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70 lines
3.9 KiB
Python
70 lines
3.9 KiB
Python
#!/usr/bin/env python
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#Dan Blankenberg
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import sys, os
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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: continue
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if 'build' in org:
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build = org['build']
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print "ORG\t%s\t%s\t%s\t%s\t%s\t%s\tUCSC" % ( build, org['name'], org['kingdom'], org['group'], org['chromosomes'], org['info url'] )
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else:
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print "ORG\t%s\t%s\t%s\t%s\t%s\t%s\tNone" % ( 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%s\t%s\t%s\t%s\t%s\t%s\t%s" % ( 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%s_%s_%s\t%s\t%s\t%s\t%s\t%s" % ( build, chr['chromosome'], feature, build, chr['chromosome'], feature, "bed", os.path.join( org['base_dir'], "%s.%s.bed" % ( chr['chromosome'], feature ) ) )
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#FASTA
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print "DATA\t%s_%s_%s\t%s\t%s\t%s\t%s\t%s" % ( 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%s_%s_%s\t%s\t%s\t%s\t%s\t%s" % ( 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%s_%s_%s\t%s\t%s\t%s\t%s\t%s" % ( 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%s_%s_%s\t%s\t%s\t%s\t%s\t%s" % ( 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__": __main__()
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