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#!/usr/bin/python3
import argparse
import glob
import json
import collections
helpMessage = """
Creates a single csv file containing summaries for the Shasta assemblies
present in the current directory.
"""
parser = argparse.ArgumentParser(description = helpMessage)
arguments = parser.parse_args()
# Find the json files containing summaries for the individual assemblies.
jsonFileNames = glob.glob('*/AssemblySummary.json')
if not jsonFileNames:
print('No Shasta assemblies found in the current directory.\n'
'Invoke this script from a directory containing one or more\n'
'Shasta assemblies.')
exit(1)
# Gather the jsons for all the assemblies.
jsons = []
for jsonFileName in jsonFileNames:
jsons.append(json.load(open(jsonFileName, 'r'), object_pairs_hook=collections.OrderedDict))
# Open the output file and write the header line.
out = open('AssembliesSummary.csv', 'w')
out.write('Assembly,',)
for jsonFileName in jsonFileNames:
assemblyName = jsonFileName[:jsonFileName.find('/')]
out.write('%s,' % assemblyName)
out.write('\n')
# Loop over sections.
firstAssemblyJson = jsons[0]
for sectionName in firstAssemblyJson:
if sectionName == 'Comment':
continue
firstAssemblySection = firstAssemblyJson[sectionName]
# Special treatment of section "Reads discarded on input"
# which contains reads and bases for each item.
if sectionName == 'Reads discarded on input':
for itemName in firstAssemblySection:
for x in json[sectionName][itemName]:
out.write('"%s: %s: %s",' % (sectionName, itemName, x))
for json in jsons:
out.write('%s,' % json[sectionName][itemName][x])
out.write('\n')
continue
# Loop over items in this section.
for itemName in firstAssemblySection:
out.write('"%s: %s",' % (sectionName, itemName))
# Write the values for all the assemblies.
for json in jsons:
out.write('%s,' % json[sectionName][itemName])
out.write('\n')
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