diff --git a/misc-scripts/protein_match/get_Xmapping.pl b/misc-scripts/protein_match/get_Xmapping.pl
index 00a5f2388be053952f299fa7b6a9c393812c1d7a..7bccda504088a8ca982108a8dee28d2af0618996 100644
--- a/misc-scripts/protein_match/get_Xmapping.pl
+++ b/misc-scripts/protein_match/get_Xmapping.pl
@@ -47,6 +47,18 @@ my $zeb_dblink = $conf{'zeb_dblink'};
my $briggsae_peptides = $conf{'briggsae_hybrid'};
+my $help;
+
+
+&GetOptions(
+ 'help' => \$help,
+ );
+
+if ($help) {
+ print STDERR $conf{'help'}."\n";
+ exit();
+}
+
#Check that the configuration file has been well filled in for each different organism
#Beginning of check
@@ -640,3 +652,4 @@ HELP
exit();
}
+
diff --git a/misc-scripts/protein_match/mapping_conf.pl b/misc-scripts/protein_match/mapping_conf.pl
index f4579c7009349e140f9a5554a3375474cabca229..b35e34f6a6c27c8b0f0a99df33e0b118268d2b83 100644
--- a/misc-scripts/protein_match/mapping_conf.pl
+++ b/misc-scripts/protein_match/mapping_conf.pl
@@ -221,6 +221,10 @@ package main;
##################
'check' => '', #obslete option?
+
+
+#Help related stuff. Put the location of the latest help file
+ 'help' => 'For an extensive help please check out ensembl-doc and have a look at protein_mapping.txt',
);
diff --git a/misc-scripts/protein_match/maps2db.pl b/misc-scripts/protein_match/maps2db.pl
index 563428af7a8e808809cb33b9773a5ca184407d9e..67793bba77b3272a3d9ea90d7c32176580d9831e 100644
--- a/misc-scripts/protein_match/maps2db.pl
+++ b/misc-scripts/protein_match/maps2db.pl
@@ -32,6 +32,17 @@ my $port = $conf{'port'};
my $organism = $conf{'organism'};
my $query_pep = $conf{'query'};
my $refseq_pred = $conf{'refseq_pred_gnp'};
+my $help;
+
+
+&GetOptions(
+ 'help' => \$help,
+ );
+
+if ($help) {
+ print STDERR $conf{'help'}."\n";
+ exit();
+}
#Organism specific options
#Drosophila
@@ -53,6 +64,10 @@ my %embl2sp;
my %errorflag;
my %ref_map_pred;
+my $help = $conf{'help'};
+
+print STDERR "$help\n";
+
#Checks
my %check;
diff --git a/misc-scripts/protein_match/pmatch.pl b/misc-scripts/protein_match/pmatch.pl
index 6f92b024fb9cc82c90beee1377a005bc0f627c7f..4d6759ec4f46193d4b50a531ca4eb342b7870cfb 100644
--- a/misc-scripts/protein_match/pmatch.pl
+++ b/misc-scripts/protein_match/pmatch.pl
@@ -11,7 +11,7 @@
use strict;
-use Getopt::Std;
+use Getopt::Long;
#use vars qw($opt_q $opt_t $opt_l $opt_o $t_thr $q_thr $opt_w $opt_s $opt_c $opt_d);
BEGIN {
@@ -39,6 +39,17 @@ my $t_thr = $conf{'target_idt'};
my $q_thr = $conf{'query_idt'};
my $pmatch_bin = $conf{'pmatch'};
my ($opt_w,$opt_l,$opt_d);
+my $help;
+
+
+&GetOptions(
+ 'help' => \$help,
+ );
+
+if ($help) {
+ print STDERR $conf{'help'}."\n";
+ exit();
+}
#Check if the configuration file is correct
my %check;
diff --git a/misc-scripts/protein_match/prepare_proteome.pl b/misc-scripts/protein_match/prepare_proteome.pl
index afa8997a8c64ddb5d30de8d4cea14f1503f2388e..0661f849530e7a93c57f87481791b032579fdc01 100755
--- a/misc-scripts/protein_match/prepare_proteome.pl
+++ b/misc-scripts/protein_match/prepare_proteome.pl
@@ -1,6 +1,6 @@
#!/usr/local/bin/perl -w
use strict;
-
+use Getopt::Long;
=head1 NAME
prepare_proteome.pl
@@ -49,8 +49,11 @@ BEGIN {
require "mapping_conf.pl";
}
+
+#Global var
my %conf = %::mapping_conf;
+my $org_list = $conf{'organism_list'};
my $refseq = $conf{'refseq_fa'};
my $sptr = $conf{'sptr_fa'};
my $protfile = $conf{'pmatch_input_fa'};
@@ -58,6 +61,148 @@ my $pmatch = $conf{'pmatch'};
my $organism = $conf{'organism'};
my $refseq_pred = $conf{'refseq_pred_fa'};
