Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Increase the usage of combined assignment operators #76

Open
elfring opened this issue Nov 27, 2021 · 0 comments
Open

Increase the usage of combined assignment operators #76

elfring opened this issue Nov 27, 2021 · 0 comments

Comments

@elfring
Copy link

elfring commented Nov 27, 2021

👀 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/annotation/tools/abinitio/augustus/gaas_junctions2hints.pl b/annotation/tools/abinitio/augustus/gaas_junctions2hints.pl
index a74a6ef..d3ee10f 100755
--- a/annotation/tools/abinitio/augustus/gaas_junctions2hints.pl
+++ b/annotation/tools/abinitio/augustus/gaas_junctions2hints.pl
@@ -47,8 +47,8 @@ while (<INFILE>) {
   unless ($_ =~ /^track/){
     my @bed_line=split(/\t/, $_);
     my ($startblock,$endblock)=split(/\,/, $bed_line[10]);
-    $bed_line[1]=$bed_line[1]+$startblock+1;
-    $bed_line[2]=$bed_line[2]-$endblock;
+    $bed_line[1] += $startblock + 1;
+    $bed_line[2] -= $endblock;
     my $key = join (':',$bed_line[0],$bed_line[1],$bed_line[2]);
     $junctions{$key} +=$bed_line[4];
   }
diff --git a/annotation/tools/comparative_genomic/gaas_orthomcl_analyzeOG.pl b/annotation/tools/comparative_genomic/gaas_orthomcl_analyzeOG.pl
index d16dacc..d01aa93 100755
--- a/annotation/tools/comparative_genomic/gaas_orthomcl_analyzeOG.pl
+++ b/annotation/tools/comparative_genomic/gaas_orthomcl_analyzeOG.pl
@@ -409,7 +409,7 @@ foreach my $keyID (keys %LossIdByAppearance){
             print $message; if ( $opt_output ){ print $outReport $message; }
 
             if(exists ($lossMergedByTaxid{$keyID2})){
-                $lossMergedByTaxid{$keyID2}=$lossMergedByTaxid{$keyID2}+$value;
+                $lossMergedByTaxid{$keyID2} += $value;
             }
             else{
                 $lossMergedByTaxid{$keyID2}=$value;
diff --git a/annotation/tools/comparative_genomic/gaas_prepare_matrice_by_window.pl b/annotation/tools/comparative_genomic/gaas_prepare_matrice_by_window.pl
index e4c6fa3..53c7823 100755
--- a/annotation/tools/comparative_genomic/gaas_prepare_matrice_by_window.pl
+++ b/annotation/tools/comparative_genomic/gaas_prepare_matrice_by_window.pl
@@ -263,7 +263,7 @@ foreach my $chr (keys %hash_chr2name){
     if( (1000000*$currentLimit) > $highvalue){$stop++};
 
     my $nbPrintedVal=0;
-    $currentLimit = $currentLimit + $opt_windowsSize;
+    $currentLimit += $opt_windowsSize;
     $currentCenter=$currentLimit-($opt_windowsSize/2);
     $currentCenter=sprintf "%.1f",$currentCenter;
     $path=$dir."/".$currentCenter."Mb.aln";
diff --git a/annotation/tools/fasta/gaas_fasta_domain_extractor.pl b/annotation/tools/fasta/gaas_fasta_domain_extractor.pl
index abb042c..200df2f 100755
--- a/annotation/tools/fasta/gaas_fasta_domain_extractor.pl
+++ b/annotation/tools/fasta/gaas_fasta_domain_extractor.pl
@@ -114,7 +114,7 @@ if(length($seq) < $end){print "End position for extraction is over the sequence
 #start is 1-based coordinate system
 # The extraction compute in 0-based coordinate system
 # Lets change the 1-based coordinate system in 0-based coordinate system for the start
-$start=$start-1;
+$start -= 1;
 my $lengtExtraction=$end-$start; #Length in 0-based coordinate (in 1-based coordinate we must add +1)
 print "Length sequence extracted: $lengtExtraction\n";
 my $extractedPart=substr($seq, $start, $lengtExtraction);
diff --git a/annotation/tools/fasta/gaas_fasta_extract_sequence_from_id.pl b/annotation/tools/fasta/gaas_fasta_extract_sequence_from_id.pl
index d962388..3408f05 100755
--- a/annotation/tools/fasta/gaas_fasta_extract_sequence_from_id.pl
+++ b/annotation/tools/fasta/gaas_fasta_extract_sequence_from_id.pl
@@ -81,7 +81,7 @@ if (-f $opt_name){
   if (! defined $col){
     $col=0;
   }
-  else{$col=$col -1 ;}
+  else{$col -= 1 ;}
 
