Newer
Older
#!/bin/sh -
# This script will send a file to netscape with database IDs linked to SRS.
# To customize this script edit the $DATABASES and $SRS_SERVER variable in the
# perl code below and the NETSCAPE variable at the top of the script.
# To enable this in Artemis, sanger_options must be set to true in the options
# file.
# Default browser is mozilla
# If you are under KDE, you should use Konqueror then
# If you are under MAC OS X, use Safari
if [ `uname` = Darwin ]; then
else
for f in /usr/bin/x-www-browser \
/usr/bin/X11/real-netscape \
/usr/bin/firefox \
/usr/bin/iceweasel \
/usr/bin/mozilla; do
if [ -f $f ]; then
NETSCAPE=$f
break
fi
done
if [ ! -f "$NETSCAPE" ]; then
NETSCAPE=`which firefox`
fi
if [ -f "$DIANA_ENVIRONMENT_FILE" ]
then
. $DIANA_ENVIRONMENT_FILE
fi
if [ $# = 0 ]
then
echo no argument given 1>&2
exit 1
fi
file_arg=$1
unique_bit=$$.`hostname`
# sanger hack:
file_arg=`echo $file_arg | sed 's@^/tmp_mnt/nfs/@/nfs/@' | sed 's@^/tmp_mnt/tmp_nfs/@/nfs/@'`
# fix for pcs3:
file_arg=`echo $file_arg | sed 's@^/yeastpub4/@/nfs/disk222/yeastpub4/@'`
# fix for pcs4:
file_arg=`echo $file_arg | sed 's@^/.automount/pcs3/root/nfs/@/nfs/@'`
if [ -f ./$file_arg ]
then
# the file is in the current directory - we need the full path so netscape
# can find the file
new_file=$PWD/$file_arg.$unique_bit.html
else
new_file=$file_arg.$unique_bit.html
fi
###
# sanger fix for /nfs/repository which isn't mounted on workstations:
REPOSITORY=`echo $new_file | sed -n -e 's|^\/nfs\/repository\/\(.*\)\(\/\)\(.*\)$|\3|p'`
if [ "$REPOSITORY" != "" ]; then
if [ ! -d $HOME/artemis_tmp ]; then
mkdir $HOME/artemis_tmp
fi
new_file="$HOME/artemis_tmp/$REPOSITORY"
fi
#
###
cat <<EOF > $new_file
<HTML>
<HEAD>
<TITLE>
Results for $file_arg
</TITLE>
</HEAD>
<BODY>
<PRE>
EOF
perl -e '
BEGIN {
# change these variable to list the databases to search for the IDs - the
# database names should be separated by spaces
$DNA_DATABASES = "embl";
# change this to point to the wgetz script of your SRS server
#$SRS_SERVER = "www.sanger.ac.uk/srs6bin/cgi-bin/wgetz?-e+";
#$SRS_SERVER = "srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+";
$SRS_SERVER = "www.bioinformatics.nl/srsbin/cgi-bin/wgetz?-e+";
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
$PROTEIN_DATABASES =~ s/ /%20/g;
$DNA_DATABASES =~ s/ /%20/g;
%GENEDB_PATTERNS = (tryp => q!Tb\d+\.\d+\.\d+|TRYP_\S+!,
leish => q!LmjF\d+.\d+!);
$GENEDB_PATTERN = join ("|", values %GENEDB_PATTERNS);
$BLAST_START_LINE = "Sequences producing High-scoring Segment Pairs|" .
