| Next changeset 1:08b71aee9b80 (2020-06-22) |
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Commit message:
Uploaded |
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added:
auto_collapse_pop/auto_collapse_pops.py auto_collapse_pop/auto_collapse_pops.xml auto_collapse_pop/test_data/input.flowclr auto_collapse_pop/test_data/output.flowclr auto_collapse_pop/test_data/profile.flowscore auto_collapse_pop/test_data/report.txt |
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| diff -r 000000000000 -r 7632562ada41 auto_collapse_pop/auto_collapse_pops.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/auto_collapse_pop/auto_collapse_pops.py Mon Feb 27 12:14:29 2017 -0500 |
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| @@ -0,0 +1,79 @@ +#!/usr/bin/env python + +###################################################################### +# Copyright (c) 2016 Northrop Grumman. +# All rights reserved. +###################################################################### +from __future__ import print_function +import sys +import pandas as pd +from argparse import ArgumentParser + + +def auto_collapse(input_file, profile_file, output, report): + profile_pop_list = {} + pop_to_collapse = [] + markers = [] + with open(profile_file, "r") as pf: + pffl = pf.readline() + markers = pffl.strip().split("\t") + for pfline in pf: + line = pfline.strip().split("\t") + pop = line[0] + profil = "\t".join(line[1:-2]) + if profil in profile_pop_list: + profile_pop_list[profil].append(pop) + else: + profile_pop_list[profil] = [pop] + i = 1 + with open(report, "w") as rt: + rt.write("New_Population\tFormer_Populations\t") + rt.write("\t".join(markers[1:-2]) + "\n") + for profs in profile_pop_list: + pop_to_collapse.append(profile_pop_list[profs]) + pop_ls = ", ".join(profile_pop_list[profs]) + rt.write("\t".join([str(i), pop_ls, profs]) + "\n") + i += 1 + df = pd.read_table(input_file, dtype={'Population': object}) + df['new_population'] = df.Population + for i, sets_pop in enumerate(pop_to_collapse): + df.loc[df['Population'].isin(sets_pop), ['new_population']] = i + 1 + + df.Population = df.new_population + df.drop(['new_population'], inplace=True, axis=1) + df.to_csv(output, sep="\t", index=False) + + +if __name__ == "__main__": + parser = ArgumentParser( + prog="auto_pop_collapse_from_profile", + description="collapses FLOCK populations based on profile.") + + parser.add_argument( + '-i', + dest="input_file", + required=True, + help="FLOCK output file") + + parser.add_argument( + '-o', + dest="output", + required=True, + help="Name of the output file.") + + parser.add_argument( + '-r', + dest="report", + required=True, + help="Name of the report file.") + + parser.add_argument( + '-p', + dest="profile", + required=True, + help="File location for the profile.txt from FLOCK.") + + args = parser.parse_args() + + auto_collapse(args.input_file, args.profile, args.output, args.report) + sys.exit(0) |
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| diff -r 000000000000 -r 7632562ada41 auto_collapse_pop/auto_collapse_pops.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/auto_collapse_pop/auto_collapse_pops.xml Mon Feb 27 12:14:29 2017 -0500 |
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| @@ -0,0 +1,85 @@ +<tool id="auto_collapse_populations" name="Collapse populations automatically" version="1.0"> + <description>based on quartile binning from FLOCK results.