MassSpec::CUtilities 0.04

MassSpec::CUtilities is a Perl extension containing C utilities for use in mass spectrometry.

SYNOPSIS

MassSpec::CUtilities is an XS module so theres a chance that you or your target user might not get it to install cleanly on the target system; therefore its recommended to make its presence optional and to offer slower-performing Perl equivalents where practical.

Also note that this module uses a 19-letter amino alphabet rather than the traditional 20-letter alphabet, since the isobars Leucine(L) and Isoleucine(I) are represented instead by "X." Furthermore some portions of this module assume that their input peptides are internally in alphabetical order.

my $haveCUtilities;
if (eval require MassSpec::CUtilities) {
import MassSpec::CUtilities;
$haveCUtilities = 1;
} else {
$haveCUtilities = 0;
}
if ($haveCUtilities) {
my $candidate = MassSpec::CUtilities::encodeAsBitString("ACCGT");
my @shortPeptides = ("ACT","CCGM","ACCGTY","CCT");
my (@list,@answer);
foreach $_ (@shortPeptides) {
push @list, MassSpec::CUtilities::encodeAsBitString($_);
}
if (MassSpec::CUtilities::testManyBitStrings($candidate,@shortPeptides,@list,@answer)) {
# should print "ACT" and "CCT" only
print "Matched: " . join(,,@answer) . "n";
}
}

see API documentation for other available subroutines

ABSTRACT

An eclectic mix of C utilities originally used in a mass spectrometry denovo sequencing project at NIH. It includes a fast Huffman decoder suitable (with minor modifications) for use with the CPAN module Algorithm::Huffman, as well as a fast peptide mass calculator and methods for encoding peptides as products of prime numbers or as bitmaps.

An eclectic mix of C utilities originally used in a mass spectrometry denovo sequencing project at NIH. It includes a fast Huffman decoder suitable (with minor modifications) for use with the CPAN module Algorithm::Huffman, as well as a fast peptide mass calculator and methods for encoding peptides as products of prime numbers or as bitmaps.