[med-svn] [Git][med-team/psortb][master] 6 commits: New upstream version 3.0.6+dfsg
Andreas Tille
gitlab at salsa.debian.org
Wed Sep 26 21:07:17 BST 2018
Andreas Tille pushed to branch master at Debian Med / psortb
Commits:
9497b2a1 by Andreas Tille at 2018-09-26T19:53:00Z
New upstream version 3.0.6+dfsg
- - - - -
287879c2 by Andreas Tille at 2018-09-26T19:54:20Z
Update upstream source from tag 'upstream/3.0.6+dfsg'
Update to upstream version '3.0.6+dfsg'
with Debian dir b6fdcd910fc551ed752d792ac55c7bb718fc6474
- - - - -
bcb2390b by Andreas Tille at 2018-09-26T19:54:20Z
New upstream version
- - - - -
f4e6b392 by Andreas Tille at 2018-09-26T19:54:22Z
Standards-Version: 4.2.1
- - - - -
ef852ff5 by Andreas Tille at 2018-09-26T20:03:24Z
Adapt patches
- - - - -
280d86fd by Andreas Tille at 2018-09-26T20:06:08Z
Upload to unstable
- - - - -
4 changed files:
- debian/changelog
- debian/control
- debian/patches/path_to_conf.patch
- psort/bin/psort
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+psortb (3.0.6+dfsg-1) unstable; urgency=medium
+
+ * New upstream version
+ * Standards-Version: 4.2.1
+
+ -- Andreas Tille <tille at debian.org> Wed, 26 Sep 2018 22:03:35 +0200
+
psortb (3.0.5+dfsg-2) unstable; urgency=medium
[ Steve Langasek ]
=====================================
debian/control
=====================================
@@ -14,7 +14,7 @@ Build-Depends: debhelper (>= 11~),
libmodhmm-dev,
pkg-config,
pftools
-Standards-Version: 4.1.4
+Standards-Version: 4.2.1
Vcs-Browser: https://salsa.debian.org/med-team/psortb
Vcs-Git: https://salsa.debian.org/med-team/psortb.git
Homepage: http://www.psort.org/
=====================================
debian/patches/path_to_conf.patch
=====================================
@@ -5,21 +5,6 @@ Description: Fix path to conf and other binaries
In case it turns out that users need to change this the files should be
moved to /etc/psortb
---- a/psort/bin/psort
-+++ b/psort/bin/psort
-@@ -59,9 +59,9 @@ MAIN: {
- my $psort_analysis = 'psort';
- my $psort_output = 'bayes';
-
-- my $root = '/usr/local/psortb-3.0';
-- my $blastdir = '/usr/local/bio/blast';
-- my $pftools = '/usr/local/bin/';
-+ my $root = '/usr/lib/psort';
-+ my $blastdir = '/usr/bin';
-+ my $pftools = '/usr/bin';
- my $pfscan_module = 'Profile';
-
- # Pull any options off of the command line.
--- a/psort/server/startup.pl
+++ b/psort/server/startup.pl
@@ -8,9 +8,9 @@ use Apache ();
@@ -35,3 +20,18 @@ Description: Fix path to conf and other binaries
our %ENV;
+--- a/psort/bin/psort
++++ b/psort/bin/psort
+@@ -61,9 +61,9 @@ MAIN: {
+ my $psort_analysis = 'psort';
+ my $psort_output = 'bayes';
+
+- my $root = '/usr/local/psortb3';
+- my $blastdir = '/usr/local/pkg/blast-2.2.26//bin';
+- my $pftools = '/usr/local/bin/';
++ my $root = '/usr/lib/psort';
++ my $blastdir = '/usr/bin';
++ my $pftools = '/usr/bin';
+ my $pfscan_module = 'Profile';
+
+ # Pull any options off of the command line.
