Mercurial > repos > galaxyp > pyteomics_mztab2tsv

annotate mztab_reader.py @ 1:a475c1906e0b draft default tip

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics commit 58fe8232b7f4659b37e8725197d63e81efae0683"
author galaxyp
date Fri, 15 Jan 2021 21:10:59 +0000
parents 84e4b5d4b7ad
children
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84e4b5d4b7ad "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics commit 49b21b01937067ffc7cf088e615d68177644640b"
galaxyp
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1 #!/usr/bin/env python
84e4b5d4b7ad "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics commit 49b21b01937067ffc7cf088e615d68177644640b"
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84e4b5d4b7ad "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics commit 49b21b01937067ffc7cf088e615d68177644640b"
galaxyp
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3 import argparse
84e4b5d4b7ad "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics commit 49b21b01937067ffc7cf088e615d68177644640b"
galaxyp
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4 import os
84e4b5d4b7ad "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics commit 49b21b01937067ffc7cf088e615d68177644640b"
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84e4b5d4b7ad "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics commit 49b21b01937067ffc7cf088e615d68177644640b"
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6 import pandas as pd
84e4b5d4b7ad "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics commit 49b21b01937067ffc7cf088e615d68177644640b"
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7 from pyteomics.mztab import MzTab
84e4b5d4b7ad "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics commit 49b21b01937067ffc7cf088e615d68177644640b"
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84e4b5d4b7ad "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics commit 49b21b01937067ffc7cf088e615d68177644640b"
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84e4b5d4b7ad "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics commit 49b21b01937067ffc7cf088e615d68177644640b"
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10 def read_mztab(input_path, output_path):
84e4b5d4b7ad "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics commit 49b21b01937067ffc7cf088e615d68177644640b"
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11 """
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a475c1906e0b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics commit 58fe8232b7f4659b37e8725197d63e81efae0683"
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12 Read and process mztab file
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84e4b5d4b7ad "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics commit 49b21b01937067ffc7cf088e615d68177644640b"
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13 """
84e4b5d4b7ad "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics commit 49b21b01937067ffc7cf088e615d68177644640b"
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14 mztab = MzTab(input_path)
84e4b5d4b7ad "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics commit 49b21b01937067ffc7cf088e615d68177644640b"
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15 mtd = pd.DataFrame.from_dict(mztab.metadata, orient='index')
84e4b5d4b7ad "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics commit 49b21b01937067ffc7cf088e615d68177644640b"
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16 mtd.to_csv(os.path.join(output_path, "mtd.tsv"), sep="\t")
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a475c1906e0b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics commit 58fe8232b7f4659b37e8725197d63e81efae0683"
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17 for name, tab in mztab:
a475c1906e0b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics commit 58fe8232b7f4659b37e8725197d63e81efae0683"
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18 if not tab.empty:
a475c1906e0b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics commit 58fe8232b7f4659b37e8725197d63e81efae0683"
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19 tab.to_csv(os.path.join(output_path, f"{name.lower()}.tsv"), sep="\t")
a475c1906e0b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics commit 58fe8232b7f4659b37e8725197d63e81efae0683"
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20 else:
a475c1906e0b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics commit 58fe8232b7f4659b37e8725197d63e81efae0683"
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21 with open(os.path.join(output_path, f"{name.lower()}.tsv"), "w"):
a475c1906e0b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics commit 58fe8232b7f4659b37e8725197d63e81efae0683"
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22 pass
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84e4b5d4b7ad "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics commit 49b21b01937067ffc7cf088e615d68177644640b"
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84e4b5d4b7ad "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics commit 49b21b01937067ffc7cf088e615d68177644640b"
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84e4b5d4b7ad "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics commit 49b21b01937067ffc7cf088e615d68177644640b"
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25 if __name__ == "__main__":
84e4b5d4b7ad "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics commit 49b21b01937067ffc7cf088e615d68177644640b"
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26 # Create the parser
84e4b5d4b7ad "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics commit 49b21b01937067ffc7cf088e615d68177644640b"
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27 my_parser = argparse.ArgumentParser(description='List of paths')
84e4b5d4b7ad "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics commit 49b21b01937067ffc7cf088e615d68177644640b"
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28 # Add the arguments
84e4b5d4b7ad "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics commit 49b21b01937067ffc7cf088e615d68177644640b"
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29 my_parser.add_argument('--path_in',
84e4b5d4b7ad "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics commit 49b21b01937067ffc7cf088e615d68177644640b"
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30 metavar='path',
84e4b5d4b7ad "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics commit 49b21b01937067ffc7cf088e615d68177644640b"
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31 type=str,
84e4b5d4b7ad "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics commit 49b21b01937067ffc7cf088e615d68177644640b"
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32 required=True,
84e4b5d4b7ad "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics commit 49b21b01937067ffc7cf088e615d68177644640b"
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33 help='the path of input .mztab file')
84e4b5d4b7ad "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics commit 49b21b01937067ffc7cf088e615d68177644640b"
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34 my_parser.add_argument('--path_out',
84e4b5d4b7ad "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics commit 49b21b01937067ffc7cf088e615d68177644640b"
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35 metavar='path',
84e4b5d4b7ad "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics commit 49b21b01937067ffc7cf088e615d68177644640b"
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36 type=str,
84e4b5d4b7ad "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics commit 49b21b01937067ffc7cf088e615d68177644640b"
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37 default=os.getcwd(),
84e4b5d4b7ad "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics commit 49b21b01937067ffc7cf088e615d68177644640b"
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38 help='the path of folder for output .tsv file')
84e4b5d4b7ad "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics commit 49b21b01937067ffc7cf088e615d68177644640b"
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84e4b5d4b7ad "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics commit 49b21b01937067ffc7cf088e615d68177644640b"
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40 # Execute parse_args()
84e4b5d4b7ad "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics commit 49b21b01937067ffc7cf088e615d68177644640b"
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41 args = my_parser.parse_args()
84e4b5d4b7ad "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics commit 49b21b01937067ffc7cf088e615d68177644640b"
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84e4b5d4b7ad "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics commit 49b21b01937067ffc7cf088e615d68177644640b"
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43 read_mztab(args.path_in, args.path_out)