Commit 264a0ab4 authored by Sebastien Moretti's avatar Sebastien Moretti
Browse files

Cleaning

parent 7e8b670c
......@@ -1199,18 +1199,18 @@ sub prepareResults4BOJ{
my $description = $annot;
my $readyname = '';
$readyname = fastaHeaders4ProtoGene($input_name);
if ( $intronLess =~ /\:.+/ || $bestOne =~ /^N[CTWZG]_/ || $bestOne =~ /^AC_/ || $nameLess =~ /^N[CTWZG]_/ || $nameLess =~ /^AC_/ ){
$readyname =~ s/_G_@@/_G_${bestOne}-IntronLess _S_ $blastHit _DESC_ / if ( $nameLess eq '' );
$readyname =~ s/_G_@@/_G_${nameLess}-IntronLess _S_ $blastHit _DESC_ / if ( $nameLess ne '' );
if ( $intronLess =~ /:.+/ || $bestOne =~ /^N[CTWZG]_/ || $bestOne =~ /^AC_/ || $nameLess =~ /^N[CTWZG]_/ || $nameLess =~ /^AC_/ ){
$readyname =~ s/_G_@@/_G_${bestOne}-IntronLess _S_ $blastHit _DESC_ / if ( $nameLess eq '' );
$readyname =~ s/_G_@@/_G_${nameLess}-IntronLess _S_ $blastHit _DESC_ / if ( $nameLess ne '' );
$readyname =~ s/(.)$/$1 MATCHES_ON $description/ if ( $description ne '' );
$bestOne = $nameLess if ( $nameLess ne '' );
$bestOne = $nameLess if ( $nameLess ne '' );
}
else{
$readyname =~ s/_G_@@/_G_Unavailable _S_ $blastHit _DESC_ /;
$bestOne = '';
}
$readyname =~ s/ +/ /g;
$resultBOJ = ">".$readyname."\n".$input_seq."\n";
$resultBOJ = '>'.$readyname."\n".$input_seq."\n";
}
return($resultBOJ, $bestOne);
......@@ -1307,7 +1307,7 @@ sub buildBOJseq{
}
else{
$countNoGapPos++;
$bojSeq .= lc($EXONBORDERS{$countNoGapPos}) if ( exists($EXONBORDERS{$countNoGapPos}) );
$bojSeq .= lc($EXONBORDERS{$countNoGapPos}) if ( exists($EXONBORDERS{$countNoGapPos}) );
$bojSeq .= uc($whatIs) if ( !exists($EXONBORDERS{$countNoGapPos}) );
}
}
......@@ -1361,7 +1361,7 @@ sub buildIntronlessBOJOutputFile{
my $annot = getFastaHeaderAnnot($NTstatus);
my $readyname = '';
$readyname = fastaHeaders4ProtoGene($original_name);
$NTstatus =~ s/\:.+$//;
$NTstatus =~ s/:.+$//;
$readyname =~ s/_G_@@/_G_$NTstatus-IntronLess _S_ $BLASTstatus _DESC_ / if ( $NTname eq '' );
$readyname =~ s/_G_@@/_G_$NTname-IntronLess _S_ $BLASTstatus _DESC_ / if ( $NTname ne '' );
$readyname =~ s/(.)$/$1 MATCHES_ON $annot/ if ( $annot ne '' );
......
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