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61 lines
2.1 KiB
Python
61 lines
2.1 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, 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))
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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("{}={}".format(chrom["chromosome"], chrom["length"]))
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print("{}\t{}\t{}".format(build, org["name"], ",".join(chrs)))
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if __name__ == "__main__":
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__main__()
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