def cogent_slice( fname ):
fasta = get_index( fname, tag='cogent', flag='c')
for rec in fasta:
seq = fasta[rec]
for i in range(NSLICE):
sub = str( seq[:100] )
break
fasta.close()
def bx_reverse_comp( fname ):
fasta = get_index( fname, tag='bx', flag='c')
for rec in fasta:
seq = fasta[rec]
rev = seq.reverse_complement( seq.text )
rev = str(rev)
fasta.close()
def bio_reverse_comp( fname ):
fasta = get_index( fname, tag='bio', flag='c')
keys = fasta.keys()
keys.sort()
for rec in keys:
seq = fasta[rec].seq.reverse_complement()
sub = seq.tostring()
fasta.close()
def bio_slice( fname ):
fasta = get_index( fname, tag='bio', flag='c')
for rec in fasta:
seq = fasta[rec].seq
for i in range(NSLICE):
sub = seq[:100].tostring()
break
fasta.close()
def bx_slice( fname ):
fasta = get_index( fname, tag='bx', flag='c')
for rec in fasta:
seq = fasta[rec]
for i in range(NSLICE):
sub = seq.get(0, 100)
break
fasta.close()
def bx_reverse_comp(fname):
fasta = get_index(fname, tag='bx', flag='c')
for rec in fasta:
seq = fasta[rec]
rev = seq.reverse_complement(seq.text)
rev = str(rev)
fasta.close()
def bio_reverse_comp(fname):
fasta = get_index(fname, tag='bio', flag='c')
keys = fasta.keys()
keys.sort()
for rec in keys:
seq = fasta[rec].seq.reverse_complement()
sub = seq.tostring()
fasta.close()
def cogent_slice(fname):
fasta = get_index(fname, tag='cogent', flag='c')
for rec in fasta:
seq = fasta[rec]
for i in range(NSLICE):
sub = str(seq[:100])
break
fasta.close()
def bx_slice(fname):
fasta = get_index(fname, tag='bx', flag='c')
for rec in fasta:
seq = fasta[rec]
for i in range(NSLICE):
sub = seq.get(0, 100)
break
fasta.close()
def bio_slice(fname):
fasta = get_index(fname, tag='bio', flag='c')
for rec in fasta:
seq = fasta[rec].seq
for i in range(NSLICE):
sub = seq[:100].tostring()
break
fasta.close()
def cogent_reverse_comp( fname ):
fasta = get_index( fname, tag='cogent', flag='c')
keys = fasta.keys()
keys.sort()
for rec in keys:
seq = fasta[rec].reversecomplement()
seq = str(seq)
sub = seq[:10]
fasta.close()
def cogent_reverse_comp(fname):
fasta = get_index(fname, tag='cogent', flag='c')
keys = fasta.keys()
keys.sort()
for rec in keys:
seq = fasta[rec].reversecomplement()
seq = str(seq)
sub = seq[:10]
fasta.close()
def cogent_iter( fname ):
fasta = get_index( fname, tag='cogent', flag='c')
for rec in fasta:
seq = fasta[rec]
fasta.close()
def bio_iter( fname ):
fasta = get_index( fname, tag='bio', flag='c')
for rec in fasta:
seq = fasta[rec]
fasta.close()
def bx_iter(fname):
fasta = get_index(fname, tag='bx', flag='c')
for rec in fasta:
seq = fasta[rec]
fasta.close()
