#!/usr/bin/perl -w

 

#use warnings;

use strict;

use DBI;

use DBD::mysql;

use BeginPerlBioinfo;      #                                                                                                                

#use Test::More tests=> 15

use Exporter;

OUR @ISA = qw(EXPORTER);

OUR @EXPORT=qw(get_file_data get_accession get_gene get_origin get_translation);

 

 

sub connect_to_db {

my ($dbh, $sth, $...., $..., $..., $...);

my $dbname = "1";

my $dbserver = "";

my $datasource = "dbi:mysql:database=$dbname;host = $dbserver";

my $username = "";

my $password = "p";

 

my $dbh= DBI->connect($datasource,$username, $password,{

    PrintError=>0,     #disable PrintError

                RaiseError=>1      #enable RaiseError

}) || die "Error opening database: $DBI::errstr\n";

     return ($dbh);

    }

 

$sth = $dbh-> prepare("INSERT INTO Chrom_4_AC (AC_number, Gene_id)

                       VALUES                 (?        ,?       )");     # use placeholders

 

#Declare and initialize variables

my $genbank='chrom_CDS-4.txt';

my record="";

my $gene_id="";

my $AC_number="";

my $DNA_seq="";

my $start_stop_cs="";

my aa_seq="";

my $transl_start_site="";

my $protein_prod_names="";

my $chromosomal_location="";

                                                                                  

#Open the Genbank file

#unless (open (GBFILE, $genbank)) {

#        print "CANNOT open Genbank file \n";

#                             exit;

#                            

# $/="//\n';   #set input separator and read in arecord to scalar

#$record = <GBFILE>

#reset input separator

#$/=$save_input_separator;

 

#$record = ~/^(LOCUS.**ORIGIN\s*\n)(.*)\/\/\n/s);

#print $record;

 

sub get_file_data {

 

my ($filename) = @_;

my @filedata =();

 

unless (open(GET_FILE_DATA, $filename)) {

print STDERR "CANNOT open file\n";

exit;

}

@filedata = <GET_FILE_DATA>;

close GET_FILE_DATA;

return @filedata;

}

 

                sub get_accession   {

   my $genbank = shift;

    if ($genbank = ~/ACCESSION\s*(\w+)/) {

     return $1;

    }  else   {

         return "error";

         }

     }                        

                                                                                   

                                                                                  

sub get_gene {

    my $genbank= shift;

    if($genbank=/gene="(.*?)"/s) {

      return $1;

    }  else {

                   return "error";

                     }

    }

               

               

                sub get_origin  {

                   my $seq;

                   chop $seq;

                   if($genbank =~/ORIGIN|s*(.*)\/\//s) {

                   $seq = $1;

                }   else   {

        return             "error";

                                }

                                $seq =~s/[\s\d]//g;

                                return uc($seq);

                                }

                               

                                sub get_translation  {

                                my $genbank=shift;

                                my $pro;

                                if($genbank=~/translation="(.*?)"/s) {

                                $pro = $1;

                                }   else  {

                                return "error";

                                }

                                $pro=~s/[\s]//g;

                                return uc($pro);

                                }