Mercurial > repos > immport-devteam > flow_overview

annotate flowstatlib.py @ 1:b5453d07f740 draft default tip

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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"
author azomics
date Wed, 29 Jul 2020 17:03:53 -0400
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b5453d07f740 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"
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1 ######################################################################
b5453d07f740 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"
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2 # Copyright (c) 2016 Northrop Grumman.
b5453d07f740 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"
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3 # All rights reserved.
b5453d07f740 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"
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4 ######################################################################
b5453d07f740 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"
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5 import pandas as pd
b5453d07f740 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"
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6 from scipy.stats import gmean
b5453d07f740 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"
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7 from argparse import ArgumentParser
b5453d07f740 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"
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8
b5453d07f740 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"
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9
b5453d07f740 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"
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10 def gen_overview_stats(file_name):
b5453d07f740 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"
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11 flow_stats = {}
b5453d07f740 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"
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12 fcs = pd.read_table(file_name)
b5453d07f740 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"
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13 (events, columns) = fcs.shape
b5453d07f740 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"
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14 flow_stats['fcs'] = fcs
b5453d07f740 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"
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15 flow_stats['events'] = events
b5453d07f740 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"
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16 flow_stats['columns'] = columns - 1
b5453d07f740 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"
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17 flow_stats['data'] = fcs.iloc[:, :-1]
b5453d07f740 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"
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18 flow_stats['population'] = fcs.iloc[:, -1:].iloc[:, 0]
b5453d07f740 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"
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19 flow_stats['population_freq'] = flow_stats['population'].value_counts()
b5453d07f740 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"
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20 flow_stats['population_sample'] = (flow_stats['population_freq'] * (20000/float(events))).round(decimals=0)
b5453d07f740 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"
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21 flow_stats['population_freq_sort'] = flow_stats['population_freq'].sort_index()
b5453d07f740 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"
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22 flow_stats['population_per'] = (flow_stats['population'].value_counts(normalize=True) * 100).round(decimals=2)
b5453d07f740 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"
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23 flow_stats['population_per_sort'] = flow_stats['population_per'].sort_index()
b5453d07f740 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"
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24 flow_stats['population_all'] = pd.concat([flow_stats['population_freq_sort'], flow_stats['population_per_sort']], axis=1)
b5453d07f740 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"
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25 flow_stats['population_all'].columns = ['Count', 'Percentage']
b5453d07f740 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"
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26 flow_stats['min'] = flow_stats['data'].values.min()
b5453d07f740 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"
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27 flow_stats['max'] = flow_stats['data'].values.max()
b5453d07f740 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"
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28 flow_stats['markers'] = list(flow_stats['data'].columns)
b5453d07f740 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"
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29 flow_stats['mfi'] = fcs.groupby('Population').mean().round(decimals=2)
b5453d07f740 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"
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30 flow_stats['mfi_pop'] = pd.merge(flow_stats['mfi'], flow_stats['population_all'], left_index=True, right_index=True)
b5453d07f740 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"
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31 flow_stats['mfi_pop']['Population'] = flow_stats['mfi_pop'].index
b5453d07f740 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"
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32 flow_stats['gmfi'] = fcs.groupby('Population').agg(lambda x: gmean(list(x))).round(decimals=2)
b5453d07f740 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"
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33 flow_stats['gmfi_pop'] = pd.merge(flow_stats['gmfi'], flow_stats['population_all'], left_index=True, right_index=True)
b5453d07f740 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"
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34 flow_stats['gmfi_pop']['Population'] = flow_stats['gmfi_pop'].index
b5453d07f740 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"
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35 flow_stats['mdfi'] = fcs.groupby('Population').median().round(decimals=2)
b5453d07f740 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"
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36 flow_stats['mdfi_pop'] = pd.merge(flow_stats['mdfi'], flow_stats['population_all'], left_index=True, right_index=True)
b5453d07f740 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"
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37 flow_stats['mdfi_pop']['Population'] = flow_stats['mdfi_pop'].index
b5453d07f740 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"
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38
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39 #
b5453d07f740 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"
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40 # If the number of events is less than 20000, then return
b5453d07f740 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"
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41 # the complete data set,
b5453d07f740 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"
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42 # Otherwise sample the data to only return 20000 events.
