mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-17 16:41:31 +08:00
Nicola Soranzo
9d74bba7fb
Upgrade syntax using `pyupgrade --py36-plus` . Manually drop several `six` imports. Also: - Remove broken pr_cache in scripts/bootstrap_history.py - Fix broken prefix removal in lib/galaxy/tool_util/deps/mulled/mulled_build.py
74 lines
3.9 KiB
Python
74 lines
3.9 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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print("ORG\t{}\t{}\t{}\t{}\t{}\t{}\tUCSC".format(build, org['name'], org['kingdom'], org['group'], org['chromosomes'], org['info url']))
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else:
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print("ORG\t{}\t{}\t{}\t{}\t{}\t{}\tNone".format(build, org['name'], org['kingdom'], org['group'], org['chromosomes'], org['info url']))
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for chr in org['chrs']:
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chr = org['chrs'][chr]
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print("CHR\t{}\t{}\t{}\t{}\t{}\t{}\t{}".format(build, chr['chromosome'], chr['name'], chr['length'], chr['gi'], chr['gb'], "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=" + chr['refseq']))
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for feature in ['CDS', 'tRNA', 'rRNA']:
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print("DATA\t{}_{}_{}\t{}\t{}\t{}\t{}\t{}".format(build, chr['chromosome'], feature, build, chr['chromosome'], feature, "bed", os.path.join(org['base_dir'], "{}.{}.bed".format(chr['chromosome'], feature))))
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# FASTA
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print("DATA\t{}_{}_{}\t{}\t{}\t{}\t{}\t{}".format(build, chr['chromosome'], "seq", build, chr['chromosome'], "sequence", "fasta", os.path.join(org['base_dir'], "%s.fna" % chr['chromosome'])))
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# GeneMark
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if os.path.exists(os.path.join(org['base_dir'], "%s.GeneMark.bed" % chr['chromosome'])):
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print("DATA\t{}_{}_{}\t{}\t{}\t{}\t{}\t{}".format(build, chr['chromosome'], "GeneMark", build, chr['chromosome'], "GeneMark", "bed", os.path.join(org['base_dir'], "%s.GeneMark.bed" % chr['chromosome'])))
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# GenMarkHMM
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if os.path.exists(os.path.join(org['base_dir'], "%s.GeneMarkHMM.bed" % chr['chromosome'])):
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print("DATA\t{}_{}_{}\t{}\t{}\t{}\t{}\t{}".format(build, chr['chromosome'], "GeneMarkHMM", build, chr['chromosome'], "GeneMarkHMM", "bed", os.path.join(org['base_dir'], "%s.GeneMarkHMM.bed" % chr['chromosome'])))
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# Glimmer3
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if os.path.exists(os.path.join(org['base_dir'], "%s.Glimmer3.bed" % chr['chromosome'])):
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print("DATA\t{}_{}_{}\t{}\t{}\t{}\t{}\t{}".format(build, chr['chromosome'], "Glimmer3", build, chr['chromosome'], "Glimmer3", "bed", os.path.join(org['base_dir'], "%s.Glimmer3.bed" % chr['chromosome'])))
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if __name__ == "__main__":
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__main__()
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