Hi Kajsa,
I don't know if there's a way of doing this in Artemis (if not, it would
certainly be a useful feature to add), but here is a simple script to do
what you want. You'll need to have Perl and BioPerl installed. The usage
is (assuming you save the program as an executable file called
"nucrestart", and your sequence is in the file "seq.embl"):
nucrestart seq.embl 1000 --format embl > newseq.embl
The file "newseq.embl" should now contain a version of the sequence with
the old base 1000 as the new base 1. You can also include the option
"--revcom" to reverse complement the sequence. All the coordinates of
the features on the sequence are adjusted appropriately.
#!/usr/bin/perl
use warnings FATAL=>qw(all);
use strict;
use Bio::SeqIO;
use Bio::SeqUtils qw(cat trunc_with_features revcom_with_features);
use Getopt::Long;
my $revcom=0;
my $format='genbank';
GetOptions('revcom!'=>\$revcom, 'format=s'=>\$format) or die 'Died';
die "Changes the start position of the sequence (assumes
circularity).\nUsage: $0 seq_file 100\n" unless defined $ARGV[1];
my $seq=Bio::SeqIO->new(-format=>$format, -file=>$ARGV[0])->next_seq;
die "Error - New start not numeric\n" if $ARGV[1]=~/\D/;
die "Error - New start not in sequence\n" if $ARGV[1]>$seq->length or
$ARGV[1]==0;
my $first=Bio::SeqUtils->trunc_with_features($seq, $ARGV[1], $seq->length);
my $second=Bio::SeqUtils->trunc_with_features($seq, 1, $ARGV[1]-1);
Bio::SeqUtils->cat($first, $second);
$first=Bio::SeqUtils->revcom_with_features($first) if $revcom;
my $out=Bio::SeqIO->newFh(-format=>$format);
print $out $first;
Let me know if you have any problems.
Roy.
On 19/03/2010 12:01, Kajsa Himmelstrand wrote:
Hello Artemis users,
I had to change the starting point for my circular mt-DNA. Then I had
to change the positions of the genes also. But that was to hard to do
in an easy way in the embl-format the genes were in. So I saved the
files with the genes in gff-format instead and changed the positions.
But then I lost a lot of information of which exons that belongs to
the same gene. I have also tried to see if it is possible to save the
genes in this Sequin Table format, change the positions and then save
the Sequin Table file to a embl format. But it doesn't seem to work
to save the Sequin Table file to a embl file in Artemis?
Is there anyone that have a good solution of how to change the
positions of the genes in an easy way without loosing any
information? Otherwise I will have to make my own scrip, but Im
rather slow in programming.
Best regards from Kajsa
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