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()