Mercurial > repos > immport-devteam > cs_overview

annotate crossSampleOverview.py @ 2:a64ece32a01a draft default tip

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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit a46097db0b6056e1125237393eb6974cfd51eb41"
author azomics
date Tue, 28 Jul 2020 08:32:36 -0400
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a64ece32a01a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit a46097db0b6056e1125237393eb6974cfd51eb41"
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1 #!/usr/bin/env python
a64ece32a01a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit a46097db0b6056e1125237393eb6974cfd51eb41"
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2
a64ece32a01a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit a46097db0b6056e1125237393eb6974cfd51eb41"
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3 ######################################################################
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4 # Copyright (c) 2016 Northrop Grumman.
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5 # All rights reserved.
a64ece32a01a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit a46097db0b6056e1125237393eb6974cfd51eb41"
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6 ######################################################################
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7
a64ece32a01a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit a46097db0b6056e1125237393eb6974cfd51eb41"
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8 # version 1.1 -- August 2017
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9 # added checks for consistency between input files
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10 # and upper limit on nb of cluster to look at
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11
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12 from __future__ import print_function
a64ece32a01a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit a46097db0b6056e1125237393eb6974cfd51eb41"
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13 import sys
a64ece32a01a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit a46097db0b6056e1125237393eb6974cfd51eb41"
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14 import os
a64ece32a01a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit a46097db0b6056e1125237393eb6974cfd51eb41"
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15 import logging
a64ece32a01a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit a46097db0b6056e1125237393eb6974cfd51eb41"
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16 import fileinput
a64ece32a01a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit a46097db0b6056e1125237393eb6974cfd51eb41"
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17 import pandas as pd
a64ece32a01a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit a46097db0b6056e1125237393eb6974cfd51eb41"
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18 from argparse import ArgumentParser
a64ece32a01a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit a46097db0b6056e1125237393eb6974cfd51eb41"
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19 from jinja2 import Environment, FileSystemLoader
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20 from shutil import copyfile
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21 from collections import defaultdict
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23
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24 def check_pops(mfi_file, stat1):
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25 df = pd.read_table(mfi_file)
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26 df1 = pd.read_table(stat1)
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27 nb_pop = len(set(df.Population))
a64ece32a01a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit a46097db0b6056e1125237393eb6974cfd51eb41"
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28 nb_pop1 = len(df1.columns) - 2
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29 if (nb_pop > 40):
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30 sys.stderr.write("There are " + str(nb_pop) + " in the input file.")
a64ece32a01a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit a46097db0b6056e1125237393eb6974cfd51eb41"
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31 sys.exit(1)
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32 if (nb_pop != nb_pop1):
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33 sys.exit(2)
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34
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35
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36 def panel_to_json_string(df):
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37 # from http://stackoverflow.com/questions/28078118/merge-many-json-strings-with-python-pandas-inputs
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38 def __merge_stream(key, stream):
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39 return '"' + key + '"' + ': ' + stream + ', '
a64ece32a01a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit a46097db0b6056e1125237393eb6974cfd51eb41"
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40 try:
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41 if 'Unnamed: 0' in df.columns:
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42 df = df.drop(['Unnamed: 0'], axis=1)
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43 stream = '{'
a64ece32a01a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit a46097db0b6056e1125237393eb6974cfd51eb41"
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44 for index, subdf in df.groupby(level=0):
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45 stream += __merge_stream(index, df.loc[index, :, :].droplevel(0).to_json())
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46 # take out extra last comma
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47 stream = stream[:-2]
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48 # add the final paren
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49 stream += '}'
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50 except:
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51 logging.exception('Panel Encoding did not work')
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52 return stream
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53
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54
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55 def get_outliers(group, upper, lower):
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56 cat = group.name
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57 out = {}
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58 for marker in group:
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59 # skip population since upper and lower don't contain it, since it was made after a group by Population
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60 if marker != 'Population':
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61 out[marker] = group[(group[marker] > upper.loc[cat][marker]) | (group[marker] < lower.loc[cat][marker])][marker]
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62 return out
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63
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64
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65 def get_boxplot_stats(all_data, mfi_file, output_json):
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66 # modified code from http://bokeh.pydata.org/en/latest/docs/gallery/boxplot.html
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67 # Get initial MFI values
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68 mfi = pd.read_table(mfi_file)
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69 mfi = mfi.set_index('Population')
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70
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71 df = pd.read_table(all_data)
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72 # check if ever some pops not in cs_files
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73 missing_pop = [x for x in mfi.index if x not in set(df.Population)]
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74
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75 if (missing_pop):
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76 zeros = {}
a64ece32a01a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit a46097db0b6056e1125237393eb6974cfd51eb41"
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77 for m in df.columns:
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78 zeros[m] = [0 for x in missing_pop]
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79 tmpdf = pd.DataFrame(zeros)
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80 tmpdf.Population = missing_pop
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81 df = df.append(tmpdf)
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82
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83 pops = df.groupby('Population')
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84 q1 = pops.quantile(q=0.25)
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85 q2 = pops.quantile(q=0.5)
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86 q3 = pops.quantile(q=0.75)
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87 iqr = q3 - q1
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88 upper = q3 + 1.5*iqr
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89 lower = q1 - 1.5*iqr
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90 resampled = False
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91 # get outliers
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92 out = pops.apply(get_outliers, upper, lower).dropna()
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93 outliers = defaultdict(dict)
