Bioinf

 view release on metacpan or  search on metacpan

Bioinf.pl  view on Meta::CPAN

	   @new_range= ($R_start1, $R_end1);
	 }else{                                #  ----
	  @new_range=(0,0);                  #        --------
	 }
	 return(\@new_range);
}

#______________________________________________________________________________
# Title     : find_source_perl_library
# Usage     : $source_library=${&find_source_perl_library};
# Function  : gets the default perl sub source library from ENV setenv
# Example   :
# Keywords  :
# Options   :
# Author    :
# Category  :
# Version   : 1.1
#------------------------------------------------------------------------------
sub find_source_perl_library{
     my($source_library);
     print "\n# $0: You did not use \"s=\" option for \$source_library\n";

Bioinf.pl  view on Meta::CPAN

				 }
			   }
			   close(FASTADB);
			   close(FASTAIDX);
			   if(-s $F_idx){
				   print "\nGood! Copy $F_idx to your DB dir and set two ENV vars\n";
				   print "absolute path ENV var \'FASTADB\' to your fastadb path\n";
				   print "absolute path ENV var \'FASTAINDEX\' to your $F_idx path\n";
				   print "e.g. #bash\> export FASTADB   =\/DB\/mySwiss\/$FASTA\n";
				   print "e.g. #bash\> export FASTAINDEX=\/DB\/mySwiss\/$F_idx\n";
				   print "e.g. #tcsh\> setenv FASTADB    \/DB\/mySwiss\/$FASTA\n";
				   print "e.g. #tcsh\> setenv FASTAINDEX \/DB\/mySwiss\/$F_idx\n";
				   print "Unless, you can specify the database each time at prompt\n\n";
				   if($create==1){ exit;  }
			   }else{
				   print "\n Creation of seq.dat or $F_idx seems to have gone wrong";
			   }
			}
		 }else{
			exit;
		 }
	  }

Bioinf.pm  view on Meta::CPAN

	   @new_range= ($R_start1, $R_end1);
	 }else{                                #  ----
	  @new_range=(0,0);                  #        --------
	 }
	 return(\@new_range);
}

#______________________________________________________________________________
# Title     : find_source_perl_library
# Usage     : $source_library=${&find_source_perl_library};
# Function  : gets the default perl sub source library from ENV setenv
# Example   :
# Keywords  :
# Options   :
# Author    :
# Category  :
# Version   : 1.1
#------------------------------------------------------------------------------
sub find_source_perl_library{
     my($source_library);
     print "\n# $0: You did not use \"s=\" option for \$source_library\n";

Bioinf.pm  view on Meta::CPAN

				 }
			   }
			   close(FASTADB);
			   close(FASTAIDX);
			   if(-s $F_idx){
				   print "\nGood! Copy $F_idx to your DB dir and set two ENV vars\n";
				   print "absolute path ENV var \'FASTADB\' to your fastadb path\n";
				   print "absolute path ENV var \'FASTAINDEX\' to your $F_idx path\n";
				   print "e.g. #bash\> export FASTADB   =\/DB\/mySwiss\/$FASTA\n";
				   print "e.g. #bash\> export FASTAINDEX=\/DB\/mySwiss\/$F_idx\n";
				   print "e.g. #tcsh\> setenv FASTADB    \/DB\/mySwiss\/$FASTA\n";
				   print "e.g. #tcsh\> setenv FASTAINDEX \/DB\/mySwiss\/$F_idx\n";
				   print "Unless, you can specify the database each time at prompt\n\n";
				   if($create==1){ exit;  }
			   }else{
				   print "\n Creation of seq.dat or $F_idx seems to have gone wrong";
			   }
			}
		 }else{
			exit;
		 }
	  }