def get(record):
return annotation_tools.join_descriptions(index[getattr(record,join_field)],'/')
def get(record):
return annotation_tools.join_descriptions(
index[getattr(record, join_field)], '/')
def run(self):
assert self.ucsc_name, 'Need a UCSC genome name'
scratch = _ucsc_scratch(self)
# Load annotations
source = 'tt-ucsc-%s-%s' % (self.ucsc_name, self.table)
table = scratch.get_table(self.table)
get_name = scratch.getter(self.name)
get_product = scratch.getter(self.product)
mrnas = [ ]
for item in table:
ann = annotation.Annotation(
seqid = item.chrom,
source = source,
type = 'mRNA',
strand = {'+':1, '-':-1}[item.strand],
start = int(item.txStart),
end = int(item.txEnd),
attr = {
'ID' : item.name,
'Name' : get_name(item),
'Product' : get_product(item),
#'UCSC_name2' : item.name2,
}
)
ann.record = item
mrnas.append(ann)
_uniquify_ids(mrnas)
annotations = [ ]
for group in _grouped_features(mrnas):
ID = '/'.join(item.attr['ID'] for item in group)
for item in group:
item.attr['Parent'] = ID
item.attr['ID'] = item.attr['ID'] + '-mRNA'
annotations.append(annotation.Annotation(
source = source,
type = 'gene',
seqid = group[0].seqid,
strand = group[0].strand,
start = min(item.start for item in group),
end = max(item.end for item in group),
attr = {
'ID' : ID,
'Name' : annotation_tools.join_descriptions([ item.attr['Name'] for item in group ], '/'),
'Product' : annotation_tools.join_descriptions([ item.attr['Product'] for item in group ], '/'),
#'UCSC_name2' : annotation_tools.join_descriptions([ item.attr['UCSC_name2'] for item in group ], '/'),
}
))
for item in group:
annotations.append(item)
exonStarts = _parse_ints(item.record.exonStarts)
exonEnds = _parse_ints(item.record.exonEnds)
cdsStart = int(item.record.cdsStart)
cdsEnd = int(item.record.cdsEnd)
for start,end in zip(exonStarts,exonEnds):
annotations.append(annotation.Annotation(
source = source,
type = 'exon',
seqid = item.seqid,
strand = item.strand,
start = start,
end = end,
attr = {
'Parent' : item.attr['ID'],
}
))
if max(cdsStart,start) < min(cdsEnd,end):
annotations.append(annotation.Annotation(
source = source,
type = 'CDS',
seqid = item.seqid,
strand = item.strand,
start = max(cdsStart,start),
end = min(cdsEnd,end),
#TODO: phase
attr = {
'Parent' : item.attr['ID'],
}
))
# Load sequence
if self.download:
io.execute(['rsync','-P','rsync://hgdownload.cse.ucsc.edu/goldenPath/'+self.ucsc_name+'/bigZips/chromFa.tar.gz',scratch.ucsc/'chromFa.tar.gz'])
with workspace.tempspace() as temp:
io.execute(['tar','-C',temp.working_dir,'-zxf',scratch.ucsc/'chromFa.tar.gz'])
sequences = [ temp/item for item in natural_sorted(os.listdir(temp.working_dir)) ]
with open(temp/'reference.gff','wb') as f:
annotation.write_gff3_header(f)
for item in annotations:
print >> f, item.as_gff()
Make_tt_reference(
self.output_dir,
filenames = sequences + [ temp/'reference.gff' ],
index = self.index,
).run()
def run(self):
assert self.ucsc_name, 'Need a UCSC genome name'
scratch = _ucsc_scratch(self)
# Load annotations
source = 'tt-ucsc-%s-%s' % (self.ucsc_name, self.table)
table = scratch.get_table(self.table)
get_name = scratch.getter(self.name)
get_product = scratch.getter(self.product)
mrnas = []
for item in table:
ann = annotation.Annotation(
seqid=item.chrom,
source=source,
type='mRNA',
strand={
'+': 1,
'-': -1
}[item.strand],
start=int(item.txStart),
end=int(item.txEnd),
attr={
'ID': item.name,
'Name': get_name(item),
'Product': get_product(item),
#'UCSC_name2' : item.name2,
})
ann.record = item
mrnas.append(ann)
_uniquify_ids(mrnas)
annotations = []
for group in _grouped_features(mrnas):
ID = '/'.join(item.attr['ID'] for item in group)
for item in group:
item.attr['Parent'] = ID
item.attr['ID'] = item.attr['ID'] + '-mRNA'
annotations.append(
annotation.Annotation(
source=source,
type='gene',
seqid=group[0].seqid,
strand=group[0].strand,
start=min(item.start for item in group),
end=max(item.end for item in group),
attr={
'ID':
ID,
'Name':
annotation_tools.join_descriptions(
[item.attr['Name'] for item in group], '/'),
'Product':
annotation_tools.join_descriptions(
[item.attr['Product'] for item in group], '/'),
#'UCSC_name2' : annotation_tools.join_descriptions([ item.attr['UCSC_name2'] for item in group ], '/'),
}))
for item in group:
annotations.append(item)
exonStarts = _parse_ints(item.record.exonStarts)
exonEnds = _parse_ints(item.record.exonEnds)
cdsStart = int(item.record.cdsStart)
cdsEnd = int(item.record.cdsEnd)
for start, end in zip(exonStarts, exonEnds):
annotations.append(
annotation.Annotation(source=source,
type='exon',
seqid=item.seqid,
strand=item.strand,
start=start,
end=end,
attr={
'Parent': item.attr['ID'],
}))
if max(cdsStart, start) < min(cdsEnd, end):
annotations.append(
annotation.Annotation(
source=source,
type='CDS',
seqid=item.seqid,
strand=item.strand,
start=max(cdsStart, start),
end=min(cdsEnd, end),
#TODO: phase
attr={
'Parent': item.attr['ID'],
}))
# Load sequence
if self.download:
io.execute([
'rsync', '-P', 'rsync://hgdownload.cse.ucsc.edu/goldenPath/' +
self.ucsc_name + '/bigZips/chromFa.tar.gz',
scratch.ucsc / 'chromFa.tar.gz'
])
with workspace.tempspace() as temp:
io.execute([
'tar', '-C', temp.working_dir, '-zxf',
scratch.ucsc / 'chromFa.tar.gz'
])
sequences = [
temp / item
for item in natural_sorted(os.listdir(temp.working_dir))
]
with open(temp / 'reference.gff', 'wb') as f:
annotation.write_gff3_header(f)
for item in annotations:
print >> f, item.as_gff()
Make_tt_reference(
self.output_dir,
filenames=sequences + [temp / 'reference.gff'],
index=self.index,
).run()
