Mercurial > repos > bcclaywell > argo_navis

annotate bin/ess.py @ 0:d67268158946 draft

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planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
author bcclaywell
date Mon, 12 Oct 2015 17:43:33 -0400
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1 #!/usr/bin/env python
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2
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3 import csv
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4 import numpy
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5 from biopy import bayesianStats as bs
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6 import argparse
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7 import re
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8
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9
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10 commented_regex = re.compile("^\s*\#.*")
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11
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12 doc_template = """
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13 <html>
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14 <body>
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15 <h1>Effective Sample Size Results</h1>
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16 <p>Recommendation: {status}</p>
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17
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18 <h2>Explanation</h2>
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19 <p>
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20 Ideally, you want all these values to be greater than or equal to 200.
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21 If any of them aren't, it's probably a good idea to perform a Resume run with BEAST.
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22 On average, running 3x as long will increase your ESS by 3.
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23 This should help give you some sense of how much longer you should run BEAST.
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24 </p>
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25 <p>
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26 Note that while ESS statistics are valuable for getting a rough sense of whether to run or not, it is
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27 <em>always</em> recommended that you manually look at your logfile traces using
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28 <a href="http://tree.bio.ed.ac.uk/software/tracer/">Tracer</a>, or another trace analysis software before
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29 accepting your analysis as "final".
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30 </p>
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31
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32 <h2>Detailed Results</h2>
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33 <table>
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34 <tr><th>Parameter</th><th>ESS</th></tr>
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35 {table_content}
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36 </table>
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37 </body>
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38 </html>
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39 """
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40
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41 tr_template = "<tr><td>{parameter}</td><td {style}>{ess}</td></tr>"
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42
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43
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44 def format_tr(result, threshold=200):
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45 "Takes a result [param, ess] pair and makes the appropriate tr html"
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46 param, ess = result
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47 passes = ess >= threshold
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48 style = "" if passes else 'style="color: red;"'
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49 return tr_template.format(parameter=param, ess=ess, style=style)
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50
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51
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52 def dict_reader_to_cols(dict_reader):
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53 d = dict()
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54 for row in dict_reader:
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55 for k, v in row.iteritems():
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56 try:
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57 v = float(v)
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58 try:
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59 d[k].append(v)
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60 except KeyError:
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61 d[k] = [v]
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62 except ValueError:
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63 if k == "" and v == "":
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64 # Don't worry about this, there is a tailing \t on each line
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65 pass
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66 else:
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67 # Otherwise... something weird is happening
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68 print "Could not cast to float for kv pair:", k, v
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69 return d
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70
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71
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72 def table_contents(results, threshold=200):
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73 trs = [format_tr(result, threshold) for result in sorted(results)]
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74 return "\n".join(trs)
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75
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76
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77 def html_contents(results, threshold):
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78 table_content = table_contents(results, threshold)
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79 within_tol = [x[1] > threshold for x in results]
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80 ess_good = all(within_tol)
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81 status = "Good to go" if all(within_tol) else "Should run longer"
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82 return doc_template.format(status=status, table_content=table_content)
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83
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84
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85 def get_args():
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86 parser = argparse.ArgumentParser()
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87 parser.add_argument('logfile', type=argparse.FileType('r'))
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88 parser.add_argument('ess_out', type=argparse.FileType('w'))
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89 parser.add_argument('-t', '--threshold', type=float, default=200,
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90 help="""For formatting html, what's the minimal ESS score to be considered high enough?
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91 (default: 200""")
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92 parser.add_argument('--html-out', action="store_true",
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93 help="Default is CSV output")
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94 return parser.parse_args()
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95
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96
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97 def main(args):
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98 non_comment_lines = (row for row in args.logfile if not commented_regex.match(row))
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99 reader = csv.DictReader(non_comment_lines, delimiter="\t")
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100 data_columns = dict_reader_to_cols(reader)
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101 results = []
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102 for colname, data in data_columns.iteritems():
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103 if colname != "Sample":
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104 results.append([colname, bs.effectiveSampleSize(data)])
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105
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106 if args.html_out:
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107 html_content = html_contents(results, args.threshold)
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108 args.ess_out.write(html_content)
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109 else:
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110 writer = csv.writer(args.ess_out)
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111 writer.writerow(["statistic", "ess"])
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112 for result in results:
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113 writer.writerow(result)
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114
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115 args.logfile.close()
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116 args.ess_out.close()
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117
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118
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119 if __name__ == '__main__':
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120 main(get_args())
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121
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122