Python keys Examples

Example #1

File: benchmark.py Project: amuralle/pygr

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()                

Example #2

File: benchmark.py Project: amuralle/pygr

def pygr_reverse_comp( fname ):
    fasta = seqdb.SequenceFileDB( fname )
    keys = fasta.keys()
    keys.sort()
    for rec in keys:
        # force full reverse complement
        seq = str(-fasta[rec])
        sub = seq[:10]

Example #3

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()

Example #4

def pygr_reverse_comp(fname):
    fasta = seqdb.SequenceFileDB(fname)
    keys = fasta.keys()
    keys.sort()
    for rec in keys:
        # force full reverse complement
        seq = str(-fasta[rec])
        sub = seq[:10]

Example #5

File: benchmark.py Project: amuralle/pygr

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()

Example #6

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()