Bioinf

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Bioinf.pl  view on Meta::CPAN

           @files_made_with_rv, @files_made, %hash, $seq, $sec_str_hash_form_given);
	my($output_file) ='default_out.fa'; ### when no output file name is given, this is used
        #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~`
        # Try and determin the output file name
        #________________________________________________________
        if(@file>0){
            if($file[0]=~/\S\.[n]?fa/){ ## to handle .nfa and .fa files
                $output_file = $file[0];   $out_file_name_provided=1;
                if(-s $output_file){
                    rename($output_file, "$output_file\.bak");
                    print "\n# (INFO) $output_file is present. $output_file\.bak will be created for backup\n";
                }
            }elsif($file[0]=~/(\S+)\.\S+/){
                $output_file = "$1\.fa";   $out_file_name_provided=1;
            }
	}else{ $output_file='default_out.fa'; }

	if($char_opt=~/s/){ $sort_seq_names='s';	}
        if($char_opt=~/o/){ $write_pure_seq_only='o' }
        if($char_opt=~/R/){ $write_rv_seq_as_well='R'; print "\n# (INFO) You wanted REVerse seq as well\n"; }

Bioinf.pl  view on Meta::CPAN

	\@raw_string=\"@raw_string\"\n\t\@array=\"@array\"\n\t\@num_opt=\"@num_opt\"
	\@char_opt=\"@char_opt\"\n\t\@file=\"@file\"\n\t\@string=\"@string\"\n" }
	#""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

	## Reading self and the template headbox in this subroutine.
	my %correct_head_box_entry = %{&read_correct_head_box()};
	for($p=0; $p < @file; $p++){
	  $in_file = $file[$p];

	  ##""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
	  ##  Make backup of the input file
	  ##""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
	  &cp( "$in_file", "$in_file\.bak$$");
	  print "\n $in_file\.bak$$ is created as a backup \n\n";
	  print chr(7);

	  ##""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
	  ##  Open files
	  ##""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
	  open(TARGET, "$in_file\.bak$$");
	  open(RESULT, ">$in_file");

	  my(@whole_file) = <TARGET>;
	  my(@keys) = keys %correct_head_box_entry;

Bioinf.pm  view on Meta::CPAN

           @files_made_with_rv, @files_made, %hash, $seq, $sec_str_hash_form_given);
	my($output_file) ='default_out.fa'; ### when no output file name is given, this is used
        #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~`
        # Try and determin the output file name
        #________________________________________________________
        if(@file>0){
            if($file[0]=~/\S\.[n]?fa/){ ## to handle .nfa and .fa files
                $output_file = $file[0];   $out_file_name_provided=1;
                if(-s $output_file){
                    rename($output_file, "$output_file\.bak");
                    print "\n# (INFO) $output_file is present. $output_file\.bak will be created for backup\n";
                }
            }elsif($file[0]=~/(\S+)\.\S+/){
                $output_file = "$1\.fa";   $out_file_name_provided=1;
            }
	}else{ $output_file='default_out.fa'; }

	if($char_opt=~/s/){ $sort_seq_names='s';	}
        if($char_opt=~/o/){ $write_pure_seq_only='o' }
        if($char_opt=~/R/){ $write_rv_seq_as_well='R'; print "\n# (INFO) You wanted REVerse seq as well\n"; }

Bioinf.pm  view on Meta::CPAN

	\@raw_string=\"@raw_string\"\n\t\@array=\"@array\"\n\t\@num_opt=\"@num_opt\"
	\@char_opt=\"@char_opt\"\n\t\@file=\"@file\"\n\t\@string=\"@string\"\n" }
	#""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

	## Reading self and the template headbox in this subroutine.
	my %correct_head_box_entry = %{&read_correct_head_box()};
	for($p=0; $p < @file; $p++){
	  $in_file = $file[$p];

	  ##""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
	  ##  Make backup of the input file
	  ##""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
	  &cp( "$in_file", "$in_file\.bak$$");
	  print "\n $in_file\.bak$$ is created as a backup \n\n";
	  print chr(7);

	  ##""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
	  ##  Open files
	  ##""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
	  open(TARGET, "$in_file\.bak$$");
	  open(RESULT, ">$in_file");

	  my(@whole_file) = <TARGET>;
	  my(@keys) = keys %correct_head_box_entry;