iPE::SequenceReader::NoLoad::Align(3)

NAME
iPE::SequenceReader::NoLoad::Align - NoLoad version of the align format.

DESCRIPTION
This SequenceReader expects a file formatted with a fasta header with space-delimited sequence names, starting from the top sequence to the bottom sequence of the alignment (left to right in the header). Each sequence should occupy a single line in the file, and each sequence should be of the same length (unaligned regions should be '.' and gapped regions should be '_').

FUNCTIONS

new (memberHash)
    Constructs a new alignment sequence reader. This doesn't read in the sequences, it simply make calculations which will enable it to later read portions of the sequence in from the file.

length ()
    Returns length of all sequences in the alignment. This assumes that all sequences are the same length. If they are not, the sequence reader will not function correctly.

numSeqs (), seqNames ()
    numSeqs () returns the number of sequences in this alignment. This is equivalent to the size of the array reference returned by seqNames (). seqNames () is inferred from the space delimited names in the first line of the file after the fasta header character '>'.

getSeq (start, length, seqNum), getRevSeq (start, length, seqNum)
    This gets sequence directly from the file. This works similarly to substr in that it takes in a start and 'offset' or length of the substring to retrieve. Note that getRevSeq also reverse-complements the sequence.

SEE ALSO
iPE::SequenceReader::NoLoad

AUTHOR
Bob Zimmermann (rpz@cse.wustl.edu). (With much acknowledgement to Sam Gross's code).