b5453d07f740 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"
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43 if events <= 20000:
b5453d07f740 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"
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44 flow_stats['sample'] = fcs
b5453d07f740 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"
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45 else:
b5453d07f740 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"
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46 fcs_np = fcs.values
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47 sample_data = []
b5453d07f740 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"
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48 pop_found = {}
b5453d07f740 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"
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49 for i in range(0, events):
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50 population_number = fcs_np[i][columns-1]
b5453d07f740 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"
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51 if population_number in pop_found:
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52 if pop_found[population_number] < flow_stats['population_sample'][population_number]:
b5453d07f740 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"
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53 pop_found[population_number] += 1
b5453d07f740 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"
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54 sample_data.append(fcs_np[i])
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55 else:
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56 pop_found[population_number] = 1
b5453d07f740 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"
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57 sample_data.append(fcs_np[i])
b5453d07f740 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"
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58 flow_stats['sample'] = pd.DataFrame(sample_data)
b5453d07f740 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"
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59 flow_stats['sample'].columns = fcs.columns
b5453d07f740 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"
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60
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61 flow_stats['sample_data'] = flow_stats['sample'].iloc[:, :-1]
b5453d07f740 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"
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62 flow_stats['sample_population'] = flow_stats['sample'].iloc[:, -1:].iloc[:, 0]
b5453d07f740 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"
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63
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64 return flow_stats
b5453d07f740 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"
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65
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66
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67 if __name__ == '__main__':
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68 parser = ArgumentParser(
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69 prog="flowstats",
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70 description="Gets statistics on FLOCK run")
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71
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72 parser.add_argument(
b5453d07f740 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"
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73 '-i',
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74 dest="input_file",
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75 required=True,
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76 help="File locations for flow clr file.")
b5453d07f740 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"
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77
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78 parser.add_argument(
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79 '-o',
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80 dest="out_file",
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81 required=True,
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82 help="Path to the directory for the output file.")
b5453d07f740 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"
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83 args = parser.parse_args()
b5453d07f740 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"
azomics
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84
b5453d07f740 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"
azomics
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85 flow_stats = gen_overview_stats(args.input_file)
b5453d07f740 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"
azomics
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86 with open(args.out_file, "w") as outf:
b5453d07f740 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"
azomics
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87 outf.write("Events: ", flow_stats['events'])
b5453d07f740 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"
azomics
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88 outf.write("Min: ", flow_stats['min'])
b5453d07f740 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"
azomics
parents:
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89 outf.write("Max: ", flow_stats['max'])
b5453d07f740 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"
azomics
parents:
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90 outf.write("Columns: ", flow_stats['columns'])
b5453d07f740 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"
azomics
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91 outf.write("Markers: ", flow_stats['markers'])
b5453d07f740 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"
azomics
parents:
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92 outf.write("Population: ", flow_stats['population'])
b5453d07f740 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"
azomics
parents:
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93 outf.write("Population Freq: ", flow_stats['population_freq'])
b5453d07f740 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"
azomics
parents:
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94 outf.write("Population Sample: ", flow_stats['population_sample'])
b5453d07f740 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"
azomics
parents:
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95 outf.write("Population Per: ", flow_stats['population_per'])
b5453d07f740 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"
azomics
parents:
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96 outf.write("Sample Data contains ", len(flow_stats['sample']), " events")
b5453d07f740 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flow_overview commit 65373effef15809f3db0e5f9603ef808f4110aa3"
azomics
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97 outf.write("MIF_POP ", flow_stats['mfi_pop'])