[Bioperl-l] parsing output from an avid alignment

[Brian Osborne]

Jon,

Unfortunately there's no parser for Avid in the AlignIO family.

Brian O.

-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Jonathan Manning
Sent: Tuesday, June 08, 2004 6:39 AM
To: Bioperl
Subject: [Bioperl-l] parsing output from an avid alignment

Hi all,

I'm preparing to incorporate Vista analysis into my script, and am
attempting to use the AVID global alignment algorithm, since they seem
to be associated, and likely to work well together.

I don't think there is, but just in case I've missed something, has
anyone written a module to parse the AVID output? Apparently it's a
hybrid of the fasta and ClustalW styles. Here's an excerpt of the kind
of thing I mean:

1419  t   |
1420  c   |
1421  a   |
1422  a   |
1423  t   |
1424  a   |
1425  g   |
1426  g   |
1427  t   |
1428  g - g  9
1429  a - a  10
1430  c - c  11
1431  t - t  12
1432  a   g  13
1433  a - a  14
1434  a - a  15
1435  a   g  16
1436  g - g  17
1437  t   |
1438  c   |
1439  t   |
1440  c   |
1441  t   |
1442  a   |
1443  a   |
1444  a   |
1445  g   |

Cheers,

Jon

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