Mercurial > repos > jjjjia > cpo_prediction
changeset 26:3dc84625d22c draft
planemo upload
| author | jjjjia |
|---|---|
| date | Wed, 29 Aug 2018 17:25:50 -0400 |
| parents | 573136f142b6 |
| children | 13bf5059984a |
| files | cpo_galaxy_tree.py |
| diffstat | 1 files changed, 4 insertions(+), 4 deletions(-) [+] |
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--- a/cpo_galaxy_tree.py Wed Aug 29 15:10:44 2018 -0400 +++ b/cpo_galaxy_tree.py Wed Aug 29 17:25:50 2018 -0400 @@ -25,7 +25,7 @@ import pandas #conda pandas import optparse import os -os.environ['QT_QPA_PLATFORM']='offscreen' +#os.environ['QT_QPA_PLATFORM']='offscreen' import datetime import sys import time @@ -40,8 +40,8 @@ #parses some parameters parser = optparse.OptionParser("Usage: %prog [options] arg1 arg2 ...") parser.add_option("-t", "--tree", dest="treePath", type="string", default="./pipelineTest/tree.txt", help="absolute file path to phylip tree") -parser.add_option("-d", "--distance", dest="distancePath", type="string", default="./pipelineTest/distance.tab", help="absolute file path to distance matrix") -parser.add_option("-m", "--metadata", dest="metadataPath", type="string", default="./pipelineTest/metadata.tsv",help="absolute file path to metadata file") +parser.add_option("-d", "--distance", dest="distancePath", type="string", default="./pipelineTest/dist.tabular", help="absolute file path to distance matrix") +parser.add_option("-m", "--metadata", dest="metadataPath", type="string", default="./pipelineTest/metadata.tabular",help="absolute file path to metadata file") parser.add_option("-o", "--output_file", dest="outputFile", type="string", default="tree.png", help="Output graphics file. Use ending 'png', 'pdf' or 'svg' to specify file format.") # sensitive data adder @@ -185,7 +185,7 @@ _results.TotalPlasmids = int(r.loc[r.index[i], 'Total Plasmids']) _results.plasmidBestMatch = str(r.loc[r.index[i], 'Plasmid Best Match']) _results.plasmididentity = str(r.loc[r.index[i], 'Plasmid Identity']) - _results.plasmidsharedhashes = float(r.loc[r.index[i], 'Plasmid Shared Hash']) + _results.plasmidsharedhashes = str(r.loc[r.index[i], 'Plasmid Shared Hash']) for j in range(0,_results.TotalPlasmids): _plasmid = plasmidObj() _plasmid.PlasmidsID =(((str(r.loc[r.index[i], 'Plasmids ID'])).split(";"))[j])