[2] | 1 | #!/usr/bin/env python
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| 2 | #Dan Blankenberg
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| 3 |
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| 4 | import sys, os
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| 5 |
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| 6 | assert sys.version_info[:2] >= ( 2, 4 )
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| 7 |
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| 8 | def __main__():
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| 9 | base_dir = os.path.join( os.getcwd(), "bacteria" )
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| 10 | try:
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| 11 | base_dir = sys.argv[1]
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| 12 | except:
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| 13 | pass
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| 14 | #print "using default base_dir:", base_dir
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| 15 |
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| 16 | organisms = {}
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| 17 | for result in os.walk(base_dir):
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| 18 | this_base_dir,sub_dirs,files = result
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| 19 | for file in files:
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| 20 | if file[-5:] == ".info":
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| 21 | dict = {}
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| 22 | info_file = open(os.path.join(this_base_dir,file),'r')
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| 23 | info = info_file.readlines()
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| 24 | info_file.close()
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| 25 | for line in info:
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| 26 | fields = line.replace("\n","").split("=")
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| 27 | dict[fields[0]]="=".join(fields[1:])
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| 28 | if 'genome project id' in dict.keys():
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| 29 | name = dict['genome project id']
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| 30 | if 'build' in dict.keys():
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| 31 | name = dict['build']
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| 32 | if name not in organisms.keys():
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| 33 | organisms[name] = {'chrs':{},'base_dir':this_base_dir}
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| 34 | for key in dict.keys():
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| 35 | organisms[name][key]=dict[key]
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| 36 | else:
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| 37 | if dict['organism'] not in organisms.keys():
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| 38 | organisms[dict['organism']] = {'chrs':{},'base_dir':this_base_dir}
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| 39 | organisms[dict['organism']]['chrs'][dict['chromosome']]=dict
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| 40 | for org in organisms:
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| 41 | org = organisms[org]
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| 42 | #if no gpi, then must be a ncbi chr which corresponds to a UCSC org, w/o matching UCSC designation
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| 43 | try:
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| 44 | build = org['genome project id']
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| 45 | except: continue
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| 46 | if 'build' in org:
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| 47 | build = org['build']
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| 48 | 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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| 49 | else:
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| 50 | 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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| 51 |
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| 52 | for chr in org['chrs']:
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| 53 | chr = org['chrs'][chr]
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| 54 | 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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| 55 | for feature in ['CDS','tRNA','rRNA']:
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| 56 | 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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| 57 | #FASTA
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| 58 | 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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| 59 | #GeneMark
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| 60 | if os.path.exists( os.path.join( org['base_dir'], "%s.GeneMark.bed" % chr['chromosome'] ) ):
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| 61 | 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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| 62 | #GenMarkHMM
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| 63 | if os.path.exists( os.path.join( org['base_dir'], "%s.GeneMarkHMM.bed" % chr['chromosome'] ) ):
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| 64 | 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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| 65 | #Glimmer3
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| 66 | if os.path.exists( os.path.join( org['base_dir'], "%s.Glimmer3.bed" % chr['chromosome'] ) ):
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| 67 | 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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| 68 |
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| 69 | if __name__ == "__main__": __main__()
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