Mercurial > repos > mvdbeek > damid_deseq2_to_bedgraph

annotate damid_to_bedgraph.py @ 0:755cbe6825b5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
author mvdbeek
date Fri, 14 Dec 2018 06:27:41 -0500
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755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
parents:
diff changeset
1 from collections import OrderedDict
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
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755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
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3 import click
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
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4 import numpy as np
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
parents:
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5 import pandas as pd
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
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6 import traces
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
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755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
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755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
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9 def order_index(df):
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
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10 """
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
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11 Split chr_start_stop in df index and order by chrom and start.
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
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12 """
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
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13 idx = df.index.str.split('_')
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
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14 idx = pd.DataFrame.from_records(list(idx))
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
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755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
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16 idx.columns = ['chr', 'start', 'stop']
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
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17 idx = idx.astype(dtype={"chr": "object",
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
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18 "start": "int32",
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
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19 "stop": "int32"})
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
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20 coordinates = idx.sort_values(['chr', 'start'])
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
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21 df.index = np.arange(len(df.index))
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
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22 df = df.loc[coordinates.index]
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
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23 df = coordinates.join(df)
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
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24 # index is center of GATC site
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
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25 df.index = df['start'] + 2
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
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26 return df
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
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755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
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755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
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29 def interpolate_values(df, sampling_width=100):
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
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30 result = []
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
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31 for chrom in df['chr'].unique():
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
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32 chrom_df = df[df['chr'] == chrom]
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
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33 time_series = traces.TimeSeries(chrom_df['log2FC'])
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
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34 s = pd.DataFrame.from_records(time_series.sample(sampling_width, interpolate='linear'))
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
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35 # Calculate new start and end of interpolated region
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
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36 start = s[0] - int(sampling_width / 2)
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
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37 start.loc[start < 0] = 1
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
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38 end = s[0] + int(sampling_width / 2)
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
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39 result.append(pd.DataFrame(OrderedDict([('chr', chrom), ('start', start), ('end', end), ('score', s[1])])))
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
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40 return pd.concat(result)
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
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755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
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755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
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43 @click.command()
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
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44 @click.argument('input_path', type=click.Path(exists=True), required=True)
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
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45 @click.argument('output_path', type=click.Path(exists=False), required=True)
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
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46 @click.option('--resolution', help="Interpolate log2 fold change at this resolution (in basepairs)", default=50)
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
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47 def deseq2_to_bedgraph(input_path, output_path, resolution=50):
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
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48 """Convert deseq2 output on GATC fragments to bedgraph file with interpolated values."""
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
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49 df = pd.read_csv(input_path, sep='\t', header=None, index_col=0, usecols=[0, 2], names=['GATC', 'log2FC'])
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
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50 df = df[~df.index.str.contains('\.')]
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
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51 df = order_index(df)
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
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52 r = interpolate_values(df, sampling_width=resolution)
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
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53 r.to_csv(output_path, sep='\t', header=None, index=None)
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
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755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
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755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
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56 if __name__ == '__main__':
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
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57 deseq2_to_bedgraph()