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94 for population in set(df.Population):
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95 for marker in df.columns:
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96 if marker != 'Population':
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97 tmp_outliers = list(out[population][marker])
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98 if (len(list(out[population][marker])) > 100):
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99 tmp_outliers = list(out[population][marker].sample(n=100))
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100 resampled = True
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101 outliers[population][marker] = tmp_outliers
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102 outdf = pd.DataFrame(outliers)
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103
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104 data = pd.concat({'q1': q1,
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105 'q2': q2,
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106 'q3': q3,
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107 'upper': upper,
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108 'lower': lower,
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109 'outliers': outdf.T,
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110 'mfi': mfi}, keys=['q1','q2','q3','upper','lower','outliers','mfi'])
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111
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112 with open(output_json, "w") as js_all:
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113 js_all.write(panel_to_json_string(data))
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114
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115 return resampled
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116
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117
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118 def cs_overview(input_file, input_mfi, init_mfi, output_file, output_dir, tools_dir, cs_files):
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119 os.mkdir(output_dir)
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120
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121 env = Environment(loader=FileSystemLoader(tools_dir + "/templates"))
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122 template = env.get_template("csOverview.template")
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123
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124 real_directory = output_dir.replace("/job_working_directory", "")
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125 context = {'outputDirectory': real_directory}
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126 overview = template.render(**context)
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127 with open(output_file, "w") as outf:
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128 outf.write(overview)
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129
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130 cs_overview_file = output_dir + "/csOverview.tsv"
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131 copyfile(input_file, cs_overview_file)
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132
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133 cs_overview_mfis = output_dir + "/csAllMFIs.tsv"
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134 copyfile(input_mfi, cs_overview_mfis)
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135
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136 # Get all the data to calculate quantiles, IRC and outliers.
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137 tmp_all_data = "csAllData.tsv"
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138 with open(tmp_all_data, "a") as alldata:
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139 # assumes that the files have ran through flock and CS and therefore have the same headers
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140 df1 = pd.read_table(cs_files[0])
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141 df1.to_csv(alldata, sep="\t", header=True, index=False)
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142 for i in range(1, len(cs_files)):
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143 df = pd.read_table(cs_files[i])
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144 df.to_csv(alldata, sep="\t", header=False, index=False)
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145
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146 cs_boxplot_data = output_dir + "/csBoxplotData.json"
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147 resampled = get_boxplot_stats(tmp_all_data, init_mfi, cs_boxplot_data)
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148 if resampled:
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149 to_find = '<div id="outlierWarning" style="display:none;">'
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150 to_replace = '<div id="outlierWarning">'
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151 ## yay python 2.7
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152 ro = fileinput.input(output_file, inplace=True, backup=".bak")
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153 for roline in ro:
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154 print(roline.replace(to_find, to_replace), end='')
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155 ro.close()
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156
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diff changeset
157 return
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158
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159
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160 if __name__ == "__main__":
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161 parser = ArgumentParser(
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162 prog="csOverview",
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163 description="Generate an overview plot of crossSample results.")
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164
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165 parser.add_argument(
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166 '-i',
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167 dest="input_file",
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168 required=True,
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169 help="File location for the summary statistics from CrossSample.")
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170
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171 parser.add_argument(
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172 '-I',
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173 dest="input_mfi",
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174 required=True,
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175 help="File location for the MFI summary statistics from CrossSample.")
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176
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177 parser.add_argument(
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178 '-s',
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179 dest="cs_outputs",
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180 required=True,
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181 action='append',
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182 help="File location for the CrossSample output files.")
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183
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184 parser.add_argument(
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185 '-o',
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186 dest="output_file",
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187 required=True,
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188 help="File location for the HTML output file.")
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189
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190 parser.add_argument(
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191 '-m',
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192 dest="mfi",
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193 required=True,
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194 help="File location for the MFI from FLOCK.")
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195
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196 parser.add_argument(
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197 '-d',
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198 dest="output_directory",
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199 required=True,
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200 help="Directory location for the html supporting files.")
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201
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202 parser.add_argument(
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203 '-t',
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204 dest="tool_directory",
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205 required=True,
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206 help="Location of the Tool Directory.")
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207
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208 args = parser.parse_args()
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209
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210 cs_files = [f for f in args.cs_outputs]
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211 check_pops(args.mfi, args.input_file)
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212 cs_overview(args.input_file, args.input_mfi, args.mfi, args.output_file, args.output_directory, args.tool_directory, cs_files)