Hi,
thanks guys and sorry for the late reply.
I finally got it going.... I was using run-mummer3 but it gave me very strange
output in plots (lots of scatter) while promer and nucmer on the same files
gave me good results I was expecting with these demo files.
Tim the awk script complained on boundaries out of range when loading the
comparison file in ACT. But the perl scripts (which basically do the same on
the coords file) worked like a charm.
I think it was not your awk script resulting in this problem but I suspect the
.out file to be erroneous of run-mummer3.
Thanks a lot!
Alex
________________________________
Van: artemis-users-boun...@sanger.ac.uk namens andrew warry (BITS)
Verzonden: di 28-4-2009 16:59
Aan: 'artemis-users@sanger.ac.uk'
Onderwerp: Re: [Artemis-users] ACT and MUMMER
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: artemis-users-boun...@sanger.ac.uk
[mailto:artemis-users-boun...@sanger.ac.uk] 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 Artemis-users@sanger.ac.uk
> http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
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