bump prosite to 2025_01

core/jms-implementation/src/main/resources/application-default.properties

@@ -208,17 +208,17 @@ fingerprintscan.binary.switches=-e 0.0001 -d 10 -E 257043 84355444 -fj -o 15
 
 # PROSITE
 # Note: Correct PROSITE binary distribution for your platform can be downloaded: ftp://ftp.expasy.org/databases/prosite/ps_scan/
-prosite.patterns.signature.library.release=2023_05
-prosite.profiles.signature.library.release=2023_05
+prosite.patterns.signature.library.release=2025_01
+prosite.profiles.signature.library.release=2025_01
 binary.prosite.psscan.pl.path=${bin.directory}/prosite/ps_scan.pl
 binary.prosite.pfscanv3.path=${bin.directory}/prosite/pfscanV3
 binary.prosite.pfsearchv3.path=${bin.directory}/prosite/pfsearchV3
 binary.prosite.runprosite.path=${bin.directory}/prosite/runprosite.py
-prosite.patterns.models.path=${data.directory}/prosite/2023_05/prosite_patterns.dat
-prosite.profiles.models.path=${data.directory}/prosite/2023_05/prosite_profiles.dat
-prosite.profiles.models.dir=${data.directory}/prosite/2023_05/prosite_profiles
-prosite.evaluator.models.path=${data.directory}/prosite/2023_05/evaluator.dat
-prosite.profiles.skip.flagged.profiles=${data.directory}/prosite/2023_05/skip_flagged_profiles.txt
+prosite.patterns.models.path=${data.directory}/prosite/2025_01/prosite_patterns.dat
+prosite.profiles.models.path=${data.directory}/prosite/2025_01/prosite_profiles.dat
+prosite.profiles.models.dir=${data.directory}/prosite/2025_01/prosite_profiles
+prosite.evaluator.models.path=${data.directory}/prosite/2025_01/evaluator.dat
+prosite.profiles.skip.flagged.profiles=${data.directory}/prosite/2025_01/skip_flagged_profiles.txt
 psscan.prosite.profiles.usepfsearch=true
 pfsearchv3.binary.switches.prosite.profiles=-f -o 7
 pfsearchv3.cpu.switch.prosite.profiles=-t 4

core/jms-implementation/support-mini-x86-32/bin/prosite/ps_scan.pl

@@ -2,7 +2,7 @@
 
 # ps_scan - a PROSITE scanning program
 #
-# Revision: 1.90
+# Revision: 1.91
 #
 # Copyright (C) 2001-2020 SIB Swiss Institute of Bioinformatics
 # Authors:
@@ -34,6 +34,7 @@
 use Carp qw(confess cluck);
 use vars qw(@ISA $VERSION $errpos $errstr);
 use strict;
+use Data::Dumper;
 
 
 ################################################################################
@@ -1472,6 +1473,9 @@ sub scanSeqFile {
                     # FIXME: should be done at the do_profile_scan level
                     # fix seqid (do_profile_scan sometimes
                     # returns ac|id instead of id)
+
+                    # EXPGE-313
+                    next if $opt_filterheader && $hit->[10] !~ /$opt_filterheader/o;
                     $hit->[3] = $psid;
                     push @{$all_hits_bypsac_byseqid->{$seq_id}->{$psac}},
                         $hit;

core/jms-implementation/support-mini-x86-32/bin/prosite/ps_scan_README

@@ -14,24 +14,24 @@ FASTA format. It requires two compiled external programs from the PFTOOLS
 package : "pfscan" used to scan a sequence against a profile library and
 "psa2msa" which is necessary for the "-o msa" output format only.
 
-Authors:
+Authors: 
  Alexandre Gattiker
- Edouard de Castro; E-mail: ecastro@isb-sib.ch
+ Edouard de Castro; E-mail: ecastro@sib.swiss
  Elisabeth Gasteiger
 
 Installation
 ------------
 
-Download a binary package for your platform from
+Download a binary package for your platform from 
 
-ftp://ftp.expasy.org/databases/prosite/ps_scan/ps_scan_<platform>.tar.gz
+https://ftp.expasy.org/databases/prosite/ps_scan/ps_scan_<platform>.tar.gz
 
 or the source packages from
 
-ftp://ftp.lausanne.isb-sib.ch/pub/software/unix/pftools/
+https://ftp.vital-it.ch/pub/software/unix/pftools/ or https://github.com/sib-swiss/pftools3
 
 in which case you will need gcc or a compatible fortran compiler to compile the
-pftools sources.
+pftools sources, see https://ftp.expasy.org/databases/prosite/README.pftools.
 
 You may need to edit the ps_scan.pl to provide absolute paths to the directory
 where you have installed the pfscan and psa2msa executables, unless you have
@@ -40,7 +40,7 @@ stored them in a directory in your PATH.
 A local copy of the PROSITE database is also needed. You may download it
 in a single file from
 
-ftp://ftp.expasy.org/databases/prosite/prosite.dat
+https://ftp.expasy.org/databases/prosite/prosite.dat
 
 Usage
 -----
@@ -53,8 +53,8 @@ Input/Output:
   -o : specify an output format : $formats_string
   -d : specify a prosite.dat file
   -p : specify a pattern or the AC of a prosite motif
-  -f : specify a motif AC to scan against together with all its
-       releated post-processing motifs (but show only specified
+  -f : specify a motif AC to scan against together with all its 
+       releated post-processing motifs (but show only specified 
        motif hits)
 Selection:
   -r : do not scan profiles
@@ -210,7 +210,7 @@ Pattern match mode:
   position to match X (unless that pattern position is an X itself, in which
   case we can accept more). The maximum number of X characters which are
   allowed to match a non-X position in a pattern can be specified with the -x
-  option. The default value is 1.
+  option. The default value is 0.
 
 Examples
 --------

core/jms-implementation/support-mini-x86-32/installer.properties

@@ -63,10 +63,10 @@ prints.kdat.path=data/prints/42.0/prints.kdat
 prints.pval.path=data/prints/42.0/prints.pval
 
 # Prosite
-prosite.patterns.signature.library.release=2023_05
-prosite.patterns.models.path=data/prosite/2023_05/prosite_patterns.dat
-prosite.profiles.signature.library.release=2023_05
-prosite.profiles.models.path=data/prosite/2023_05/prosite_profiles.dat
+prosite.patterns.signature.library.release=2025_01
+prosite.patterns.models.path=data/prosite/2025_01/prosite_patterns.dat
+prosite.profiles.signature.library.release=2025_01
+prosite.profiles.models.path=data/prosite/2025_01/prosite_profiles.dat
 
 # SFLD
 sfld.signature.library.release=4