Mercurial > repos > mvdbeek > damidseq_consecutive_peaks
changeset 0:7ca388514216 draft
planemo upload for repository https://github.com/bardin-lab/damid_galaxy_tools commit c753dd4f3e1863aae7ba45dcc7efdf6937b03542-dirty
| author | mvdbeek |
|---|---|
| date | Fri, 26 Oct 2018 11:56:10 -0400 |
| parents | |
| children | ce32ecf89099 |
| files | consecutive_peaks.py consecutive_peaks.xml test-data/deseq2_peaks.bed test-data/grouped.bed |
| diffstat | 4 files changed, 110 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/consecutive_peaks.py Fri Oct 26 11:56:10 2018 -0400 @@ -0,0 +1,34 @@ +import click +import numpy as np +import pandas as pd + +SHIFTED_PADJ_COLUMN = 'shifted' +CONSECUTIVE_MAX = 'consecutive_max' +PEAKS_PER_GROUP = 'peaks_per_group' + + +@click.command() +@click.argument('input_file', type=click.Path(exists=True)) +@click.argument('output_file', type=click.Path()) +@click.argument('padj_column', default=8) +@click.argument('groupby_column', default=9) +@click.argument('add_number_of_peaks', default=True) +def determine_consecutive_peaks(input_file, output_file, padj_column, groupby_column, add_number_of_peaks): + """Finds the two lowest consecutives peaks for a group and reports""" + df = pd.read_csv(input_file, sep='\t', header=None) + grouped = df.groupby(groupby_column, sort=False) + if add_number_of_peaks: + df[PEAKS_PER_GROUP] = grouped[groupby_column].transform(np.size) + df[SHIFTED_PADJ_COLUMN] = grouped[8].shift() + df[CONSECUTIVE_MAX] = df[[padj_column, SHIFTED_PADJ_COLUMN]].max(axis=1) + grouped = df.groupby(groupby_column, sort=False) + idx = grouped[CONSECUTIVE_MAX].transform(min) # index of groupwise consecutive minimum + new_df = df[df[CONSECUTIVE_MAX] == idx] + new_df.sort_values(by=CONSECUTIVE_MAX) + new_df[padj_column].replace(new_df[CONSECUTIVE_MAX]) + new_df = new_df.drop(labels=[CONSECUTIVE_MAX, SHIFTED_PADJ_COLUMN], axis=1) + new_df.to_csv(output_file, sep='\t', header=None, na_rep="NaN") + + +if __name__ == '__main__': + determine_consecutive_peaks()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/consecutive_peaks.xml Fri Oct 26 11:56:10 2018 -0400 @@ -0,0 +1,27 @@ +<tool id="consecutive_peaks" name="Consecutive peaks" version="0.1.0"> + <requirements> + <requirement type="package" version="7.0">click</requirement> + <requirement type="package" version="0.23.4">pandas</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ +python '$__tool_directory__/consecutive_peaks.py' '$input_file' '$output_file' + ]]></command> + <inputs> + <param name="input_file" type="data" format="tabular" label="Input file" help="file containing peaks and genes"/> + <param name="padj_column" type="data_column" data_ref="input_file" value="c8" label="Column containing padj value"/> + <param name="groupby" type="data_column" data_ref="input_file" value="c9" label="Group values by this column" help="Usually gene id."/> + </inputs> + <outputs> + <data name="output_file" format_source="input_file"/> + </outputs> + <tests> + <test> + <param name="input_file" value="deseq2_peaks.bed"/> + <output name="output_file" value="grouped.bed"/> + </test> + </tests> + <help><![CDATA[ +Can be used to get the lowest p.adj for 2 consecutive peaks in a gene. +The reported p.adj is the higher p.adj of the 2 consecutive peaks. + ]]></help> +</tool>
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