def setUp(self):
self.assembly = Assembly('ce6')
self.assembly.genrep = GenRep(url='http://bbcftools.epfl.ch/genrep/',
root='/db/genrep')
self.assembly.intype = '0'
self.chromosomes = {
(3066, u'NC_003279', 6): {
'length': 15072421,
'name': u'chrI'
},
(3067, u'NC_003280', 7): {
'length': 15279323,
'name': u'chrII'
},
(3068, u'NC_003281', 8): {
'length': 13783681,
'name': u'chrIII'
},
(3069, u'NC_003282', 5): {
'length': 17493785,
'name': u'chrIV'
},
(3070, u'NC_003283', 8): {
'length': 20919568,
'name': u'chrV'
},
(3071, u'NC_003284', 7): {
'length': 17718854,
'name': u'chrX'
},
(2948, u'NC_001328', 1): {
'length': 13794,
'name': u'chrM'
}
}
def adn(self, ass, chr, id, **kw):
id = int(id)
g = GenRep()
chrs = g.get_genrep_objects('chromosomes',
'chromosome',
filters={'name': chr},
params={'assembly_id': ass})
ass = Assembly(ass)
for chrid, chrs in ass.chromosomes.iteritems():
if chrs['name'] == chr:
start = id * chunk
end = start + chunk
return g.get_sequence(chrid[0], [[start, end]])
return ''
def merge_junc_files(trackList, assembly):
out = track('all.junc',
format='txt',
fields=['chr', 'start', 'end', 'strand', 'score'])
from bbcflib.genrep import Assembly
a = Assembly(assembly)
for c in a.chromosomes:
tl = [
track(t,
fields=['chr', 'start', 'end', 'strand', 'score'],
format='txt').read(str(c[0]) + '_' + c[1] + '.' + str(c[2]))
for t in trackList
]
#all = concatenate(tl,remove_duplicates=True)
all = concatenate(tl,
group_by=['chr', 'start', 'end'],
aggregate={'score': lambda x: sum(x)})
out.write(all, mode='append')
def main(assembly, filename):
a = Assembly(assembly)
tmap = a.get_transcript_mapping()
# Get total num of reads
f = open(filename)
g = open('simulation/count_simulation.txt', 'wb')
header = [
'ID', 'Count', 'RPKM', 'Chrom', 'Start', 'End', 'Strand', 'GeneName',
'Length', 'Type', 'Sense', 'Synonyms'
]
g.write('\t'.join(header) + '\n')
for line in f:
loc, tid, coding, length, \
expr_fraction, expr_number, lib_fraction, lib_number, seq_fraction, seq_number, \
cov_fraction, chisq, var_coeff = line.split('\t')
chrom, coord = loc.split(':')
start, end = coord[:-1].split('-')
strand = '1' if coord[-1] == 'W' else '-1'
nreads = float(seq_number)
if nreads != 0:
ntotal = nreads / float(seq_fraction)
rpkm = 1e9 * nreads / (float(length) * ntotal)
else:
rpkm = 0.0
t = tmap.get(tid)
if t is not None:
newline = [
tid, seq_number,
str(rpkm), chrom, start, end, strand, t.gene_name, length,
'transcript', '.', '.'
]
g.write('\t'.join(newline) + '\n')
f.close()
g.close()
def add_new_sequence(sequence):
'''
Method called when a new sequence is created on GDV.
It should import fast from JBrowse
'''
print 'add new sequence'
file_url = Assembly(sequence).get_sqlite_url()
print file_url
out = os.path.join(filemanager.temporary_directory(), 'Genes.sql')
fileinfo = filemanager.FileInfo(inputtype='url',
inpath=file_url,
trackname='Genes',
extension='sql',
outpath=out,
admin=True)
print fileinfo
user = DBSession.query(User).filter(
User.key == constants.admin_user_key()).first()
user_info = {'id': user.id, 'name': user.name, 'email': user.email}
sequence_info = {'id': sequence.id, 'name': sequence.name}
# track
t = Track()
t.name = fileinfo.trackname
t.sequence_id = sequence.id
t.user_id = user.id
DBSession.add(t)
DBSession.flush()
# send task
async = tasks.new_input.delay(user_info, fileinfo, sequence_info, t.id)
t.task_id = async .task_id
DBSession.add(t)
sequence.default_tracks.append(t)
DBSession.add(sequence)
DBSession.flush()
#!/usr/bin/env python
import sys
if len(sys.argv) < 2:
print "Usage: header_translation <assembly_name>"
sys.exit(1)
from bbcflib.genrep import Assembly
assembly = sys.argv[1]
a = Assembly(assembly)
ac2name = {}
for k, v in a.chrmeta.items():
ac2name[v['ac']] = k
f = open("header.sam")
#g = open("reheader.txt", "wb")
h = open("reheader.sam", "wb")
for line in f:
L = line.split('\t')
chrom = L[1].split(':')[1]
length = L[2].split(':')[1]
newchrom = ac2name[chrom]
#g.write('%s\t%s' % (newchrom,length))
h.write(line.replace(chrom, newchrom))
f.close()
g.close()
from bbcflib.genrep import Assembly
a = Assembly('hg38')
chrmeta = a.chrmeta
md5 = "cbcc5aeeb39d29065c6641aafd5ccaa430706008"
filename = "%s_ENSEMBL.gtf" % md5
to = "%s_REFSEQ.gtf" % md5
f = open(filename)
g = open(to, "wb")
for line in f:
L = line.split('\t')
ensembl = L[0]
refseq = chrmeta[ensembl]['ac']
newline = [refseq] + L[1:]
g.write('\t'.join(newline))
f.close()
g.close()
def setUp(self):
self.assembly = Assembly('ce6')
self.root = self.assembly.genrep.root
self.intype = 0
"""
