Mercurial > repos > mvdbeek > damidseq_consecutive_peaks

annotate consecutive_peaks.py @ 1:f3ca59e53b73 draft default tip

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planemo upload for repository https://github.com/bardin-lab/damid_galaxy_tools commit c753dd4f3e1863aae7ba45dcc7efdf6937b03542-dirty
author mvdbeek
date Mon, 29 Oct 2018 06:49:17 -0400
parents 7f827a8e4ec5
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7f827a8e4ec5 planemo upload for repository https://github.com/bardin-lab/damid_galaxy_tools commit c753dd4f3e1863aae7ba45dcc7efdf6937b03542-dirty
mvdbeek
parents:
diff changeset
1 import click
7f827a8e4ec5 planemo upload for repository https://github.com/bardin-lab/damid_galaxy_tools commit c753dd4f3e1863aae7ba45dcc7efdf6937b03542-dirty
mvdbeek
parents:
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2 import numpy as np
7f827a8e4ec5 planemo upload for repository https://github.com/bardin-lab/damid_galaxy_tools commit c753dd4f3e1863aae7ba45dcc7efdf6937b03542-dirty
mvdbeek
parents:
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3 import pandas as pd
7f827a8e4ec5 planemo upload for repository https://github.com/bardin-lab/damid_galaxy_tools commit c753dd4f3e1863aae7ba45dcc7efdf6937b03542-dirty
mvdbeek
parents:
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7f827a8e4ec5 planemo upload for repository https://github.com/bardin-lab/damid_galaxy_tools commit c753dd4f3e1863aae7ba45dcc7efdf6937b03542-dirty
mvdbeek
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5 SHIFTED_PADJ_COLUMN = 'shifted'
7f827a8e4ec5 planemo upload for repository https://github.com/bardin-lab/damid_galaxy_tools commit c753dd4f3e1863aae7ba45dcc7efdf6937b03542-dirty
mvdbeek
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6 CONSECUTIVE_MAX = 'consecutive_max'
7f827a8e4ec5 planemo upload for repository https://github.com/bardin-lab/damid_galaxy_tools commit c753dd4f3e1863aae7ba45dcc7efdf6937b03542-dirty
mvdbeek
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7 PEAKS_PER_GROUP = 'peaks_per_group'
7f827a8e4ec5 planemo upload for repository https://github.com/bardin-lab/damid_galaxy_tools commit c753dd4f3e1863aae7ba45dcc7efdf6937b03542-dirty
mvdbeek
parents:
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7f827a8e4ec5 planemo upload for repository https://github.com/bardin-lab/damid_galaxy_tools commit c753dd4f3e1863aae7ba45dcc7efdf6937b03542-dirty
mvdbeek
parents:
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7f827a8e4ec5 planemo upload for repository https://github.com/bardin-lab/damid_galaxy_tools commit c753dd4f3e1863aae7ba45dcc7efdf6937b03542-dirty
mvdbeek
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10 @click.command()
7f827a8e4ec5 planemo upload for repository https://github.com/bardin-lab/damid_galaxy_tools commit c753dd4f3e1863aae7ba45dcc7efdf6937b03542-dirty
mvdbeek
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11 @click.argument('input_file', type=click.Path(exists=True))
7f827a8e4ec5 planemo upload for repository https://github.com/bardin-lab/damid_galaxy_tools commit c753dd4f3e1863aae7ba45dcc7efdf6937b03542-dirty
mvdbeek
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12 @click.argument('output_file', type=click.Path())
7f827a8e4ec5 planemo upload for repository https://github.com/bardin-lab/damid_galaxy_tools commit c753dd4f3e1863aae7ba45dcc7efdf6937b03542-dirty
mvdbeek
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13 @click.argument('padj_column', default=8)
7f827a8e4ec5 planemo upload for repository https://github.com/bardin-lab/damid_galaxy_tools commit c753dd4f3e1863aae7ba45dcc7efdf6937b03542-dirty
mvdbeek
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14 @click.argument('groupby_column', default=9)
7f827a8e4ec5 planemo upload for repository https://github.com/bardin-lab/damid_galaxy_tools commit c753dd4f3e1863aae7ba45dcc7efdf6937b03542-dirty
mvdbeek
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15 @click.argument('add_number_of_peaks', default=True)
7f827a8e4ec5 planemo upload for repository https://github.com/bardin-lab/damid_galaxy_tools commit c753dd4f3e1863aae7ba45dcc7efdf6937b03542-dirty
mvdbeek
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16 def determine_consecutive_peaks(input_file, output_file, padj_column, groupby_column, add_number_of_peaks):
7f827a8e4ec5 planemo upload for repository https://github.com/bardin-lab/damid_galaxy_tools commit c753dd4f3e1863aae7ba45dcc7efdf6937b03542-dirty
mvdbeek
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17 """Finds the two lowest consecutives peaks for a group and reports"""
