Free binhex 1.119 software for linux

Convert::BinHex can extract data from Macintosh BinHex files.

ALPHA WARNING: this code is currently in its Alpha release. Things may change drastically until the interface is hammered out: if you have suggestions or objections, please speak up now!

SYNOPSIS

Simple functions:

use Convert::BinHex qw(binhex_crc macbinary_crc);

# Compute HQX7-style CRC for data, pumping in old CRC if desired:
$crc = binhex_crc($data, $crc);

# Compute the MacBinary-II-style CRC for the data:
$crc = macbinary_crc($data, $crc);

Hex to bin, low-level interface. Conversion is actually done via an object ("Convert::BinHex::Hex2Bin") which keeps internal conversion state:
# Create and use a "translator" object:
my $H2B = Convert::BinHex->hex2bin; # get a converter object
while (< STDIN >) {
print $STDOUT $H2B->next($_); # convert some more input
}
print $STDOUT $H2B->done; # no more input: finish up

Hex to bin, OO interface. The following operations must be done in the order shown!
# Read data in piecemeal:
$HQX = Convert::BinHex->open(FH=>*STDIN) || die "open: $!";
$HQX->read_header; # read header info
@data = $HQX->read_data; # read in all the data
@rsrc = $HQX->read_resource; # read in all the resource

Bin to hex, low-level interface. Conversion is actually done via an object ("Convert::BinHex::Bin2Hex") which keeps internal conversion state:
# Create and use a "translator" object:
my $B2H = Convert::BinHex->bin2hex; # get a converter object
while (< STDIN >) {
print $STDOUT $B2H->next($_); # convert some more input
}
print $STDOUT $B2H->done; # no more input: finish up

Bin to hex, file interface. Yes, you can convert to BinHex as well as from it!
# Create new, empty object:
my $HQX = Convert::BinHex->new;

# Set header attributes:
$HQX->filename("logo.gif");
$HQX->type("GIFA");
$HQX->creator("CNVS");

# Give it the data and resource forks (either can be absent):
$HQX->data(Path => "/path/to/data"); # here, data is on disk
$HQX->resource(Data => $resourcefork); # here, resource is in core

# Output as a BinHex stream, complete with leading comment:
$HQX->encode(*STDOUT);

PLANNED!!!! Bin to hex, "CAP" interface. Thanks to Ken Lunde for suggesting this.
# Create new, empty object from CAP tree:
my $HQX = Convert::BinHex->from_cap("/path/to/root/file");
$HQX->encode(*STDOUT);

BinHex is a format used by Macintosh for transporting Mac files safely through electronic mail, as short-lined, 7-bit, semi-compressed data streams. Ths module provides a means of converting those data streams back into into binary data.

Bio::Tools::Run::TribeMCL is a method for clustering proteins into related groups, which are termed protein families.
SYNOPSIS
use Bio::Tools::Run::TribeMCL;
use Bio::SearchIO;
# 3 methods to input the blast results
# straight forward raw blast output (NCBI or WU-BLAST)
my @params = (inputtype=>blastfile);
# OR
# markov program format
# protein_id1 protein_id2 evalue_magnitude evalue_factor
# for example:
# proteins ENSP00000257547 and ENSP00000261659
# with a blast score evalue of 1e-50
# and proteins O42187 and ENSP00000257547
# with a blast score evalue of 1e-119
# entry would be
my @array = [[qw(ENSP00000257547 ENSP00000261659 1 50)],
[qw(O42187 ENSP00000257547 1 119)]];
my @params = (pairs=>@array,I=>2.0);
# OR
# pass in a searchio object
# slowest of the 3 methods as it does more rigourous parsing
# than required for us here
my $sio = Bio::SearchIO->new(-format=>blast,
-file=>blast.out);
my @params=(inputtype=>searchio,I=>2.0);
# you can specify the path to the executable manually in the following way
my @params=(inputtype=>blastfile,I=>2.0,
mcl=>/home/shawn/software/mcl-02-150/src/shmcl/mcl,
matrix=>/home/shawn/software/mcl-02-150/src/contrib/tribe/tribe-matrix);
my $fact = Bio::Tools::Run::TribeMCL->new(@params);
# OR
$fact->matrix_executable(/home/shawn/software/mcl-02-150/src/contrib/tribe/tribe-matrix);
$fact->mcl_executable(/home/shawn/software/mcl-02-150/src/shmcl/mcl);
# to run
my $fact = Bio::Tools::Run::TribeMCL->new(@params);
# Run the program
# returns an array reference to clusters where members are the ids
# for example :2 clusters with 3 members per cluster:
# $fam = [ [mem1 mem2 mem3],[mem1 mem2 mem3]]
# pass in either the blastfile path/searchio obj/the array ref to scores
my $fam = $fact->run($sio);
# print out your clusters
for (my $i = 0; $i
print "Cluster $i t ".scalar(@{$fam->[$i]})." membersn";
foreach my $member (@{$fam->[$i]}){
print "t$membern";
}
}
This clustering is achieved by analysing similarity patterns between proteins in a given dataset, and using these patterns to assign proteins into related groups. In many cases, proteins in the same protein family will have similar functional properties.
Enhancements:
- Perl