cjfields

pyrimidine1:biomoose cjfields$ cat benchmark_fasta.pl 
#!/usr/bin/perl -w

use strict;
use warnings;
use Bio::PrimarySeq;
use Bio::Moose::PrimarySeq;
use Benchmark ':hireswallclock';
use Modern::Perl;

cjfields

            my $gs = ${$self->symbols}{GAP};
            # map gaps prior and post start/end
            my ($newst, $newend) = ($start, $end);
            while ($rawseq =~ m{([$gs]+)}g) {
                my $len = CORE::length($1);
                my $current = pos($rawseq) - $len;
                # optimization : bail if current gap is past the end
                last if $current >= $newend;
                $newst += $len if $current <= $newst;

cjfields

pyrimidine1:HMM cjfields$ perl Makefile.PL 
Writing Makefile for Bio::Ext::HMM
pyrimidine1:HMM cjfields$ make
cp HMM.pm blib/lib/Bio/Ext/HMM.pm
/opt/perl/bin/perl /opt/perl/lib/5.10.0/ExtUtils/xsubpp  -typemap /opt/perl/lib/5.10.0/ExtUtils/typemap -typemap typemap  HMM.xs > HMM.xsc && mv HMM.xsc HMM.c
Please specify prototyping behavior for HMM.xs (see perlxs manual)
cc -c   -fno-common -DPERL_DARWIN -no-cpp-precomp -nostdinc -B/Developer/SDKs/MacOSX10.5.sdk/usr/include/gcc -B/Developer/SDKs/MacOSX10.5.sdk/usr/lib/gcc -isystem/Developer/SDKs/MacOSX10.5.sdk/usr/include -F/Developer/SDKs/MacOSX10.5.sdk/System/Library/Frameworks -fno-strict-aliasing -pipe -I/opt/local/include -O3   -DVERSION=\"0.1\" -DXS_VERSION=\"0.1\"  "-I/opt/perl/lib/5.10.0/darwin-64int-ld-2level/CORE"   HMM.c
HMM.c: In function ‘XS_Bio__Ext__HMM_HMM_statistical_training’:
HMM.c:44: warning: cast to pointer from integer of different size
HMM.c: In function ‘XS_Bio__Ext__HMM_HMM_likelihood’:

cjfields

cjfields4:HMM cjfields$ make test
PERL_DL_NONLAZY=1 /usr/bin/perl "-Iblib/lib" "-Iblib/arch" test.pl
Baum-Welch Training
===================
S should be monotonic increasing!
make: *** [test_dynamic] Error 255
cjfields4:HMM cjfields$ make test
PERL_DL_NONLAZY=1 /usr/bin/perl "-Iblib/lib" "-Iblib/arch" test.pl
Baum-Welch Training
===================

cjfields

#### dev.open-bio.org, perl 5.8.8 ####

[cjfields@dev HMM]$ perl -V
Summary of my perl5 (revision 5 version 8 subversion 8) configuration:
  Platform:
    osname=linux, osvers=2.6.9-67.0.15.elvm, archname=i386-linux-thread-multi
    uname='linux v20z-x86-64.home.local 2.6.9-67.0.15.elvm #1 wed may 7 13:53:04 edt 2008 i686 athlon i386 gnulinux '
    config_args='-des -Doptimize=-O2 -g -pipe -m32 -march=i386 -mtune=pentium4 -Dversion=5.8.8 -Dmyhostname=localhost -Dperladmin=root@localhost -Dcc=gcc -Dcf_by=Red Hat, Inc. -Dinstallprefix=/usr -Dprefix=/usr -Darchname=i386-linux -Dvendorprefix=/usr -Dsiteprefix=/usr -Duseshrplib -Dusethreads -Duseithreads -Duselargefiles -Dd_dosuid -Dd_semctl_semun -Di_db -Ui_ndbm -Di_gdbm -Di_shadow -Di_syslog -Dman3ext=3pm -Duseperlio -Dinstallusrbinperl=n -Ubincompat5005 -Uversiononly -Dpager=/usr/bin/less -isr -Dd_gethostent_r_proto -Ud_endhostent_r_proto -Ud_sethostent_r_proto -Ud_endprotoent_r_proto -Ud_setprotoent_r_proto -Ud_endservent_r_proto -Ud_setservent_r_proto -Dinc_v

cjfields

#!/usr/bin/perl -w
#svn_bioperl_irc.pl

use strict;
use warnings;
use WWW::Shorten 'TinyURL';

my $server = "irc.freenode.net";
my $port = 6667;
my $nick = "driveby_bot";

cjfields

# this is mainly GFF3-specific, GFF2/GTF to be added

my ($io, $f, $s, $fcount, $scount);

################################################################################
#
# use FeatureIO::gff to read a FASTA file.
#
$fcount = 0;
$scount = 0;

cjfields

use v6;

use Test;

use MONKEY_TYPING;

augment class Cool {
    
    # could build this up as a regex, use progressive matching
    # and a default Callable that grabs the mapped value and uses

cjfields

ID   AQP1_HUMAN              Reviewed;         269 AA.
AC   P29972; B5BU39; Q8TBI5; Q8TDC1;
DT   01-APR-1993, integrated into UniProtKB/Swiss-Prot.
DT   23-JAN-2007, sequence version 3.
DT   18-MAY-2010, entry version 122.
DE   RecName: Full=Aquaporin-1;
DE            Short=AQP-1;
DE   AltName: Full=Aquaporin-CHIP;
DE   AltName: Full=Water channel protein for red blood cells and kidney proximal tubule;
DE   AltName: Full=Urine water channel;

cjfields

$VAR1 = bless( {
                 '_secondary_ids' => [],
                 '_dblinks' => {},
                 'short_name' => undef,
                 '_ontology' => bless( {
                                         'engine' => bless( {
                                                              '_relationship_type_store' => {
                                                                                              'InterPro|IS_A' => bless( {
                                                                                                                          '_secondary_ids' => [],
                                                                                                                          '_dblinks' => {},