep="\t")
+    pep = mztab.peptide_table
+    pep.to_csv(os.path.join(output_path, "pep.tsv"), sep="\t")
+    psm = mztab.spectrum_match_table
+    psm.to_csv(os.path.join(output_path, "psm.tsv"), sep="\t")
+    sml = mztab.small_molecule_table
+    sml.to_csv(os.path.join(output_path, "sml.tsv"), sep="\t")
+
+
+def read_mztab_m(mztab, output_path):
+    """
+    Processing mztab "M"
+    """
+    mtd = pd.DataFrame.from_dict(mztab.metadata, orient='index')
+    mtd.to_csv(os.path.join(output_path, "mtd.tsv"), sep="\t")
+    sml = mztab.small_molecule_table
+    sml.to_csv(os.path.join(output_path, "sml.tsv"), sep="\t")
+    smf = mztab.small_molecule_feature_table
+    smf.to_csv(os.path.join(output_path, "smf.tsv"), sep="\t")
+    sme = mztab.small_molecule_evidence_table
+    sme.to_csv(os.path.join(output_path, "sme.tsv"), sep="\t")
+
+
+if __name__ == "__main__":
+    # Create the parser
+    my_parser = argparse.ArgumentParser(description='List of paths')
+    # Add the arguments
+    my_parser.add_argument('--path_in',
+                           metavar='path',
+                           type=str,
+                           required=True,
+                           help='the path of input .mztab file')
+    my_parser.add_argument('--path_out',
+                           metavar='path',
+                           type=str,
+                           default=os.getcwd(),
+                           help='the path of folder for output .tsv file')
+
+    # Execute parse_args()
+    args = my_parser.parse_args()
+
+    read_mztab(args.path_in, args.path_out)