Hi
I agree with Roy and had written a very similar script but took a slightly
different approach.
I thought it was simpler to use the crunch format for the comparison file but
also created a crude match score rather than just using the match length
(however I don't know if that was really a good idea + I'm sure there are
better ways of generating a score :-)
For what it's worth (for use with nucmer --coords output):
#!/usr/bin/perl
use warnings;
use strict;
while (<>)
{
unless ($_ =~ /^(\s*)\d/){next}
$_ =~ s/\|//g;
my @f = split;
# create crude match score = ((length_of_match *
%identity)-(length_of_match * (100 - %identity))) /20
my $crude_plus_score=($f[4]*$f[6]);
my $crude_minus_score=($f[4]*(100-$f[6]));
my $crude_score= int(($crude_plus_score - $crude_minus_score) / 20);
# reorganise columns and print crunch format to stdout
# score %id S1 E1 seq1 S2 E2 seq2 (description)
print " $crude_score $f[6] $f[0] $f[1] $f[7] $f[2] $f[3] $f[8] nucmer
comparison coordinates\n"
}
Andrew
-----Original Message-----
From: [email protected]
[mailto:[email protected]] On Behalf Of Roy Chaudhuri
Sent: 24 April 2009 13:29
To:
Subject: Re: [Artemis-users] ACT and MUMMER
Hi Alex.
It's relative straightforward to parse the "coords" file output by
NUCmer/PROmer (which is produced when you specify the --coords flag on the
command line), and produce something resembling the BLAST m8 format that ACT
expects.
Here is some example Perl code for NUCmer:
#!/usr/bin/perl
use warnings;
use strict;
while (<>) {last if /^=+/};
while (<>) {
$_=~s/\|//g;
my @split=split;
next if defined $split[9] and $split[9]=~/SHADOWED|DUPLICATE/;
print join("\t", @split[7..8], $split[6],
$split[4]>$split[5]?$split[4]:$split[5], '#', '#', @split[2..3], @split[0..1],
'#', $split[6]), "\n"; }
For PROmer you'll need to change the print statement to:
print join("\t", @split[11..12], $split[6], $length, '#', '#', @split[2..3],
@split[0..1], '#', $split[7]), "\n";
Hope this helps,
Roy.
Bossers, Alex wrote:
> Hello all,
>
> I am a big fan of artemis and have ported some of my annotation files
> automatically to it.
>
> Currently I am interested in doing multiple genome comparisons. I know
> I can use webact or double act to generate big_blast alignments which
> should be appropriate for opening in ACT. However, I have been working
> with mummer (nucmer in particular) and even though the artemis/act
> "manual" tells I should be able to open them I can nowhere find which
> files to use (they all seem to fail). Do I need to run mummer with
> specific options or do I need a differentparser for that?
>
> Thanks for any help..... this is already costing me several nights to
> find out :-(
>
> Alex
>
>
>
> _______________________________________________ Artemis-users mailing
> list [email protected]
> http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
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