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👀 Some source code analysis tools can help to find opportunities for improving software components.
💭 I propose to increase the usage of combined operators accordingly.
diff --git a/fdog/bin/hamstr.pl b/fdog/bin/hamstr.pl
index 3feb01e..c56ecdb 100755
--- a/fdog/bin/hamstr.pl+++ b/fdog/bin/hamstr.pl@@ -1150,7 +1150,7 @@ sub checkInput {
elsif (-e $blastpathtmp . '_prot' . $blastdbend){
## the check for the file naming '_prot' is only to maintain backward compatibility
$blastapp = '_prot';
- $blastpathtmp = $blastpathtmp . $blastapp;+ $blastpathtmp .= $blastapp;
push @log, "\tcheck for $blastpathtmp succeeded";
printOUT("succeeded\n");
}
diff --git a/fdog/bin/oneSeq.pl b/fdog/bin/oneSeq.pl
index a99e1e6..6a8a61b 100755
--- a/fdog/bin/oneSeq.pl+++ b/fdog/bin/oneSeq.pl@@ -586,7 +586,7 @@ if (!$coreex) {
print "Added TAXON: $addedTaxon\t$addedTaxonName\n";
#if a new core ortholog was found
if($addedTaxon ne "") {
- $hamstrSpecies = $hamstrSpecies . "," . $addedTaxon;+ $hamstrSpecies .= "," . $addedTaxon;
clearTmpFiles();
@@ -865,7 +865,7 @@ sub getAlnScores{
unless ($silent) {
print "Cumulative alignmentscore is: $score\n";
}
- $scores{$key} = $scores{$key} / $maxAlnScore;+ $scores{$key} /= $maxAlnScore;
$score = $scores{$key};
unless ($silent) {
print "Normalised alignmentscore is: $score\n";
@@ -1151,7 +1151,7 @@ sub checkOptions {
}
my $output = '';
for (my $i = 0; $i < @refTaxonlist; $i++) {
- $output = $output . "[$i]" . "\t" . $refTaxonlist[$i] . "\n";+ $output .= "[$i]\t" . $refTaxonlist[$i] . "\n";
}
### for debug?
# for (keys %taxa){
@@ -1279,7 +1279,7 @@ sub checkOptions {
}
print "Your sequence was named: " . $seqName . "\n\n";
}
- $outputPath = $outputPath . "/$seqName";+ $outputPath .= "/$seqName";
if (! -d "$outputPath"){
mkdir "$outputPath", 0777 or die "could not create the output directory $outputPath";
}
@@ -1526,7 +1526,7 @@ sub fetchSequence {
my $line = $_;
chomp($line);
unless($line =~ /^\>.*/) {
- $seq = $seq . $line;+ $seq .= $line;
}
}
close INPUT;
@@ -1719,7 +1719,7 @@ sub cumulativeAlnScore{
if($line[0] && ($line[0] eq $shortedId)){
if(exists $cumscores{$key}) {
$gotScore = 1;
- $cumscores{$key} = $cumscores{$key} + $line[2];+ $cumscores{$key} += $line[2];
}else{
$gotScore = 1;
$cumscores{$key} = $line[2];
@@ -1938,7 +1938,7 @@ sub runHamstr {
if (! -e $taxaDir) {
## backward compatibility. I used to name the dirs with the ending .dir
if (-e "$taxaDir.dir"){
- $taxaDir = $taxaDir . '.dir';+ $taxaDir .= '.dir';
}
}
$taxaDir =~ s/\s*//g;
diff --git a/fdog/bin/translate.pl b/fdog/bin/translate.pl
index 68ee444..2fe04dd 100755
--- a/fdog/bin/translate.pl+++ b/fdog/bin/translate.pl@@ -167,7 +167,7 @@ sub checkIds {
$id =~ s/|.*//;
}
elsif ($check == 2) {
- $id = $id . '_' . $seq_object[$i]->desc;+ $id .= '_' . $seq_object[$i]->desc;
$id =~ s/(.{0,$limit}).*/$1/;
}
if (defined $counter->{$id}) {
The text was updated successfully, but these errors were encountered:
👀 Some source code analysis tools can help to find opportunities for improving software components.
💭 I propose to increase the usage of combined operators accordingly.
The text was updated successfully, but these errors were encountered: