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147 lines
5.5 KiB
Python
147 lines
5.5 KiB
Python
#!/usr/bin/env python
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"""
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Walk downloaded Genome Projects and Convert, in place, IDs to match the UCSC Archaea browser, where applicable.
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Uses UCSC Archaea DSN.
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"""
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import sys, os
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import urllib
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from elementtree import ElementTree
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from BeautifulSoup import BeautifulSoup
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from shutil import move
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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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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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if dict['genome project id'] not in organisms.keys():
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organisms[dict['genome project id']] = {'chrs':{},'base_dir':this_base_dir}
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for key in dict.keys():
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organisms[dict['genome project id']][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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##get UCSC data
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URL = "http://archaea.ucsc.edu/cgi-bin/das/dsn"
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try:
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page = urllib.urlopen(URL)
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except:
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print "#Unable to open " + URL
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print "?\tunspecified (?)"
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sys.exit(1)
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text = page.read()
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try:
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tree = ElementTree.fromstring(text)
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except:
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print "#Invalid xml passed back from " + URL
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print "?\tunspecified (?)"
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sys.exit(1)
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builds = {}
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#print "#Harvested from http://archaea.ucsc.edu/cgi-bin/das/dsn"
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#print "?\tunspecified (?)"
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for dsn in tree:
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build = dsn.find("SOURCE").attrib['id']
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try:
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org_page = urllib.urlopen("http://archaea.ucsc.edu/cgi-bin/hgGateway?db="+build).read().replace("\n","").split("<table border=2 cellspacing=2 cellpadding=2>")[1].split("</table>")[0].split("</tr>")
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except:
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print "NO CHROMS FOR",build
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continue
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org_page.pop(0)
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if org_page[-1]=="":
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org_page.pop(-1)
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for row in org_page:
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chr = row.split("</a>")[0].split(">")[-1]
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refseq = row.split("</a>")[-2].split(">")[-1]
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for org in organisms:
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for org_chr in organisms[org]['chrs']:
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if organisms[org]['chrs'][org_chr]['chromosome']==refseq:
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if org not in builds:
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builds[org]={'chrs':{},'build':build}
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builds[org]['chrs'][refseq]=chr
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#print build,org,chr,refseq
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print
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ext_to_edit = ['bed', 'info', ]
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for org in builds:
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print org,"changed to",builds[org]['build']
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#org info file
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info_file_old = os.path.join(base_dir+org,org+".info")
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info_file_new = os.path.join(base_dir+org,builds[org]['build']+".info")
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old_dir = base_dir+org
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new_dir = base_dir+builds[org]['build']
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#open and edit org info file
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info_file_contents = open(info_file_old).read()
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info_file_contents = info_file_contents+"build="+builds[org]['build']+"\n"
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for chrom in builds[org]['chrs']:
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info_file_contents = info_file_contents.replace(chrom,builds[org]['chrs'][chrom])
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for result in os.walk(base_dir+org):
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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[0:len(chrom)]==chrom:
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#rename file
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old_name = os.path.join(this_base_dir,file)
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new_name = os.path.join(this_base_dir,builds[org]['chrs'][chrom]+file[len(chrom):])
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move(old_name,new_name)
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#edit contents of file, skiping those in list
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if file.split(".")[-1] not in ext_to_edit: continue
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file_contents = open(new_name).read()
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file_contents = file_contents.replace(chrom,builds[org]['chrs'][chrom])
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#special case fixes...
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if file[-5:] == ".info":
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file_contents = file_contents.replace("organism="+org,"organism="+builds[org]['build'])
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file_contents = file_contents.replace("refseq="+builds[org]['chrs'][chrom],"refseq="+chrom)
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#write out new file
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file_out = open(new_name,'w')
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file_out.write(file_contents)
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file_out.close()
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#write out org info file and remove old file
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org_info_out = open(info_file_new,'w')
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org_info_out.write(info_file_contents)
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org_info_out.close()
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os.unlink(info_file_old)
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#change org directory name
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move(old_dir,new_dir)
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if __name__ == "__main__": __main__()
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