def append_to_description(seqrecord, text):
'it appends the text to the seqrecord description'
desc = get_description(seqrecord)
if desc in (None, get_name(seqrecord), '<unknown description>'):
desc = ''
desc += text
seqrecord.object.description = desc
def append_to_description(seqrecord, text):
'it appends the text to the seqrecord description'
desc = get_description(seqrecord)
if desc in (None, get_name(seqrecord), '<unknown description>'):
desc = ''
desc += text
seqrecord.object.description = desc
def _read_estcan_result(fhand, result, file_type):
'It reads a dna or pep ESTscan result file'
for seq in read_seqs([fhand], file_format='fasta'):
items = [i.strip() for i in get_description(seq).split(';')]
strand = -1 if 'minus strand' in items else 1
start, end = items[0].split(' ', 3)[1:3]
# estscan changes the name, we have to fix it
seqid = get_name(seq).strip(';')
try:
seq_orfs = result[seqid]
except KeyError:
seq_orfs = {}
result[seqid] = seq_orfs
orf_key = (int(start), int(end), strand)
if orf_key in seq_orfs:
orf = seq_orfs[orf_key]
else:
orf = {}
seq_orfs[orf_key] = orf
orf[file_type] = get_str_seq(seq)
def _read_estcan_result(fhand, result, file_type):
'It reads a dna or pep ESTscan result file'
for seq in read_seqs([fhand], file_format='fasta'):
items = [i.strip() for i in get_description(seq).split(';')]
strand = -1 if 'minus strand' in items else 1
start, end = items[0].split(' ', 3)[1:3]
# estscan changes the name, we have to fix it
seqid = get_name(seq).strip(';')
try:
seq_orfs = result[seqid]
except KeyError:
seq_orfs = {}
result[seqid] = seq_orfs
orf_key = (int(start), int(end), strand)
if orf_key in seq_orfs:
orf = seq_orfs[orf_key]
else:
orf = {}
seq_orfs[orf_key] = orf
orf[file_type] = get_str_seq(seq)