"Sequences producing significant alignments:";
$FASTA_START_LINE = "The best scores are";
# the list of IDs we have seen so far
@ids = ();
# the list of IDs we have made anchors for so far
@anchored_ids = ();
$db_type = "unknown";
}
sub hyperlink_to_anchor
{
$id = shift;
qq(<a href="#$id">$id</a>);
}
sub hyperlink_id
{
$id = shift;
if ($db_type eq "dna") {
$r = qq#<a href="http://$SRS_SERVER\[\{$DNA_DATABASES\}-ID:$id*]|[\{$DNA_DATABASES\}-AccNumber:$id*]">$id</a>#;
} else {
for my $org (keys %GENEDB_PATTERNS) {
my $pattern = $GENEDB_PATTERNS{$org};
if ($id =~ /$pattern/) {
$r = qq#<a href="http://www.genedb.org/genedb/Search?organism=$org&name=$id">$id</a>#;
return $r
}
}
$r = qq#<a href="http://www.uniprot.org/uniprot/$id">$id</a>#;
#$r = qq#<a href="http://$SRS_SERVER-id+1+\[\{$PROTEIN_DATABASES\}-ID:$id*]|[\{$PROTEIN_DATABASES\}-AccNumber:$id*]+-vn+2">$id</a>#;
#$r = qq#<a href="http://$SRS_SERVER-id+1+\[\{$PROTEIN_DATABASES\}-ID:$id*]|[\{$PROTEIN_DATABASES\}-AccNumber:$id*]">$id</a>#;
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
}
return $r
}
$file_name = $ARGV[0];
if ($file_name =~ /\.gz$/) {
open IN_FILE, "gzip -d < $file_name |" or die "failed to open $file_name\n";
} else {
open IN_FILE, "$file_name" or die "failed to open $file_name\n";
}
while (<IN_FILE>) {
if ($. == 1) {
if (/^\s*([^\s]+)/) {
if (lc $1 eq "blastn" or lc $1 eq "tblastn" or lc $1 eq "tblastx") {
$db_type = "dna";
} else {
if (lc $1 eq "fasta" or lc $1 eq "blastp" or lc $1 eq "blastx") {
$db_type = "protein";
} else {
print "\nWARNING: could not identify file type: $1\n";
}
}
} else {
print "\nWARNING: could not identify file type\n";
}
}
# ignore header lines
if (1..m/$BLAST_START_LINE|$FASTA_START_LINE/) {
print;
next;
}
if (@ids && /^\s*$/) {
$summary_finished = 1;
}
if (/^>?\w+\|\w+\|(\w+)|^(?:(?:>?>?(?:[A-Z]+:)?)(\w+)|($GENEDB_PATTERN))|^(?:(?:>?>?(?:[A-Z]+:)?)(\w+)\\.\d+\s+) /) {
$id = $1;
if (!defined $id) {
$id = $2;
}
if ($summary_finished) {
if ((grep {$_ eq $id} @ids) && (!grep {$_ eq $id} @anchored_ids)) {
# not anchored yet so make it an anchor
if (s/\b$id\b/"<a name=\"$id\">" . (hyperlink_id($id)) . "<\/a>"/e) {
push @anchored_ids, $id;
}
}
} else {
if (!grep {$_ eq $id} @ids) {
push @ids, $id;
}
s/$id/hyperlink_to_anchor($id)/ei;
# if the id occurs once in the line put a link at end of line
s/$/" LINK:" . hyperlink_id($id)/e;
}
}
print;
}
' $file_arg >> $new_file
cat <<EOF >> $new_file;
</PRE>
</BODY>
</HTML>
EOF
# delete it at some point
echo "rm -f $new_file > /dev/null 2>&1" | at now + 12 hours
# MAC OS X => Safari browser
# The command then is the following
if [ -f "/usr/bin/open" -a `uname` = Darwin ]
then
/usr/bin/open $new_file
exit 0
elif [ -f "/Applications/Safari.app/Contents/MacOS/Safari" ]
# For Netscape or mozilla
exit 0
else
echo starting new netscape 2>&1
# netscape isn't running - so start it
($NETSCAPE &)&
# now send the URL. we do things this way so that the script doesn't exit
# until netscape has successfully shown the URL
sleep 1
# don't exit the script until the file is successfully displayed or until
# 40 seconds is up
for i in 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
do
if $NETSCAPE -remote "openURL($new_file)" 2> /dev/null
then