def combine_field_from_intervals( infasta, ingff, outfasta, field, filt ):
intervals = read_interval( infasta )
fields = ['seqid','source','type','start','end','score','strand','phase','attributes']
template = '\t'.join(['%%(%s)s' % f for f in fields]) + '\n'
features = read_gff( ingff, fields )
#features = add_ID( features )
parents = by_key( features, 'ID' )
fff = by_key( features, field )
with outfasta as out:
for ff in sorted(fff.keys()):
seqs = ''
note = ''
name = ''
for f in parents[ff]:
if f['type'] in ['mRNA', 'transcript', 'gene']:
if 'Note' in f['atts']:
note = urllib.unquote(f['atts']['Note'])
elif 'note' in f:
note = urllib.unquote(f['atts']['note'])
if 'Name' in f['atts'] and f['atts']['Name'] != ff:
name = f['atts']['Name']
elif 'name' in f['atts'] and f['atts']['name'] != ff:
name = f['atts']['name']
for f in sorted(fff[ff], lambda x,y: cmp(int(x['start']), int(y['start']))):
if f['type'] in [filt] and (f['seqid'], f['start'], f['end']) in intervals:
if 'name' in f['atts'] and f['atts']['name'] != ff:
name = f['atts']['name']
if f['strand'] == '-':
seqs = intervals[(f['seqid'], f['start'], f['end'])] + seqs
else:
seqs += intervals[(f['seqid'], f['start'], f['end'])]
if seqs != '':
out.write( '>%s %s|%s %s(%s)\n%s' % (name, ff, note, ','.join(['%s:%s' %(f['start'], f['end']) for f in fff[ff]]), f['strand'], seqs ) )
def get_name_from_intervals( infasta, ingff, outfasta, field, filt ):
intervals = read_interval( infasta )
fields = ['seqid','source','type','start','end','score','strand','phase','attributes']
template = '\t'.join(['%%(%s)s' % f for f in fields]) + '\n'
with outfasta as out:
for feature in read_gff( ingff, fields ):
if type(feature) is dict and (feature['seqid'], feature['start'], feature['end']) in intervals:
if field in feature['atts']:
out.write( '>%s %s:%s(%s)\n%s' % (feature['atts'][field], feature['start'], feature['end'], feature['strand'], intervals[(feature['seqid'], feature['start'], feature['end'])]))
elif field in feature:
out.write( '>%s\n%s' % (feature[field], intervals[(feature['seqid'], feature['start'], feature['end'])]))
def gff3_to_hints( ingff3, outhints ):
gff = gff_utils.read_gff( ingff3 )
hints = []
for f in gff:
if type(f) is str:
hints.append( f )
elif f['type'] == 'CDS':
f['attributes'] = 'src=M;pri=100;grp=%s' % f['atts']['Parent']
f['type'] = 'CDSpart'
hints.append( f )
gff_utils.write_gff( outhints, hints )
