Mercurial > repos > immport-devteam > txt_diagnosis

annotate txtdiagnosis.py @ 1:b94872d65050 draft default tip

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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
author azomics
date Thu, 16 Jul 2020 07:35:26 -0400
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b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
azomics
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1 #!/usr/bin/env python
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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2 ######################################################################
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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3 # Copyright (c) 2016 Northrop Grumman.
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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4 # All rights reserved.
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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5 ######################################################################
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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6 import pandas as pd
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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7 from argparse import ArgumentParser
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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8 import sys
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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9
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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10
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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11 def is_number(s):
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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12 try:
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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13 float(s)
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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14 return True
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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15 except ValueError:
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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16 return False
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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17
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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18
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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19 def error_report(input_file, fname, output_file):
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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20 errors = 0
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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21 df = pd.read_table(input_file)
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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22 with open(output_file, "w") as outf:
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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23 for cols in df.columns.values:
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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24 if df[cols].count() != len(df[cols]):
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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25 with open(input_file, "r") as checkfile:
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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26 fl = checkfile.readline()
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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27 count_lines = 1
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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28 for checklines in checkfile:
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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29 to_check = checklines.strip().split("\t")
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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30 count_lines += 1
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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31 for item in to_check:
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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32 if not is_number(item):
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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33 errors += 1
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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34 outf.write(" ".join(["WARNING: line", str(count_lines), "in", fname, "contains non-numeric results\n"]))
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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35 if errors == 0:
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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36 outf.write("No errors in the file.\n")
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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37 return
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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38
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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39
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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40 if __name__ == "__main__":
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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41 parser = ArgumentParser(
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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42 prog="txtDiagnosis",
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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43 description="Reports potential errors in text-converted FCS files")
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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44
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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45 parser.add_argument(
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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46 '-i',
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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47 dest="input_file",
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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48 required=True,
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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49 help="File location for the text file.")
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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50
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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51 parser.add_argument(
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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52 '-n',
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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53 dest="filename",
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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54 required=True,
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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55 help="Filename location for the text file.")
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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56
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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57 parser.add_argument(
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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58 '-o',
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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59 dest="output_file",
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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60 required=True,
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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61 help="Name of the output file.")
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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62
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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63 args = parser.parse_args()
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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64
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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65 error_report(args.input_file, args.filename, args.output_file)