Mercurial > repos > bgruening > flexynesis_cbioportal_import

annotate convert.py @ 8:461b8e2d79d5 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit bcee55468e70cd025cc5359bef5e9991e893eca9
author bgruening
date Thu, 16 Oct 2025 20:15:31 +0000
parents 693011647a67
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3f7481deaff1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
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1 #!/usr/bin/env python
3f7481deaff1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
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3f7481deaff1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
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3 import sys
3f7481deaff1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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3f7481deaff1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
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5 import pandas as pd
3f7481deaff1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
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3f7481deaff1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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3f7481deaff1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
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8 def tabular_to_csv(tabular_file, csv_file):
3f7481deaff1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
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9 """Convert tabular (TSV) to CSV"""
3f7481deaff1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
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10 data = pd.read_csv(tabular_file, sep="\t")
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693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
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11 if data.columns[0] == '' or data.columns[0].startswith('Unnamed:'):
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
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12 data.columns = ['ID'] + list(data.columns[1:])
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3f7481deaff1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
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13 data.to_csv(csv_file, index=False)
3f7481deaff1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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3f7481deaff1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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3f7481deaff1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
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16 def csv_to_tabular(csv_file, tabular_file):
3f7481deaff1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
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17 """Convert CSV to tabular (TSV)"""
3f7481deaff1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
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18 data = pd.read_csv(csv_file)
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693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
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19 if data.columns[0] == '' or data.columns[0].startswith('Unnamed:'):
693011647a67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 6
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20 data.columns = ['ID'] + list(data.columns[1:])
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3f7481deaff1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
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21 data.to_csv(tabular_file, sep="\t", index=False)
3f7481deaff1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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3f7481deaff1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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3f7481deaff1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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24 if __name__ == "__main__":
3f7481deaff1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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25 input_file = sys.argv[1]
3f7481deaff1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
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26 output_file = sys.argv[2]
3f7481deaff1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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3f7481deaff1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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28 if input_file.endswith('.csv'):
3f7481deaff1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
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29 csv_to_tabular(input_file, output_file)
3f7481deaff1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
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30 else:
3f7481deaff1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
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31 tabular_to_csv(input_file, output_file)