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All Samples(13)  |  Call(11)  |  Derive(0)  |  Import(2)
an array posing as a sequence.

This class conserves memory as it uses only 1 byte per letter,
while python strings use the machine word size for a letter.

It exports a mixture of the methods in the python string and 
python array classes.

.. note::
(more...)

src/c/g/CGAT-0.2.0/CGAT/Genomics.py   CGAT(Download)
    parsed = {}
    key = None
    p = AString.AString()
    if regex_identifier:
        rx = regex_identifier
 
            key = rx.search( line[1:-1]).groups()[0]
            p = AString.AString()
            continue
 
        p.extend( AString.AString( re.sub( "\s", "", line[:-1])) )
            if key:
                if not filter or key in filter:
                    parsed[key] = AString.AString( re.sub( "\s", "", string.join( fragments, "")))
 
            key = re.match(">(\S+)", line[:-1]).groups()[0]
 
    if not filter or key in filter:
        parsed[key] = AString.AString( re.sub( "\s", "", string.join( fragments, "")))
 
    return parsed

src/c/g/CGAT-0.2.0/CGAT/IndexedFasta.py   CGAT(Download)
import cStringIO
import Experiment as E
from AString import AString
import pysam
 
        assert first_pos < last_pos, "first position %i is larger than last position %i " % (first_pos, last_pos)
 
        p = AString()
 
        if self.mNoSeek:
        if str(strand) in ("-", "0", "-1"):
            p.reverse()            
            p = AString( string.translate( p[:],
                                           string.maketrans("ACGTacgt", "TGCAtgca") ) )
 

src/c/g/cgat-HEAD/CGAT/IndexedFasta.py   cgat(Download)
import cStringIO
from CGAT import Experiment as E
from AString import AString
import pysam
 
            first_pos, last_pos)
 
        p = AString()
 
        if self.mNoSeek:
        if str(strand) in ("-", "0", "-1"):
            p.reverse()
            p = AString(string.translate(p[:],
                                         string.maketrans("ACGTacgt", "TGCAtgca")))