# HG changeset patch
# User clifinder
# Date 1581503558 18000
# Node ID 6d7caeea1e74c3cb9c388b07307d9f023a60ed81
# Parent  feecd33c83901f9bb1910d0ed56df615c4df8914
"planemo upload for repository https://github.com/GReD-Clermont/CLIFinder/ commit 2a3a263fc5a2123e6988872d23057f8797231a76"

diff -r feecd33c8390 -r 6d7caeea1e74 script/CLIFinder.pl
--- a/script/CLIFinder.pl	Tue Feb 11 09:28:56 2020 -0500
+++ b/script/CLIFinder.pl	Wed Feb 12 05:32:38 2020 -0500
@@ -45,8 +45,8 @@
   "min_L1:i"      => \(my $min_L1 = 50),
   "mis_L1:i"      => \(my $mis_L1 = 2),
   "threads:i"     => \(my $threads = 1),
-  'help'          => sub { HelpMessage(0); },
-  'version'       => sub { VersionMessage(0); },
+  "help"          => sub { HelpMessage(0); },
+  "version"       => sub { VersionMessage(0); },
 ) or HelpMessage(1);
 
 HelpMessage(1) unless @fastq1 && @fastq2 && @name && defined($TE) && defined($ref) && defined($rmsk_source) && defined($refseq) && defined($html) && defined($html_repertory);
@@ -95,10 +95,10 @@
   # Paired end mapping against L1 promoter sequences#
   ###################################################
   
-  print STDOUT "Alignement of $name[$tabR] to L1\n";
+  print STDOUT "Alignment of $name[$tabR] to L1\n";
   my $sam = $html_repertory.'/'.$name[$tabR]."_L1.sam"; push(@garbage, $sam);
   align_paired( $TE, $fastq1[$tabR], $fastq2[$tabR], $sam, $threads, $mis_auth);
-  print STDOUT "Alignement done\n";
+  print STDOUT "Alignment done\n";
   
   ##################################################
   # Creation of two fastq for paired halfed mapped:#
@@ -107,18 +107,15 @@
   ##################################################
   
   print STDOUT "Getting pairs with one mate matched to L1 and the other mate undetected by repeatmasker as a repeat sequence\n";
-  
   my $out_ASP_1 = $html_repertory.'/'.$name[$tabR]."_1.fastq"; push(@garbage, $out_ASP_1);
   my $out_ASP_2 = $html_repertory.'/'.$name[$tabR]."_2.fastq"; push(@garbage, $out_ASP_2);
   
   ##split mate that matched to L1 and others##
   my ($ASP_readsHashR, $half_num_out) = get_half($sam, $mis_L1, $min_L1, $Bdir);
-  # $ASP_reads{$line[0]}[0] mapped - $ASP_reads{$line[0]}[1] unmapped
+  print STDOUT "Number of half mapped pairs: $half_num_out\n";
   
   ##pairs obtained after repeatmasker on the other mate##
   my $left = sort_out($threads, $out_ASP_1, $out_ASP_2, $dprct, $eprct, $ASP_readsHashR, $html_repertory);
-
-  print STDOUT "Number of half mapped pairs : $half_num_out\n";
   print STDOUT "Number of pairs after repeatmasker: $left\n";
   
   ##################################################
@@ -168,9 +165,9 @@
 my $merge_target = $html_repertory.'/target_merged.bed'; push(@garbage, $merge_target);
 my $merge = $html_repertory.'/merged.bed'; push(@garbage, $merge);
 
-open (my $mT, ">".$merge_target) || die "cannot open $merge_target\n";
-open (my $m, ">".$merge) || die "cannot open $merge\n";
-open (my $in, $repMsecond) || die "cannot open secondM\n";
+open (my $mT, ">".$merge_target) || die "Cannot open $merge_target\n";
+open (my $m, ">".$merge) || die "Cannot open $merge\n";
+open (my $in, $repMsecond) || die "Cannot open $repMsecond\n";
 my $cmp = 0;
 while (<$in>)
 {
@@ -185,7 +182,7 @@
 }
 
 $cmp = 0;
-open ($in, $repMfirst) || die "cannot open firstM\n";
+open ($in, $repMfirst) || die "Cannot open $repMfirst\n";
 while (<$in>)
 {
   chomp $_;
@@ -313,9 +310,9 @@
 sub filter_convert_rmsk
 {
   my ($source, $bed, $line_only) = @_;
-  open(my $input, $source) || die "cannot open rmsk file! $!\n"; ## Open source file
-  open(my $bedfile, ">".$bed) || die "cannot open output bed file for rmsk! $!\n"; ## Open bed file
-  open(my $linefile, ">".$line_only) || die "cannot open output LINE-only file for rmsk! $!\n"; ## Open line_only file
+  open(my $input, $source) || die "Cannot open rmsk file! $!\n"; ## Open source file
+  open(my $bedfile, ">".$bed) || die "Cannot open output bed file for rmsk! $!\n"; ## Open bed file
+  open(my $linefile, ">".$line_only) || die "Cannot open output LINE-only file for rmsk! $!\n"; ## Open line_only file
   my @headers;
   my %indices;
 
