Question: How to get script for inserting information in a table to work?
gravatar for Mimmi Ahlmén
20 months ago by
Mimmi Ahlmén20 wrote:

I have a file which looks like this:

    >orf_1 364-2160
    >orf_2 2453-5197

and a script that is supposed to insert the file content into a table:


use strict;
use warnings;
use Bio::Index::Fasta;
use DBI; # The perl database module

my $NucleotideFasta     = $ARGV[0];
my $ProteinFasta    = $ARGV[1];

die "Give the name of existing nucleotide fasta file and a file name for protein translations to be saved." unless (defined($NucleotideFasta) && defined($ProteinFasta));

# Replace with your mysql details
my $database    = "my_database.db";     #Change accordingly

# Create a connection to the database
my $dbh = DBI->connect("DBI:SQLite:$database","","") or die "Could not connect to the database $database.\n";

my $table_orfs  = 'orfs';   #Change accordingly
# Insert genes, make sure to use the correct table names etc = same as when you created the database
my $sth_insert = $dbh->prepare("INSERT INTO $table_orfs (orf_name,sequence,length,protein) VALUES (?,?,?,?)");

#read in nucleotide sequences
my $seq_nucleotide  = Bio::SeqIO->new( -format => 'fasta' , -file => $NucleotideFasta);
my $seq_protein     = Bio::SeqIO->new( -format => 'fasta' , -file => ">$ProteinFasta");

while (my $seq = $seq_nucleotide->next_seq() ) {
    #save protein translations to a file
    my $protein=$seq->translate();
    #prepare for database input
    my $orf_id = $seq->display_id();
    my $nucleotides = $seq->seq();
    my $aminoacids  = $protein->seq();
    my $length = length($aminoacids);
    #print "$orf_id $length\n$nucleotides\n$aminoacids\n";


My question is now, how can I create the table before using the script and which command should I use to run the script?

I know how to create a table, but in order for the script to work properly, what names in the tables should I use? Is it like this:

create table orfs( orf_name TEXT, sequence TEXT, length REAL, aminoacids TEXT );

When I do this I get:

DBD::SQLite::db prepare failed: table orfs has no column named orf_name at line 21.
Can't call method "execute" on an undefined value at line 37, <GEN0> line 1

. Maybe I misunderstood the task or am I supposed to create other names for the table?

sql • 436 views
ADD COMMENTlink written 20 months ago by Mimmi Ahlmén20

what's the output of

$ sqlite3 -header my_database.db '.schema orfs'


ADD REPLYlink written 20 months ago by Pierre Lindenbaum129k

CREATE TABLE orfs( orf_name TEXT, sequence TEXT, length REAL, protein TEXT );

When I look at the file my_database.db it looks like a mess.

ADD REPLYlink written 20 months ago by Mimmi Ahlmén20
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1560 users visited in the last hour