ideogram
Version:
Chromosome visualization for the web
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# DEBUG
'''
post_body = (
'jsh_pageVertPos=0' +
'&clade=monocots' +
'&org=Zea+mays' +
'&db=zeaMay_b73_v2' +
'&hgta_group=map' +
'&hgta_track=cytoBandIdeo' +
'&hgta_table=cytoBandIdeo' +
'&hgta_regionType=genome' +
'&position=chr1%3A1-301354135' +
'&hgta_outputType=primaryTable' +
'&boolshad.sendToGalaxy=0' +
'&boolshad.sendToGreat=0' +
'&hgta_outFileName=' +
'&hgta_compressType=none' +
'&hgta_doTopSubmit=get+output'
)
post_body = post_body.encode()
url = 'http://genomaize.org/cgi-bin/hgTables'
data = request(url, request_body=post_body)
rows = data.split('\n')[1:-1]
for row in rows:
# Headers: chrom, chromStart, chromEnd, name, score
chr, start, stop = row.split('\t')[:3]
chr = chr.replace('chr', '')
centromeres_by_chr[chr] = [start, stop]
'''
def fetch_maize_centromeres(output_dir):
"""Reads local copy of centromeres from B73 v2 genome assembly for Zea mays
Old documentation:
Requests maize centromere data from Genomaize
This is a special case for maize, a request for which began this module.
To debug:
curl 'http://genomaize.org/cgi-bin/hgTables' --data 'jsh_pageVertPos=0&clade=monocots&org=Zea+mays&db=zeaMay_b73_v2&hgta_group=map&hgta_track=cytoBandIdeo&hgta_table=cytoBandIdeo&hgta_regionType=genome&position=chr1%3A1-301354135&hgta_outputType=primaryTable&boolshad.sendToGalaxy=0&boolshad.sendToGreat=0&hgta_outFileName=&hgta_compressType=none&hgta_doTopSubmit=get+output'
"""
centromeres_by_chr = {}
rows = open(output_dir + 'zea-mays-b73-v2-centromeres.tsv').readlines()
for row in rows[1:]:
chr, start, stop = row.split('\t')[:3]
chr = chr.replace('chr', '')
centromeres_by_chr[chr] = [start, stop]
return centromeres_by_chr