</description> + <requirements> + <requirement type="package" version="0.17.1">pandas</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + </stdio> + <command><![CDATA[ + python $__tool_directory__/auto_collapse_pops.py -o "${output}" -i "${input}" -p "${profile}" -r "${report}" + ]]> + </command> + <inputs> + <param format="flowclr" name="input" type="data" label="FLOCK or Cross-Sample output file"/> + <param format="flowscore" name="profile" type="data" label="Population score profiles from FLOCK"/> + </inputs> + <outputs> + <data format="flowclr" name="output" label="Auto-collapsed pops in ${input.name}"/> + <data format="tabular" name="report" label="Auto-collapse report for ${input.name} with ${profile.name}"/> + </outputs> + <tests> + <test> + <param name="input" value="input.flowclr"/> + <param name="profile=" value="profile.flowscore"/> + <param name="report" value="report.txt"/> + <output name="output" file="output.flowclr"/> + </test> + </tests> + <help><![CDATA[ + This tool automatically collapses populations together based on FLOCK score profiles. + +----- + +.. class:: warningmark + +*FLOCK score profiles are assigned based on quartile binning of the data. As always, use this tool with caution and be critical of your results* + +----- + +**Input** + +FLOCK or Cross Sample output - a table of the fluorescence intensities for each event and the population associated with each, as well as the file containing the score profiles for each FLOCK population. + +**Output** + +The input file with selected populations replaced by the indicated population. This tool also generates a report. + +----- + +**Example** + +*Input* - fluorescence intensities per marker and population ID per event:: + + Marker1 Marker2 Marker3 Population + 34 45 12 1 + 33 65 10 5 + 19 62 98 2 + 12 36 58 3 + +*Population profile file*:: + + Population_ID Marker1 Marker2 Marker3 Count Percentage + 1 2 2 3 3885 6.44 + 2 1 3 4 2774 4.62 + 3 2 2 3 2151 3.59 + 4 1 3 2 1207 2.01 + +*Output* - fluorescence intensities per marker and population ID per event:: + + Marker1 Marker2 Marker3 Population + 34 45 12 1 + 33 65 10 4 + 19 62 98 2 + 12 36 58 1 + +*Output* - fluorescence intensities per marker and population ID per event:: + + New_Population Former_Populations Marker1 Marker2 Marker3 + 1 1, 3 2 2 3 + 2 2 1 3 4 + 3 4 1 3 2 + 4 5, 8, 12 3 1 1 + ]]> + </help> +</tool> |
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| diff -r 000000000000 -r 7632562ada41 auto_collapse_pop/test_data/input.flowclr --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/auto_collapse_pop/test_data/input.flowclr Mon Feb 27 12:14:29 2017 -0500 |
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| b |
| diff -r 000000000000 -r 7632562ada41 auto_collapse_pop/test_data/output.flowclr --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/auto_collapse_pop/test_data/output.flowclr Mon Feb 27 12:14:29 2017 -0500 |
| b |
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8\t1023\t115\t247\t174\t266\t1\n+637\t1023\t203\t289\t255\t175\t1\n+649\t902\t155\t165\t213\t262\t1\n+322\t148\t0\t187\t87\t115\t10\n' |
| b |
| diff -r 000000000000 -r 7632562ada41 auto_collapse_pop/test_data/profile.flowscore --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/auto_collapse_pop/test_data/profile.flowscore Mon Feb 27 12:14:29 2017 -0500 |
| b |
| @@ -0,0 +1,31 @@ +Population_ID FSC SSC CD4 CCR3 CD8 CCR7 +1 1 1 3 1 1 1 +2 1 1 1 1 1 1 +3 1 1 1 1 1 1 +4 1 2 1 2 1 1 +5 1 1 3 1 1 1 +6 1 1 1 1 3 2 +7 1 1 3 1 1 1 +8 1 1 1 1 1 1 +9 1 1 3 1 1 1 +10 1 1 1 1 3 2 +11 1 1 1 1 3 1 +12 1 1 3 1 1 2 +13 1 1 3 1 1 1 +14 1 1 1 1 2 1 +15 1 1 3 1 1 1 +16 1 1 3 1 1 1 +17 1 1 3 1 1 2 +18 3 2 3 1 1 2 +19 2 4 1 1 1 2 +20 2 4 1 1 1 1 +21 3 4 1 2 2 2 +22 3 4 1 1 1 1 +23 2 4 2 2 2 3 +24 3 4 1 2 1 1 +25 4 4 2 2 2 2 +26 3 2 3 1 1 1 +27 2 4 1 1 1 2 +28 2 4 1 1 1 1 +29 4 4 3 2 2 3 +30 4 4 3 4 2 3 |
| b |
| diff -r 000000000000 -r 7632562ada41 auto_collapse_pop/test_data/report.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/auto_collapse_pop/test_data/report.txt Mon Feb 27 12:14:29 2017 -0500 |
| b |
| @@ -0,0 +1,12 @@ +New_Population Former_Populations FSC SSC CD4 CCR3 +1 19, 20, 27, 28 2 4 1 1 +2 4 1 2 1 2 +3 30 4 4 3 4 +4 21, 24 3 4 1 2 +5 29 4 4 3 2 +6 18, 26 3 2 3 1 +7 25 4 4 2 2 +8 1, 5, 7, 9, 12, 13, 15, 16, 17 1 1 3 1 +9 22 3 4 1 1 +10 2, 3, 6, 8, 10, 11, 14 1 1 1 1 +11 23 2 4 2 2 |