mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-10-28 02:58:18 +08:00
Nicola Soranzo
d1bc98dfcb
Remove some debugging prints. Fix import order. Consolidate exception logging in ToolShed database migrations.
90 lines
2.8 KiB
Python
90 lines
2.8 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:
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print("using default base_dir:", base_dir)
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loc_out = os.path.join(base_dir, "seq.loc")
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try:
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loc_out = os.path.join(base_dir, sys.argv[2])
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except:
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print("using default seq.loc:", loc_out)
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organisms = {}
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loc_out = open(loc_out, 'wb')
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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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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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seq_path = os.path.join(org['base_dir'], "seq")
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# create seq dir, if exists go to next org
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# TODO: add better checking, i.e. for updating
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try:
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os.mkdir(seq_path)
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except:
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print("Skipping", build)
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# continue
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loc_out.write("seq %s %s\n" % (build, seq_path))
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# Print org info
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for chr in org['chrs']:
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chr = org['chrs'][chr]
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fasta_file = os.path.join(org['base_dir'], "%s.fna" % chr['chromosome'])
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nib_out_file = os.path.join(seq_path, "%s.nib " % chr['chromosome'])
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# create nibs using faToNib binary
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# TODO: when bx supports writing nib, use it here instead
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command = "faToNib %s %s" % (fasta_file, nib_out_file)
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os.system(command)
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loc_out.close()
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if __name__ == "__main__":
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__main__()
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