[Bioperl-l] [Bioperl-guts-l] Notification: incoming/1077 (fwd)
Jason Stajich
jason@cgt.mc.duke.edu
Tue, 5 Feb 2002 18:27:53 -0500 (EST)
Lana -
Any reason you can't use fasta format as input to clustal?
We have basically stopped supporting PIR format because none of our
developers use it and after sending out request of interest on the list
severl months ago no one responded that were using it. If there are indeed
users out there we would be happy to add the appropriate code if we can
get good use cases and example files that do not work with the current
code.
In any event I would certainly upgrade to bioperl 0.7.2 in the near future
and the future 1.0 release as I suspect the pir handling is not so great
in that 0.7.0 release.
-jason
--
Jason Stajich
Duke University
jason@cgt.mc.duke.edu
---------- Forwarded message ----------
Date: Tue, 5 Feb 2002 18:02:18 -0500
From: bioperl-bugs@bioperl.org
To: bioperl-guts-l@bioperl.org
Subject: [Bioperl-guts-l] Notification: incoming/1077
JitterBug notification
new message incoming/1077
Message summary for PR#1077
From: Lana Schaffer <lschaffe@agouron.com>
Subject: file formats
Date: Tue, 05 Feb 2002 15:08:37 -0800
0 replies 0 followups
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Date: Tue, 05 Feb 2002 15:08:37 -0800
From: Lana Schaffer <lschaffe@agouron.com>
Organization: Agouron
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To: bioperl-bugs@bioperl.org
Subject: file formats
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I am starting to use Bioperl and presently have Bioperl 0.7
and unix OS IRIX64 6.5.
I have used a small script to change the protein sequence format
from fasta to PIR. The output perl file from Bioperl is:
-------------------------------------------------------------------
>P1;CDK2
>P1;CDK2
MENFQKVEKI GEGTYGVVYK ARNKLTGEVV ALKKIRLDTE TEGVPSTAIR EISLLKELNH
PNIVKLLDVI HTENKLYLVF EFLHQDLKKF MDASALTGIP LPLIKSYLFQ LLQGLAFCHS
HRVLHRDLKP QNLLINTEGA IKLADFGLAR AFGVPVRTYT HEVVTLWYRA PEILLGCKYY
STAVDIWSLG CIFAEMVTRR ALFPGDSEID QLFRIFRTLG TPDEVVWPGV TSMPDYKPSF
PKWARQDFSK VVPPLDEDGR SLLSQMLHYD PNKRISAKAA LAHPFFQDVT KPVPHLRL
-------------------------------------------------------------------
and the output/input perl file for clustalw is:
-------------------------------------------------------------------
>P1;CDK2
MENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVPSTAIREISLLKELNH
PNIVKLLDVIHTENKLYLVFEFLHQDLKKFMDASALTGIPLPLIKSYLFQLLQGLAFCHS
HRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYTHEVVTLWYRAPEILLGCKYY
STAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTPDEVVWPGVTSMPDYKPSF
PKWARQDFSKVVPPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPVPHLRL
*
-------------------------------------------------------------------
The clustalw program will produce an error when an import is attempted
with the Bioperl format. The "*" is missing and the ">P1;CDK2" is
repeated twice.
I don't know if this format is corrected in more updated releases of
Bioperl. However, this format needs to be compatible with other
programs. Please update me on this problem.
Thanks,
--
Lana Schaffer Computational Chemistry
schaffer@pfizer.com Pfizer Global R&D-LJ
phone (858) 622-3002 10777 Science Center Drive
fax (858) 678-8244 San Diego, CA 92122-1111
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