accession_pat = re.compile('ACC.*ID="([^"]*)";')
with DeleteOnError(outputfile, gzip.open) as output:
for line in urllib.urlopen(Paths.MIRBASE_URL):
if line.startswith('#'):
continue
fields = line[:-1].split('\t')
name = accession_pat.findall(fields[8])[0]
print >> output, '\t'.join([
'chr'+fields[0], str(int(fields[3])-1), fields[4],
'miRNA|%s|%s' % (name, name), '.', fields[6]
])
@files([(None, Paths.repeatmasker_original(chrom), chrom)
for chrom in Options.UCSC_REPEATMASKER_CHROMOSOMES])
@jobs_limit(Options.MAX_PARALLEL_DOWNLOADING, 'download')
def download_repeatmasker_catalogs(inputfile, outputfile, chrom):
import urllib
url = Paths.REPEATMASKER_URL % (Options.GENOME, chrom)
print 'Downloading %s ...' % url
urllib.urlretrieve(url, outputfile)
@files([Paths.repeatmasker_original(chrom)
for chrom in Options.UCSC_REPEATMASKER_CHROMOSOMES],
Paths.repeatmasker_catalog)
@follows(download_repeatmasker_catalogs)
def merge_repeatmasker_catalogs(inputfiles, outputfile):