------ Forwarded Message
From: Roy Chaudhuri <roy.chaudh...@gmail.com>
Date: Fri, 24 Apr 2009 13:22:24 +0100
To: "Bossers, Alex" <alex.boss...@wur.nl>
Cc: <artemis-users@sanger.ac.uk>
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
--
Dr. Roy Chaudhuri
Department of Veterinary Medicine
University of Cambridge, U.K.
------ End of Forwarded Message
--- Begin Message ---
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
--
Dr. Roy Chaudhuri
Department of Veterinary Medicine
University of Cambridge, U.K.
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