   #Manage line to avoid
   if (! defined $lineToAvoid){
diff --git a/annotation/tools/fasta/gaas_fasta_splitter.pl b/annotation/tools/fasta/gaas_fasta_splitter.pl
index 44290ed..8767440 100755
--- a/annotation/tools/fasta/gaas_fasta_splitter.pl
+++ b/annotation/tools/fasta/gaas_fasta_splitter.pl
@@ -342,7 +342,7 @@ sub split_fasta{
 
 								if ($next_size < ceil($split_size/2) ){
 
-									$size = $size+$next_size;
+									$size += $next_size;
 									$continue = undef;
 									print "attach: attach because next_size $next_size < $split_size / 2(ceil) \n";
 
diff --git a/annotation/tools/fastq/gaas_fastq_check_sync_pair1_pair2.pl b/annotation/tools/fastq/gaas_fastq_check_sync_pair1_pair2.pl
index 42fbfc1..098d37e 100755
--- a/annotation/tools/fastq/gaas_fastq_check_sync_pair1_pair2.pl
+++ b/annotation/tools/fastq/gaas_fastq_check_sync_pair1_pair2.pl
@@ -114,7 +114,7 @@ while (!eof($in1) and !eof($in2)) {
 }
 
 my $percent = ($read_fail / $read_cpt) * 100 ;
-$percent = $percent * 100; # make it percent
+$percent *= 100; # make it percent
 $percent = sprintf("%.2f", $percent);
 
 my $end_run = time();
@@ -141,7 +141,7 @@ sub concat_list_from_left{
 
   my $result="";
   foreach my $element (@{$list}){
-    $result = $result.$element;
+    $result .= $element;
   }
 
   return $result;
diff --git a/annotation/tools/fastq/gaas_fastq_deinterleave_bash.pl b/annotation/tools/fastq/gaas_fastq_deinterleave_bash.pl
index 9176713..1771ae0 100755
--- a/annotation/tools/fastq/gaas_fastq_deinterleave_bash.pl
+++ b/annotation/tools/fastq/gaas_fastq_deinterleave_bash.pl
@@ -112,7 +112,7 @@ sub concat_list_from_left{
 
   my $result="";
   foreach my $element (@{$list}){
-    $result = $result.$element;
+    $result .= $element;
   }
 
   return $result;
diff --git a/annotation/tools/ncbi/gaas_ncbi_get_sequence_from_list.pl b/annotation/tools/ncbi/gaas_ncbi_get_sequence_from_list.pl
index 524846d..3c620a4 100755
--- a/annotation/tools/ncbi/gaas_ncbi_get_sequence_from_list.pl
+++ b/annotation/tools/ncbi/gaas_ncbi_get_sequence_from_list.pl
@@ -82,7 +82,7 @@ else{
 if (! defined $col){
 	$col=0;
 }
-else{$col=$col -1 ;}
+else{$col -= 1 ;}
 
 #Manage line to avoid
 if (! defined $lineToAvoid){
diff --git a/bin/gaas_fasta_domain_extractor.pl b/bin/gaas_fasta_domain_extractor.pl
index abb042c..200df2f 100755
--- a/bin/gaas_fasta_domain_extractor.pl
+++ b/bin/gaas_fasta_domain_extractor.pl
@@ -114,7 +114,7 @@ if(length($seq) < $end){print "End position for extraction is over the sequence
 #start is 1-based coordinate system
 # The extraction compute in 0-based coordinate system
 # Lets change the 1-based coordinate system in 0-based coordinate system for the start
-$start=$start-1;
+$start -= 1;
 my $lengtExtraction=$end-$start; #Length in 0-based coordinate (in 1-based coordinate we must add +1)
 print "Length sequence extracted: $lengtExtraction\n";
 my $extractedPart=substr($seq, $start, $lengtExtraction);
diff --git a/bin/gaas_fasta_extract_sequence_from_id.pl b/bin/gaas_fasta_extract_sequence_from_id.pl
index d962388..3408f05 100755
--- a/bin/gaas_fasta_extract_sequence_from_id.pl
+++ b/bin/gaas_fasta_extract_sequence_from_id.pl
@@ -81,7 +81,7 @@ if (-f $opt_name){
   if (! defined $col){
     $col=0;
   }
-  else{$col=$col -1 ;}
+  else{$col -= 1 ;}
 
