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61 lines
2.0 KiB
Python
61 lines
2.0 KiB
Python
#!/usr/bin/env python
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# Dan Blankenberg
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import os
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import sys
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assert sys.version_info[:2] >= ( 2, 4 )
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def __main__():
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base_dir = os.path.join( os.getcwd(), "bacteria" )
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try:
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base_dir = sys.argv[1]
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except:
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pass
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# print "using default base_dir:", base_dir
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organisms = {}
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for result in os.walk(base_dir):
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this_base_dir, sub_dirs, files = result
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for file in files:
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if file[-5:] == ".info":
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dict = {}
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info_file = open(os.path.join(this_base_dir, file), 'r')
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info = info_file.readlines()
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info_file.close()
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for line in info:
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fields = line.replace("\n", "").split("=")
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dict[fields[0]] = "=".join(fields[1:])
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if 'genome project id' in dict.keys():
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name = dict['genome project id']
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if 'build' in dict.keys():
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name = dict['build']
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if name not in organisms.keys():
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organisms[name] = {'chrs': {}, 'base_dir': this_base_dir}
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for key in dict.keys():
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organisms[name][key] = dict[key]
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else:
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if dict['organism'] not in organisms.keys():
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organisms[dict['organism']] = {'chrs': {}, 'base_dir': this_base_dir}
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organisms[dict['organism']]['chrs'][dict['chromosome']] = dict
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for org in organisms:
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org = organisms[org]
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# if no gpi, then must be a ncbi chr which corresponds to a UCSC org, w/o matching UCSC designation
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try:
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build = org['genome project id']
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except:
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continue
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if 'build' in org:
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build = org['build']
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chrs = []
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for chrom in org['chrs']:
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chrom = org['chrs'][chrom]
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chrs.append( "%s=%s" % ( chrom['chromosome'], chrom['length'] ) )
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print "%s\t%s\t%s" % ( build, org['name'], ",".join( chrs ) )
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if __name__ == "__main__":
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__main__()
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