my $sub_genes = $conf{'submitted_genes'};
+my $help;
+
+
+&GetOptions(
+ 'help' => \$help,
+ );
+
+if ($help) {
+ print STDERR $conf{'help'}."\n";
+ exit();
+}
+
+
+#Check that the configuration file has been well filled in for each different organism
+#Beginning of check
+
+my %check;
+my $seenorg = 0;
+
+#Check if the organism is correct
+foreach my $or (@{$org_list}) {
+ if ($or eq $organism) {
+ $seenorg = 1;
+ }
+}
+
+if ($seenorg == 0) {
+ print STDERR "Either the organism name you are using ($organism) is not define or is not allowed\n";
+ print STDERR "Here is a list of authorised organisms:\n";
+ foreach my $or (@{$org_list}) {
+ print STDERR "$or\n";
+ }
+
+ exit();
+}
+
+
+#Organism specific checks
+if($organism eq "human") {
+ $check{'sptr_swiss'} = $conf{'sptr_swiss'};
+ $check{'refseq_gnp'} = $conf{'refseq_gnp'};
+ $check{'pmatch_input_fa'} = $conf{'pmatch_input_fa'};
+ $check {'pmatch'} = $conf{'pmatch'};
+
+ foreach my $k (keys %check) {
+ if ($check{$k} !~ /(\S+)/) {
+ usage();
+ }
+ }
+
+}
+
+if ($organism eq "mouse") {
+ $check{'sptr_swiss'} = $conf{'sptr_swiss'};
+ $check{'refseq_gnp'} = $conf{'refseq_gnp'};
+ $check{'pmatch_input_fa'} = $conf{'pmatch_input_fa'};
+ $check {'pmatch'} = $conf{'pmatch'};
+
+ foreach my $k (keys %check) {
+ print STDERR $check{$k}."\n";
+ if ($check{$k} !~ /(\S+)/) {
+ usage();
+ }
+ }
+
+}
+
+if ($organism eq "elegans") {
+ $check{'sptr_swiss'} = $conf{'sptr_swiss'};
+ $check{'pmatch_input_fa'} = $conf{'pmatch_input_fa'};
+ $check {'pmatch'} = $conf{'pmatch'};
+
+ foreach my $k (keys %check) {
+ print STDERR $check{$k}."\n";
+ if ($check{$k} !~ /(\S+)/) {
+ usage();
+ }
+ }
+
+}
+
+if ($organism eq "anopheles") {
+ $check{'sptr_swiss'} = $conf{'sptr_swiss'};
+ $check{'submitted_genes'} = $conf{'submitted_genes'};
+ $check{'pmatch_input_fa'} = $conf{'pmatch_input_fa'};
+ $check {'pmatch'} = $conf{'pmatch'};
+
+ foreach my $k (keys %check) {
+ print STDERR $check{$k}."\n";
+ if ($check{$k} !~ /(\S+)/) {
+ usage();
+ }
+ }
+}
+
+if ($organism eq "drosophila") {
+ $check{'sptr_swiss'} = $conf{'sptr_swiss'};
+ $check{'refseq_gnp'} = $conf{'refseq_gnp'};
+ $check{'pmatch_input_fa'} = $conf{'pmatch_input_fa'};
+ $check {'pmatch'} = $conf{'pmatch'};
+
+ foreach my $k (keys %check) {
+ print STDERR $check{$k}."\n";
+ if ($check{$k} !~ /(\S+)/) {
+ usage();
+ }
+ }
+
+}
+
+if ($organism eq "rat") {
+ $check{'sptr_swiss'} = $conf{'sptr_swiss'};
+ $check{'refseq_gnp'} = $conf{'refseq_gnp'};
+ $check{'pmatch_input_fa'} = $conf{'pmatch_input_fa'};
+ $check {'pmatch'} = $conf{'pmatch'};
+
+ foreach my $k (keys %check) {
+ print STDERR $check{$k}."\n";
+ if ($check{$k} !~ /(\S+)/) {
+ usage();
+ }
+ }
+
+}
+
+if ($organism eq "zebrafish") {
+ $check{'sptr_swiss'} = $conf{'sptr_swiss'};
+ $check{'pmatch_input_fa'} = $conf{'pmatch_input_fa'};
+ $check {'pmatch'} = $conf{'pmatch'};
+
+ foreach my $k (keys %check) {
+ print STDERR $check{$k}."\n";
+ if ($check{$k} !~ /(\S+)/) {
+ usage();
+ }
+ }
+
+}
+
+
+#End of checks
+
print STDERR "Prepare proteome using following files: SPTR ($sptr)\nREFSEQ ($refseq)\nPROTFILE ($protfile)\n";
@@ -286,3 +431,26 @@ sub test_protfile {
unlink $tmpfile;
}
+
+
+sub usage {
+
+ print STDERR <<HELP
+
+Usage: get_Xmapping.pl
+One of the element of the configuration file has not been properly loaded
+for the organism $organism
+Please fill in properly your configuration file
+
+Here is your set up:
+HELP
+;
+
+ foreach my $k (keys %check) {
+ print STDERR "$k:\t$check{$k}\n";
+ }
+
+
+
+ exit();
+}