From: Sasha Sherstnev <a.sherstnev@dundee.ac.uk>
Date: Fri, 2 Aug 2013 10:28:30 +0000 (+0100)
Subject: JWS-67 Update internal man for jpred.pl
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=ab3a154bf48a5a143b05eab120f53396fc53bda3;p=jabaws.git

JWS-67 Update internal man for jpred.pl
---

diff --git a/binaries/src/jpred/jpred.pl b/binaries/src/jpred/jpred.pl
index 085b515..88c4f58 100755
--- a/binaries/src/jpred/jpred.pl
+++ b/binaries/src/jpred/jpred.pl
@@ -6,12 +6,12 @@ jpred - Secondary structure prediction program
 
 =head1 SYNOPSIS
 
-  jpred --sequence <fasta file> [--output <output prefix>] [--db <database>] [--psi <psiblast output>] [--pred-nohits] [--verbose] [--debug] [--help] [--man]
+./jpred.pl -in/-sequence <FILE1> [-out/-output <FILEPREFIX>] [-dbname <DBNAME>] [-dbpath <PATH>] [-ncpu NNN] [-psi <psiblast output>] [-pred-nohits] [-verbose] [-debug] [-help] [-man]
 
 =head1 DESCRIPTION
 
-This is a program which predicts the secondary structure of a sequence given a path to a FASTA sequence. 
-It does all the PSI-BLAST searching and alignment 'meddling' as required by Jnet.
+This is a program which predicts the secondary structure of a protein sequence given a path to a 
+FASTA sequence. It does all the PSI-BLAST searching and alignment 'meddling' as required by Jnet.
 
 The program is primarily design for use by the Jpred server, but it can be used directly by any user. 
 Some of the output may not be meaningful if used directly - it can be safely ignored.
@@ -20,41 +20,50 @@ Some of the output may not be meaningful if used directly - it can be safely ign
 
 =over 5
 
-=item -sequence path to input FASTA file
+=item -in/-sequence FILE
 
-The path to the sequence (in FASTA format) you want to predict.
+The path to the sequence file (in FASTA format) you want to predict.
 
-=item -output file
+=item -out/-output FILEPREFIX
 
-A prefix to the filenames created by Jpred, defaults to the value set by --sequence.
+A prefix to the filenames created by Jpred, defaults to the value set by -sequence/-in.
 
-=item --db database
+=item -dbpath PATH
 
-Database to use for PSI-BLAST querying. This only accepts databases from a list which is pre-defined in the code. Crap I know, but that's the way it is at the moment. It's probably best to stick the default for the time being.
+Path to the uniref database used for PSI-BLAST querying.
+Default: .
 
+=item -dbname database
+
+Database to use for PSI-BLAST querying. This only accepts databases from a list which is pre-defined in the code.
 Default: uniref90
 
 =item -psi path
 
 Path to a PSIBLAST output file.
 
-=item --pred-nohits
+=item -ncpu NNN
+
+Number of CPU used by jpred.pl. Maximum value is 8
+Default: NNN = 1
+
+=item -pred-nohits
 
 Toggle allowing Jpred to make predictions even when there are no PSI-BLAST hits.
 
-=item --verbose
+=item -verbose
 
 Verbose mode. Print more information while running jpred.
 
-=item --debug
+=item -debug
 
 Debug mode. Print debugging information while running jpred. 
 
-=item --help
+=item -help
 
 Gives help on the programs usage.
 
-=item --man
+=item -man
 
 Displays this man page.
 
@@ -66,7 +75,7 @@ Can't cope with gaps in the query sequence.
 
 Doesn't accept alignments.
 
-If you find any others please contact me.
+If you find any others please contact authors.
 
 =head1 AUTHORS
 
@@ -212,7 +221,6 @@ my $database = {
   ## these other DBs are experimental ones used during development.
   ## check they exist before using them.
   swall => {
-
     # generic entry for use with validate_jnet.pl
     # real db location defined by validate_jnet.pl
     database   => $db_path . "/swall/swall.filt",
@@ -220,19 +228,19 @@ my $database = {
   },
 
   uniprot => {
-
     # Path to PSIBLAST db
     database   => $db_path . "/3/swall.filt",
     unfiltered => $db_path . "/3/swall",
   },
+
   uniref50 => {
     database   => $db_path . "/6/swall.filt",
     unfiltered => $db_path . "/6/swall",
   },
 };
 
-pod2usage(' --sequence argument not provided') unless $infile;
-die "--db $db_entry not recognised" unless exists $database->{$db_entry};
+pod2usage(' -sequence argument not provided') unless $infile;
+die "-db $db_entry not recognised" unless exists $database->{$db_entry};
 $output = $infile . ".res" unless $output;
 $ncpu = 1 if ( 1 > $ncpu or 8 < $ncpu );
 
@@ -305,7 +313,7 @@ for ( $psi->get_all ) {
 ## Accuracy won't be as good, but at least it's a prediction
 if ( @seqs == 0 ) {
   if ( $predNoHits == 0 ) {
-    warn "\nJPRED: Warning! no PSI-BLAST hits found and '--pred-nohits' option not set. Exiting...\n";
+    warn "\nJPRED: Warning! no PSI-BLAST hits found and '-pred-nohits' option not set. Exiting...\n";
     print ">>100% complete\n";
     exit;
   } else {