=====================================
psort/bin/psort
=====================================
@@ -1,13 +1,15 @@
#! /usr/bin/perl
+use IO::String;
+use Getopt::Long;
+#use Data::Dumper;
+
+use lib '../lib';
use Bio::Tools::PSort::Report::Formatter;
use Bio::Tools::PSort;
use Bio::SeqIO;
use Bio::Tools::PSort::Constants qw(:all);
-use Getopt::Long;
-use Data::Dumper;
-
use strict;
our $ENV;
@@ -59,8 +61,8 @@ MAIN: {
my $psort_analysis = 'psort';
my $psort_output = 'bayes';
- my $root = '/usr/local/psortb-3.0';
- my $blastdir = '/usr/local/bio/blast';
+ my $root = '/usr/local/psortb3';
+ my $blastdir = '/usr/local/pkg/blast-2.2.26//bin';
my $pftools = '/usr/local/bin/';
my $pfscan_module = 'Profile';
@@ -361,11 +363,10 @@ MAIN: {
['CWSVM_a', sub {1},
['Signal_a']
]]]]]]]]]); # add a bracket back later
- } else {
- die "We should never be here.\n";
+ } else {
+ die "We should never be here.\n";
}
-
} else {
# Create a new PSort object.
print(STDERR "* Using \"$server\" as remote PSort server\n")
@@ -378,18 +379,19 @@ MAIN: {
# Figure out whether or not we're getting the sequences from a file or from
# STDIN and open up a Bio::SeqIO on it.
+ my $seqfh;
if($fname) {
if((-f $fname) && (-r $fname)) {
print(STDERR "* Reading sequences from file \"$fname\"\n") if($verbose);
- open(SEQS, $fname) || die("Error: open $fname: $!\n");
- $sio = new Bio::SeqIO(-fh => \*SEQS, -format => $format);
+ $seqfh = make_seq_input_uppercase($fname);
} else {
die("Error: file \"$fname\" doesn't exist or isn't readable\n");
}
} else {
print(STDERR "* Reading sequences from STDIN\n") if($verbose);
- $sio = new Bio::SeqIO(-fh => \*STDIN, -format => $format);
+ $seqfh = make_seq_input_uppercase();
}
+ $sio = new Bio::SeqIO(-fh => $seqfh, -format => $format);
# Ready for prime time - go forth and PSort.
my $format = new Bio::Tools::PSort::Report::Formatter();
@@ -404,3 +406,35 @@ MAIN: {
}
print($format->format($output, {-cutoff => $cutoff, -gram => $gram, -mcutoff => $divergent, -psort => $psort, -skiplocalizations => \@skippedlocalizations}, @reps));
}
+
+sub make_seq_input_uppercase {
+
+ my $fname = shift;
+
+ my $seqinput;
+ if (defined $fname) {
+ open(SEQS, $fname) || die("Error: open $fname: $!\n");
+ #$seqinput = <SEQS>;
+ $seqinput = do { local $/; <SEQS> };
+ }
+ else {
+ $seqinput = <>;
+ }
+
+ # hack to convert sequences (not headers) to uppercase (lowercase
+ # seems to bring back no psortb results)
+ my @seqs2uc = split(">", $seqinput);
+ shift(@seqs2uc); # remove blank first element (after doing split on > where > is the first character)
+
+ my $uc_seqs;
+ foreach my $header_seq (@seqs2uc) {
+ my ($h1, $s1) = split(/[\n\r]+/, $header_seq, 2);
+ if ($s1 =~ /[a-z]/) {
+ $s1 = uc($s1);
+ }
+ $uc_seqs .= ">$h1\n$s1";
+ }
+
+ my $seqfh = new IO::String($uc_seqs);
+ return($seqfh);
+}
View it on GitLab: https://salsa.debian.org/med-team/psortb/compare/176c269e295a70fa4d525f8a3de1aab6264abc99...280d86fd339119c75aad38c676d04d7c91b17be7
--
View it on GitLab: https://salsa.debian.org/med-team/psortb/compare/176c269e295a70fa4d525f8a3de1aab6264abc99...280d86fd339119c75aad38c676d04d7c91b17be7
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