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62 lines
2.1 KiB
Python
62 lines
2.1 KiB
Python
#!/usr/bin/env python
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# Dan Blankenberg
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from __future__ import print_function
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import os
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import sys
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assert sys.version_info[:2] >= (2, 6)
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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 IndexError:
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pass
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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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tmp_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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tmp_dict[fields[0]] = "=".join(fields[1:])
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if 'genome project id' in tmp_dict.keys():
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name = tmp_dict['genome project id']
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if 'build' in tmp_dict.keys():
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name = tmp_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 tmp_dict.keys():
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organisms[name][key] = tmp_dict[key]
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else:
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if tmp_dict['organism'] not in organisms.keys():
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organisms[tmp_dict['organism']] = {'chrs': {}, 'base_dir': this_base_dir}
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organisms[tmp_dict['organism']]['chrs'][tmp_dict['chromosome']] = tmp_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 KeyError:
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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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