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Commit c4204a2b authored by Ian Longden's avatar Ian Longden
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reduce description to the RecNAME full or if that is not present the Subname... 

reduce description to the RecNAME full or if that is not present the Subname Full. Also remove EC numbers
parent fbb48359
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misc-scripts/xref_mapping/XrefParser/UniProtParser.pm
+ 12
− 84
View file @ c4204a2b
......@@ -349,64 +349,13 @@ sub create_xrefs {
# extract ^DE lines only & build cumulative description string
my $description = " ";
my $name = "";
my $flags = " ";
my $mode = "";
my $sub_description = "";
foreach my $line (@all_lines) {
next if(!($line =~ /^DE/));
# Set up the mode first
if($line =~ /^DE RecName:/){
if($mode eq "RecName"){
$description .= ";";
}
$mode = "RecName";
}
elsif($line =~ /^DE SubName:/){
if($mode eq "RecName"){
$description .= ";";
}
$mode = "RecName";
}
elsif($line =~ /^DE AltName:/){
$mode = "AltName";
}
elsif($line =~ /^DE Contains:/){
if($mode eq "Contains"){
$description .= ";";
}
elsif($mode eq "Includes"){
$description .= "][Contains ";
}
else{
$description .= " [Contains ";
}
$mode = "Contains";
next;
}
elsif($line =~ /^DE Includes:/){
if($mode eq "Includes"){
$description .= ";";
}
elsif($mode eq "Contains"){
$description .= "][Includess";
}
else{
$description .= " [Includes ";
}
$mode = "Includes";
next;
}
elsif($line =~ /^DE Flags: (.*);/){
$flags .= "$1 ";
next;
}
# now get the data
# get the data
if($line =~ /^DE RecName: Full=(.*);/){
$name .= $1;
}
......@@ -416,40 +365,19 @@ sub create_xrefs {
elsif($line =~ /SubName: Full=(.*);/){
$name .= $1;
}
elsif($line =~ /AltName: Full=(.*);/){
$description .= "(".$1.")";
}
elsif($line =~ /Short=(.*);/){
$description .= "(".$1.")";
}
elsif($line =~ /EC=(.*);/){
$description .= "(EC ".$1.")";
}
elsif($line =~ /Allergen=(.*);/){
$description .= "(Allergen ".$1.")";
}
elsif($line =~ /INN=(.*);/){
$description .= "(".$1.")";
}
elsif($line =~ /Biotech=(.*);/){
$description .= "(".$1.")";
}
elsif($line =~ /CD_antigen=(.*);/){
$description .= "(".$1." antigen)";
}
else{
print STDERR "unable to process *$line* for $acc\n";
}
}
if($mode eq "Contains" or $mode eq "Includes"){
$description .= "]";
}
$description =~ s/^\s*//g;
$description =~ s/\s*$//g;
$description =~ s/^\s*//g;
$description =~ s/\s*$//g;
$xref->{DESCRIPTION} = $name.$flags.$description;
my $desc = $name.$description;
if(!length($desc)){
$desc = $sub_description;
}
$desc =~ s/\(\s*EC\s*\S*\)//g;
$xref->{DESCRIPTION} = $desc;
}
# extract sequence
my ($seq) = $_ =~ /SQ\s+(.+)/s; # /s allows . to match newline
......
misc-scripts/xref_mapping/XrefParser/UniProtParser_descriptions_only.pm
+ 10
− 80
View file @ c4204a2b
......@@ -282,61 +282,13 @@ sub create_xrefs {
# extract ^DE lines only & build cumulative description string
my $description = " ";
my $name = "";
my $flags = " ";
my $mode = "";
my $sub_description = "";
foreach my $line (@all_lines) {
next if(!($line =~ /^DE/));
# Set up the mode first
if($line =~ /^DE RecName:/){
if($mode eq "RecName"){
$description .= "; ";
}
$mode = "RecName";
}
elsif($line =~ /^DE SubName:/){
if($mode eq "RecName"){
$description .= "; ";
}
$mode = "RecName";
}
elsif($line =~ /^DE AltName:/){
$mode = "AltName";
}
elsif($line =~ /^DE Contains:/){
if($mode eq "Contains"){
$description .= "; ";
}
elsif($mode eq "Includes"){
$description .= "][Contains ";
}
else{
$description .= " [Contains ";
}
$mode = "Contains";
next;
}
elsif($line =~ /^DE Includes:/){
if($mode eq "Includes"){
$description .= "; ";
}
elsif($mode eq "Contains"){
$description .= "][Includess";
}
else{
$description .= " [Includes ";
}
$mode = "Includes";
next;
}
elsif($line =~ /^DE Flags: (.*);/){
$flags .= "$1 ";
next;
}
# now get the data
# get the data
if($line =~ /^DE RecName: Full=(.*);/){
$name .= $1;
}
......@@ -344,41 +296,19 @@ sub create_xrefs {
$description .= $1;
}
elsif($line =~ /SubName: Full=(.*);/){
$description .= $1;
}
elsif($line =~ /AltName: Full=(.*);/){
$description .= "(".$1.")";
$sub_description .= $1;
}
elsif($line =~ /Short=(.*);/){
$description .= "(".$1.")";
}
elsif($line =~ /EC=(.*);/){
$description .= "(EC ".$1.")";
}
elsif($line =~ /Allergen=(.*);/){
$description .= "(Allergen ".$1.")";
}
elsif($line =~ /INN=(.*);/){
$description .= "(".$1.")";
}
elsif($line =~ /Biotech=(.*);/){
$description .= "(".$1.")";
}
elsif($line =~ /CD_antigen=(.*);/){
$description .= "(".$1." antigen)";
}
else{
print STDERR "unable to process *$line* for $acc\n";
}
}
if($mode eq "Contains" or $mode eq "Includes"){
$description .= "]";
}
$description =~ s/^\s*//g;
$description =~ s/\s*$//g;
$xref->{DESCRIPTION} = $name.$flags.$description;
my $desc = $name.$description;
if(!length($desc)){
$desc = $sub_description;
}
$desc =~ s/\(\s*EC\s*\S*\)//g;
$xref->{DESCRIPTION} = $desc;
push @xrefs, $xref;
......
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