[2] | 1 | #!/usr/bin/env python |
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| 2 | |
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| 3 | """ |
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| 4 | Walk downloaded Genome Projects and Convert, in place, IDs to match the UCSC Archaea browser, where applicable. |
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| 5 | Uses UCSC Archaea DSN. |
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| 6 | """ |
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| 7 | |
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| 8 | import sys, os |
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| 9 | import urllib |
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| 10 | from elementtree import ElementTree |
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| 11 | from BeautifulSoup import BeautifulSoup |
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| 12 | from shutil import move |
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| 13 | |
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| 14 | def __main__(): |
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| 15 | base_dir = os.path.join( os.getcwd(), "bacteria" ) |
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| 16 | try: |
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| 17 | base_dir = sys.argv[1] |
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| 18 | except: |
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| 19 | print "using default base_dir:", base_dir |
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| 20 | |
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| 21 | organisms = {} |
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| 22 | for result in os.walk(base_dir): |
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| 23 | this_base_dir,sub_dirs,files = result |
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| 24 | for file in files: |
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| 25 | if file[-5:] == ".info": |
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| 26 | dict = {} |
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| 27 | info_file = open(os.path.join(this_base_dir,file),'r') |
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| 28 | info = info_file.readlines() |
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| 29 | info_file.close() |
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| 30 | for line in info: |
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| 31 | fields = line.replace("\n","").split("=") |
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| 32 | dict[fields[0]]="=".join(fields[1:]) |
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| 33 | if 'genome project id' in dict.keys(): |
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| 34 | if dict['genome project id'] not in organisms.keys(): |
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| 35 | organisms[dict['genome project id']] = {'chrs':{},'base_dir':this_base_dir} |
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| 36 | for key in dict.keys(): |
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| 37 | organisms[dict['genome project id']][key]=dict[key] |
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| 38 | else: |
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| 39 | if dict['organism'] not in organisms.keys(): |
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| 40 | organisms[dict['organism']] = {'chrs':{},'base_dir':this_base_dir} |
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| 41 | organisms[dict['organism']]['chrs'][dict['chromosome']]=dict |
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| 42 | |
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| 43 | ##get UCSC data |
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| 44 | |
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| 45 | URL = "http://archaea.ucsc.edu/cgi-bin/das/dsn" |
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| 46 | |
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| 47 | |
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| 48 | try: |
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| 49 | page = urllib.urlopen(URL) |
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| 50 | except: |
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| 51 | print "#Unable to open " + URL |
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| 52 | print "?\tunspecified (?)" |
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| 53 | sys.exit(1) |
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| 54 | |
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| 55 | text = page.read() |
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| 56 | try: |
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| 57 | tree = ElementTree.fromstring(text) |
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| 58 | except: |
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| 59 | print "#Invalid xml passed back from " + URL |
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| 60 | print "?\tunspecified (?)" |
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| 61 | sys.exit(1) |
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| 62 | |
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| 63 | |
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| 64 | builds = {} |
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| 65 | |
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| 66 | |
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| 67 | #print "#Harvested from http://archaea.ucsc.edu/cgi-bin/das/dsn" |
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| 68 | #print "?\tunspecified (?)" |
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| 69 | for dsn in tree: |
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| 70 | build = dsn.find("SOURCE").attrib['id'] |
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| 71 | try: |
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| 72 | 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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| 73 | except: |
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| 74 | print "NO CHROMS FOR",build |
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| 75 | continue |
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| 76 | org_page.pop(0) |
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| 77 | if org_page[-1]=="": |
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| 78 | org_page.pop(-1) |
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| 79 | |
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| 80 | for row in org_page: |
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| 81 | chr = row.split("</a>")[0].split(">")[-1] |
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| 82 | refseq = row.split("</a>")[-2].split(">")[-1] |
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| 83 | for org in organisms: |
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| 84 | for org_chr in organisms[org]['chrs']: |
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| 85 | if organisms[org]['chrs'][org_chr]['chromosome']==refseq: |
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| 86 | if org not in builds: |
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| 87 | builds[org]={'chrs':{},'build':build} |
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| 88 | builds[org]['chrs'][refseq]=chr |
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| 89 | #print build,org,chr,refseq |
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| 90 | |
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| 91 | print |
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| 92 | ext_to_edit = ['bed', 'info', ] |
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| 93 | for org in builds: |
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| 94 | print org,"changed to",builds[org]['build'] |
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| 95 | |
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| 96 | #org info file |
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| 97 | info_file_old = os.path.join(base_dir+org,org+".info") |
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| 98 | info_file_new = os.path.join(base_dir+org,builds[org]['build']+".info") |
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| 99 | |
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| 100 | |
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| 101 | old_dir = base_dir+org |
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| 102 | new_dir = base_dir+builds[org]['build'] |
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| 103 | |
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| 104 | #open and edit org info file |
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| 105 | info_file_contents = open(info_file_old).read() |
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| 106 | info_file_contents = info_file_contents+"build="+builds[org]['build']+"\n" |
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| 107 | for chrom in builds[org]['chrs']: |
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| 108 | info_file_contents = info_file_contents.replace(chrom,builds[org]['chrs'][chrom]) |
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| 109 | for result in os.walk(base_dir+org): |
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| 110 | this_base_dir,sub_dirs,files = result |
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| 111 | for file in files: |
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| 112 | if file[0:len(chrom)]==chrom: |
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| 113 | #rename file |
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| 114 | old_name = os.path.join(this_base_dir,file) |
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| 115 | new_name = os.path.join(this_base_dir,builds[org]['chrs'][chrom]+file[len(chrom):]) |
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| 116 | move(old_name,new_name) |
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| 117 | |
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| 118 | #edit contents of file, skiping those in list |
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| 119 | if file.split(".")[-1] not in ext_to_edit: continue |
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| 120 | |
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| 121 | file_contents = open(new_name).read() |
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| 122 | file_contents = file_contents.replace(chrom,builds[org]['chrs'][chrom]) |
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| 123 | |
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| 124 | #special case fixes... |
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| 125 | if file[-5:] == ".info": |
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| 126 | file_contents = file_contents.replace("organism="+org,"organism="+builds[org]['build']) |
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| 127 | file_contents = file_contents.replace("refseq="+builds[org]['chrs'][chrom],"refseq="+chrom) |
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| 128 | |
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| 129 | #write out new file |
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| 130 | file_out = open(new_name,'w') |
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| 131 | file_out.write(file_contents) |
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| 132 | file_out.close() |
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| 133 | |
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| 134 | |
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| 135 | |
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| 136 | #write out org info file and remove old file |
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| 137 | org_info_out = open(info_file_new,'w') |
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| 138 | org_info_out.write(info_file_contents) |
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| 139 | org_info_out.close() |
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| 140 | os.unlink(info_file_old) |
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| 141 | |
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| 142 | #change org directory name |
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| 143 | move(old_dir,new_dir) |
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| 144 |
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| 145 |
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| 146 | if __name__ == "__main__": __main__()
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