def splicer(gff, ftype, dline):
seq=dict()
roots = [line for line in gff.lines if line['line_type'] == 'feature' and not line['attributes'].has_key('Parent')]
for root in roots:
#if ftype[0] == 'CDS' and root['type'] == 'pseudogene': # pseudogene should not contain cds
#continue
rid = 'NA'
if root['attributes'].has_key('ID'):
rid = root['attributes']['ID']
children = root['children']
for child in children:
cid = 'NA'
if child['attributes'].has_key('ID'):
cid = child['attributes']['ID']
cname = cid
if child['attributes'].has_key('Name'):
cname = child['attributes']['Name']
defline='>{0:s}'.format(cid)
if ftype[0] == 'CDS':
defline='>{0:s}-CDS'.format(cid)
if dline == 'complete':
defline = '>{0:s}:{1:d}..{2:d}:{3:s}|{4:s}({8:s})|Parent={5:s}|ID={6:s}|Name={7:s}'.format(child['seqid'], child['start'], child['end'], child['strand'], child['type'], rid, cid, cname, ftype[0])
segments = []
gchildren = child['children']
for gchild in gchildren:
if gchild['type'] in ftype:
segments.append(gchild)
flag = 0
if len(segments)==0:
flag += 1
for gchild in gchildren:
if gchild['type'] == 'CDS':
segments.append(gchild)
if len(segments)==0 and ftype[0] == 'CDS':
flag += 1
print("WARNING There is no CDS feature for {0:s} in the input gff. The sequence of {0:s} is not generated.".format(cid))
continue
elif len(segments)==0:
flag += 1
print("WARNING There is no exon, nor CDS feature for {0:s} in the input gff. The sequence of {0:s} is not generated.".format(cid))
continue
if flag == 1:
print("WARNING There is no exon feature for {0:s} in the input gff. CDS features are used for splicing instead.".format(cid))
sort_seg = function4gff.featureSort(segments)
if gchild['strand'] == '-':
sort_seg = function4gff.featureSort(segments, reverse=True)
tmpseq = ''
for s in sort_seg:
tmpseq = tmpseq + get_subseq(gff, s)
seq[defline] = tmpseq
return seq
def check_duplicate(gff, linelist):
'''
This function assumes that,
1. Each gnee is unique
2. Children features such as Exons/CDSs do not contain multiple Parent IDs
Note: If there are additional transcript type in the input gfff, then you should go to intra_model.featureSort, and add the new transcript type to the dict of FEATURECODE.
'''
eCode = 'Emr0001'
eSet = list()
pairs = list()
for i in range(len(linelist)-1):
for j in range(i+1, len(linelist)):
source, target = linelist[i], linelist[j]
if source['seqid'] == target['seqid']:
s7 = '{0:s}\t{1:s}\t{2:s}\t{3:d}\t{4:d}\t{5:s}\t{6:s}'.format(source['seqid'], source['source'], source['type'], source['start'], source['end'], source['score'], source['strand'], source['phase'])
t7 = '{0:s}\t{1:s}\t{2:s}\t{3:d}\t{4:d}\t{5:s}\t{6:s}'.format(target['seqid'], target['source'], target['type'], target['start'], target['end'], target['score'], target['strand'], target['phase'])
if s7 == t7:
pairs.append({'source':source, 'target':target})
for pair in pairs:
result = dict()
same_target = False
if pair['source'].has_key('children') and pair['target'].has_key('children'):
schildren = pair['source']['children']
tchildren = pair['target']['children']
if len(schildren) == len(tchildren):
sort_schildren = function4gff.featureSort(schildren, reverse=True if pair['source']['strand'] == '-' else False)
sort_tchildren = function4gff.featureSort(tchildren, reverse=True if pair['source']['strand'] == '-' else False)
for i in range(len(sort_schildren)):
s7 = '{0:s}\t{1:s}\t{2:s}\t{3:d}\t{4:d}\t{5:s}\t{6:s}'.format(sort_schildren[i]['seqid'], sort_schildren[i]['source'], sort_schildren[i]['type'], sort_schildren[i]['start'], sort_schildren[i]['end'], sort_schildren[i]['score'], sort_schildren[i]['strand'], sort_schildren[i]['phase'])
t7 = '{0:s}\t{1:s}\t{2:s}\t{3:d}\t{4:d}\t{5:s}\t{6:s}'.format(sort_tchildren[i]['seqid'], sort_tchildren[i]['source'], sort_tchildren[i]['type'], sort_tchildren[i]['start'], sort_tchildren[i]['end'], sort_tchildren[i]['score'], sort_tchildren[i]['strand'], sort_tchildren[i]['phase'])
if s7 == t7:
same_target=True
else:
same_target=False
break
if same_target:
key = [pair['source']['attributes']['ID'], pair['target']['attributes']['ID']]
result['ID'] = key
result['eCode'] = eCode
result['eLines'] = [pair['source'], pair['target']]
result['eTag'] = 'Duplicate transcripts found between {0:s} and {1:s}'.format(pair['source']['attributes']['ID'], pair['target']['attributes']['ID'])
eSet.append(result)
gff.add_line_error(pair['source'], {'message': 'Duplicate transcripts found between {0:s} and {1:s}'.format(pair['source']['attributes']['ID'], pair['target']['attributes']['ID']), 'error_type': 'INTER_MODEL', 'eCode': eCode})
gff.add_line_error(pair['target'], {'message': 'Duplicate transcripts found between {0:s} and {1:s}'.format(pair['source']['attributes']['ID'], pair['target']['attributes']['ID']), 'error_type': 'INTER_MODEL', 'eCode': eCode})
if len(eSet):
return eSet