   #Manage line to avoid
   if (! defined $lineToAvoid){
diff --git a/bin/gaas_fasta_splitter.pl b/bin/gaas_fasta_splitter.pl
index 44290ed..8767440 100755
--- a/bin/gaas_fasta_splitter.pl
+++ b/bin/gaas_fasta_splitter.pl
@@ -342,7 +342,7 @@ sub split_fasta{
 
 								if ($next_size < ceil($split_size/2) ){
 
-									$size = $size+$next_size;
+									$size += $next_size;
 									$continue = undef;
 									print "attach: attach because next_size $next_size < $split_size / 2(ceil) \n";
 
diff --git a/bin/gaas_fastq_check_sync_pair1_pair2.pl b/bin/gaas_fastq_check_sync_pair1_pair2.pl
index 42fbfc1..098d37e 100755
--- a/bin/gaas_fastq_check_sync_pair1_pair2.pl
+++ b/bin/gaas_fastq_check_sync_pair1_pair2.pl
@@ -114,7 +114,7 @@ while (!eof($in1) and !eof($in2)) {
 }
 
 my $percent = ($read_fail / $read_cpt) * 100 ;
-$percent = $percent * 100; # make it percent
+$percent *= 100; # make it percent
 $percent = sprintf("%.2f", $percent);
 
 my $end_run = time();
@@ -141,7 +141,7 @@ sub concat_list_from_left{
 
   my $result="";
   foreach my $element (@{$list}){
-    $result = $result.$element;
+    $result .= $element;
   }
 
   return $result;
diff --git a/bin/gaas_fastq_deinterleave_bash.pl b/bin/gaas_fastq_deinterleave_bash.pl
index 9176713..1771ae0 100755
--- a/bin/gaas_fastq_deinterleave_bash.pl
+++ b/bin/gaas_fastq_deinterleave_bash.pl
@@ -112,7 +112,7 @@ sub concat_list_from_left{
 
   my $result="";
   foreach my $element (@{$list}){
-    $result = $result.$element;
+    $result .= $element;
   }
 
   return $result;
diff --git a/bin/gaas_junctions2hints.pl b/bin/gaas_junctions2hints.pl
index a74a6ef..d3ee10f 100755
--- a/bin/gaas_junctions2hints.pl
+++ b/bin/gaas_junctions2hints.pl
@@ -47,8 +47,8 @@ while (<INFILE>) {
   unless ($_ =~ /^track/){
     my @bed_line=split(/\t/, $_);
     my ($startblock,$endblock)=split(/\,/, $bed_line[10]);
-    $bed_line[1]=$bed_line[1]+$startblock+1;
-    $bed_line[2]=$bed_line[2]-$endblock;
+    $bed_line[1] += $startblock + 1;
+    $bed_line[2] -= $endblock;
     my $key = join (':',$bed_line[0],$bed_line[1],$bed_line[2]);
     $junctions{$key} +=$bed_line[4];
   }
diff --git a/bin/gaas_ncbi_get_sequence_from_list.pl b/bin/gaas_ncbi_get_sequence_from_list.pl
index 524846d..3c620a4 100755
--- a/bin/gaas_ncbi_get_sequence_from_list.pl
+++ b/bin/gaas_ncbi_get_sequence_from_list.pl
@@ -82,7 +82,7 @@ else{
 if (! defined $col){
 	$col=0;
 }
-else{$col=$col -1 ;}
+else{$col -= 1 ;}
 
 #Manage line to avoid
 if (! defined $lineToAvoid){
diff --git a/bin/gaas_orthomcl_analyzeOG.pl b/bin/gaas_orthomcl_analyzeOG.pl
index d16dacc..d01aa93 100755
--- a/bin/gaas_orthomcl_analyzeOG.pl
+++ b/bin/gaas_orthomcl_analyzeOG.pl
@@ -409,7 +409,7 @@ foreach my $keyID (keys %LossIdByAppearance){
             print $message; if ( $opt_output ){ print $outReport $message; }
 
             if(exists ($lossMergedByTaxid{$keyID2})){
-                $lossMergedByTaxid{$keyID2}=$lossMergedByTaxid{$keyID2}+$value;
+                $lossMergedByTaxid{$keyID2} += $value;
             }
             else{
                 $lossMergedByTaxid{$keyID2}=$value;
diff --git a/bin/gaas_prepare_matrice_by_window.pl b/bin/gaas_prepare_matrice_by_window.pl
index e4c6fa3..53c7823 100755
--- a/bin/gaas_prepare_matrice_by_window.pl
+++ b/bin/gaas_prepare_matrice_by_window.pl
@@ -263,7 +263,7 @@ foreach my $chr (keys %hash_chr2name){
     if( (1000000*$currentLimit) > $highvalue){$stop++};
 
     my $nbPrintedVal=0;
-    $currentLimit = $currentLimit + $opt_windowsSize;
+    $currentLimit += $opt_windowsSize;
     $currentCenter=$currentLimit-($opt_windowsSize/2);
     $currentCenter=sprintf "%.1f",$currentCenter;
     $path=$dir."/".$currentCenter."Mb.aln";
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
1 participant
@elfring