@@ -491,7 +488,7 @@
   my $mis_L1 = shift;
   my $min_L1 = shift;
   my $Bdir = shift;
-  open(my $fic, $sam) || die "cannot open sam file! $!\n"; ## Open file
+  open(my $fic, $sam) || die "Cannot open sam file! $!\n"; ## Open file
   my (%ASP_reads); my $cmp = 0; ## Declare variables for
   my $sequence = '';
   my $score = '';
@@ -594,7 +591,7 @@
   
   ##Write on file containing of readssHashTabR
   
-  open(my $tmp, ">".$second) || die "cannot open temp file $second\n";
+  open(my $tmp, ">".$second) || die "Cannot open temp file $second\n";
   while ( my ($k,$v) = each %{$readsHashTabR} )
   {
     print $tmp ${$v}[1] if defined(${$v}[1]);
@@ -609,7 +606,7 @@
   
   `RepeatMasker -s -pa $threads -dir $repout -engine hmmer -species human $fa`;
   my $repfile = $repout.$name.".fa.out";
-  open (my $rep, $repfile) || die "cannot open $repfile $!\n";
+  open (my $rep, $repfile) || die "Cannot open $repfile $!\n";
   while(<$rep>)
   {
     chomp;
@@ -635,8 +632,8 @@
   }
   
   ##write resulting reads in both files for paired ##
-  open(my $accepted_1, ">".$out1 ) || die "cannot open $out1 file $!\n";
-  open(my $accepted_2, ">".$out2 ) || die "cannot open $out2 file $!\n";
+  open(my $accepted_1, ">".$out1 ) || die "Cannot open $out1 file $!\n";
+  open(my $accepted_2, ">".$out2 ) || die "Cannot open $out2 file $!\n";
   while ( my ($k,$v) = each %{$readsHashTabR} )
   {
     if ( defined (${$v}[0]) && defined (${$v}[1]) )
@@ -752,8 +749,8 @@
   }
   
   ## get only first mate that have less tant $iprct repeats ##
-  open (my $tmp_fi, 'temp_name_first') || die "cannot open $namefirst!\n";
-  open (my $nam_fi, ">".$namefirst) || die "cannot open $namefirst!\n";
+  open (my $tmp_fi, 'temp_name_first') || die "Cannot open $namefirst!\n";
+  open (my $nam_fi, ">".$namefirst) || die "Cannot open $namefirst!\n";
   while (<$tmp_fi>)
   {
     my @line = split /\t/, $_;
@@ -771,8 +768,8 @@
   
   ## get only  second mate that have less than $iprct repeats ##
 
-  open (my $tmp_sec, 'temp_name_second') || die "cannot open $namesecond!\n";
-  open (my $nam_sec, ">".$namesecond) || die "cannot open $namesecond!\n";
+  open (my $tmp_sec, 'temp_name_second') || die "Cannot open $namesecond!\n";
+  open (my $nam_sec, ">".$namesecond) || die "Cannot open $namesecond!\n";
   while (<$tmp_sec>)
   {
     my @line = split /\t/, $_;
@@ -785,22 +782,6 @@
   close $tmp_sec; close $nam_sec;
 }
 
-#sub results
-#{
-#  my ($out_repertory, $file, $name, $hashRef,$ps) = @_;
-#  my $namefirst = $out_repertory.'/'.$name.'-first.bed'; push(@garbage, $namefirst);
-#  my $namesecond = $out_repertory.'/'.$name.'-second.bed'; push(@garbage, $namesecond);
-#  `samtools view -Sb -f66 $file | bedtools bamtobed -i /dev/stdin > $namefirst`;
-#  `samtools view -Sb -f130 $file | bedtools bamtobed -i /dev/stdin > $namesecond`;
-#  open( my $in, $out_repertory.'/'.$name.'-first.bed') || die "cannot open first read bed\n";
-#  while (<$in>)
-#  {
-#    my @line = split /\t/, $_;
-#    $line[3] =~ /(.*?)\/1/;
-#    ${$hashRef}{$1}= $ps;
-#  }
-#}
-
 
 ############################################################
 ##Function blast: blast nucleotide sequences on ref      ###
@@ -833,7 +814,7 @@
 {
   my $file = shift;
   my %hash = ();
-  open (my $f, $file) || die "cannot open $file\n";
+  open (my $f, $file) || die "Cannot open $file\n";
   while (<$f>)
   {
     chomp $_;
@@ -910,7 +891,7 @@
 
   my $chimOut = $html;
   
-  open(my $tab, ">".$chimOut) || die "cannot open $chimOut";
+  open(my $tab, ">".$chimOut) || die "Cannot open $chimOut";
   print_header($tab,"Chimerae");
   print $tab "\t\t<tr>\n\t\t\t<th>L1 chromosome</th>\n\t\t\t<th>L1 start</th>\n\t\t\t<th>L1 end</th>\n\t\t\t<th>L1 strand</th>\n";
   for my $i (0..$#fastq1)
@@ -1022,7 +1003,7 @@
   # save result in csv file ##
   
   my $filed = $out1;
-  open(my $tab, ">".$filed) || die "cannot open $filed";
+  open(my $tab, ">".$filed) || die "Cannot open $filed";
   print $tab "L1 chromosome \t L1 start \t L1 end \t L1 strand";;
   for my $i (0..$#fastq1)
   {