7f827a8e4ec5 planemo upload for repository https://github.com/bardin-lab/damid_galaxy_tools commit c753dd4f3e1863aae7ba45dcc7efdf6937b03542-dirty
mvdbeek
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18 df = pd.read_csv(input_file, sep='\t', header=None)
7f827a8e4ec5 planemo upload for repository https://github.com/bardin-lab/damid_galaxy_tools commit c753dd4f3e1863aae7ba45dcc7efdf6937b03542-dirty
mvdbeek
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19 grouped = df.groupby(groupby_column, sort=False)
7f827a8e4ec5 planemo upload for repository https://github.com/bardin-lab/damid_galaxy_tools commit c753dd4f3e1863aae7ba45dcc7efdf6937b03542-dirty
mvdbeek
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20 if add_number_of_peaks:
7f827a8e4ec5 planemo upload for repository https://github.com/bardin-lab/damid_galaxy_tools commit c753dd4f3e1863aae7ba45dcc7efdf6937b03542-dirty
mvdbeek
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21 df[PEAKS_PER_GROUP] = grouped[groupby_column].transform(np.size)
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f3ca59e53b73 planemo upload for repository https://github.com/bardin-lab/damid_galaxy_tools commit c753dd4f3e1863aae7ba45dcc7efdf6937b03542-dirty
mvdbeek
parents: 0
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22 df[SHIFTED_PADJ_COLUMN] = grouped[padj_column].shift()
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7f827a8e4ec5 planemo upload for repository https://github.com/bardin-lab/damid_galaxy_tools commit c753dd4f3e1863aae7ba45dcc7efdf6937b03542-dirty
mvdbeek
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23 df[CONSECUTIVE_MAX] = df[[padj_column, SHIFTED_PADJ_COLUMN]].max(axis=1)
7f827a8e4ec5 planemo upload for repository https://github.com/bardin-lab/damid_galaxy_tools commit c753dd4f3e1863aae7ba45dcc7efdf6937b03542-dirty
mvdbeek
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24 grouped = df.groupby(groupby_column, sort=False)
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f3ca59e53b73 planemo upload for repository https://github.com/bardin-lab/damid_galaxy_tools commit c753dd4f3e1863aae7ba45dcc7efdf6937b03542-dirty
mvdbeek
parents: 0
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25 idx = grouped[CONSECUTIVE_MAX].idxmin() # index of groupwise consecutive minimum
f3ca59e53b73 planemo upload for repository https://github.com/bardin-lab/damid_galaxy_tools commit c753dd4f3e1863aae7ba45dcc7efdf6937b03542-dirty
mvdbeek
parents: 0
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26 new_df = df.loc[idx]
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7f827a8e4ec5 planemo upload for repository https://github.com/bardin-lab/damid_galaxy_tools commit c753dd4f3e1863aae7ba45dcc7efdf6937b03542-dirty
mvdbeek
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27 new_df.sort_values(by=CONSECUTIVE_MAX)
7f827a8e4ec5 planemo upload for repository https://github.com/bardin-lab/damid_galaxy_tools commit c753dd4f3e1863aae7ba45dcc7efdf6937b03542-dirty
mvdbeek
parents:
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28 new_df[padj_column].replace(new_df[CONSECUTIVE_MAX])
7f827a8e4ec5 planemo upload for repository https://github.com/bardin-lab/damid_galaxy_tools commit c753dd4f3e1863aae7ba45dcc7efdf6937b03542-dirty
mvdbeek
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29 new_df = new_df.drop(labels=[CONSECUTIVE_MAX, SHIFTED_PADJ_COLUMN], axis=1)
7f827a8e4ec5 planemo upload for repository https://github.com/bardin-lab/damid_galaxy_tools commit c753dd4f3e1863aae7ba45dcc7efdf6937b03542-dirty
mvdbeek
parents:
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30 new_df.to_csv(output_file, sep='\t', header=None, na_rep="NaN")
7f827a8e4ec5 planemo upload for repository https://github.com/bardin-lab/damid_galaxy_tools commit c753dd4f3e1863aae7ba45dcc7efdf6937b03542-dirty
mvdbeek
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7f827a8e4ec5 planemo upload for repository https://github.com/bardin-lab/damid_galaxy_tools commit c753dd4f3e1863aae7ba45dcc7efdf6937b03542-dirty
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7f827a8e4ec5 planemo upload for repository https://github.com/bardin-lab/damid_galaxy_tools commit c753dd4f3e1863aae7ba45dcc7efdf6937b03542-dirty
mvdbeek
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33 if __name__ == '__main__':
7f827a8e4ec5 planemo upload for repository https://github.com/bardin-lab/damid_galaxy_tools commit c753dd4f3e1863aae7ba45dcc7efdf6937b03542-dirty
mvdbeek
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34 determine_consecutive_peaks()