diff 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"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/runFlockMFI.py	Fri Jul 17 09:06:54 2020 -0400
@@ -0,0 +1,116 @@
+#!/usr/bin/env python
+######################################################################
+#                  Copyright (c) 2016 Northrop Grumman.
+#                          All rights reserved.
+######################################################################
+# version 2
+
+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):
+    run_command = 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(
+            '-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)