diff run_flock/runFlockMFI.py @ 2:b6b4d08b6858 draft default tip

"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/run_flock commit 7e94637827c3637229f3b568fa7f9d38428d6607"

--- a/run_flock/runFlockMFI.py	Mon Feb 27 13:30:23 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,125 +0,0 @@
-#!/usr/bin/env python
-######################################################################
-#                  Copyright (c) 2016 Northrop Grumman.
-#                          All rights reserved.
-######################################################################
-# version 2
-from __future__ import print_function
-
-import sys
-import os
-from argparse import ArgumentParser
-import pandas as pd
-from scipy.stats import gmean
-
-
-def run_FLOCK(input_file, method, bins, density, output_file, mfi_file,
-              mfi_calc, profile, tool_directory):
-    run_command = tool_directory + "/bin/" + method + " " + input_file
-    if bins:
-        run_command += " " + bins
-    if density:
-        run_command += " " + density
-
-    os.system(run_command)
-
-    move_command = "mv flock_results.txt " + output_file
-    os.system(move_command)
-
-    # Here add some way to calculate the count and tack it on to profile file.
-    flockdf = pd.read_table(output_file)
-    if mfi_calc == "mfi":
-        MFIs = flockdf.groupby('Population').mean().round(decimals=2)
-    elif mfi_calc == "gmfi":
-        MFIs = flockdf.groupby('Population').agg(lambda x: gmean(list(x))).round(decimals=2)
-    else:
-        MFIs = flockdf.groupby('Population').median().round(decimals=2)
-
-    with open(mfi_file, "w") as outf:
-        MFIs.to_csv(outf, sep="\t", float_format='%.0f')
-
-    (events, columns) = flockdf.shape
-    fstats = {}
-    fstats['population'] = flockdf.iloc[:, -1:].iloc[:, 0]
-    fstats['population_freq'] = fstats['population'].value_counts()
-    fstats['population_freq_sort'] = fstats['population_freq'].sort_index()
-    fstats['population_per'] = (fstats['population'].value_counts(normalize=True) * 100).round(decimals=2)
-    fstats['population_per_sort'] = fstats['population_per'].sort_index()
-    fstats['population_all'] = pd.concat([fstats['population_freq_sort'], fstats['population_per_sort']], axis=1)
-    fstats['population_all'].columns = ['Count', 'Percentage']
-    fstats['population_all']['Population_ID'] = fstats['population_all'].index
-
-    flock_profile = pd.read_table('profile.txt')
-    profile_pop = flock_profile.merge(fstats['population_all'], on='Population_ID')
-    profile_pop.to_csv(profile, sep="\t", float_format='%.2f', index=False)
-
-#    get_profile = "mv profile.txt " + profile
-#    os.system(get_profile)
-    return
-
-
-if __name__ == "__main__":
-    parser = ArgumentParser(
-             prog="runFlockMFI",
-             description="Run Flock on text file and generate centroid file")
-
-    parser.add_argument(
-            '-i',
-            dest="input_file",
-            required=True,
-            help="File location for the FCS file.")
-
-    parser.add_argument(
-            '-m',
-            dest="method",
-            required=True,
-            help="Run flock1 or flock2.")
-
-    parser.add_argument(
-            '-M',
-            dest="mfi_calc",
-            required=True,
-            help="what to calculate for centroids.")
-
-    parser.add_argument(
-            '-b',
-            dest="bins",
-            required=False,
-            help="Number of Bins.")
-
-    parser.add_argument(
-            '-d',
-            dest="density",
-            required=False,
-            help="Density.")
-
-    parser.add_argument(
-            '-o',
-            dest="output_file",
-            required=True,
-            help="File location for the output file.")
-
-    parser.add_argument(
-            '-t',
-            dest="tool_directory",
-            required=True,
-            help="File location for the output file.")
-
-    parser.add_argument(
-            '-c',
-            dest="centroids",
-            required=True,
-            help="File location for the output centroid file.")
-
-    parser.add_argument(
-            '-p',
-            dest="profile",
-            required=True,
-            help="File location for the output profile file.")
-
-    args = parser.parse_args()
-    run_FLOCK(args.input_file, args.method, args.bins,
-              args.density, args.output_file, args.centroids, args.mfi_calc,
-              args.profile, args.tool_directory)
-
-    sys.exit(0)