[Bioperl-l] TBLAST Parsing
Jason Raymond
jasonraymond@asu.edu
Fri, 19 Oct 2001 14:58:44 -0700
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This is a pretty basic problem I seem to have hit, so I'm sure it's on =
the mail list somewhere but I haven't been able to dig it up. I've been =
parsing BLASTP files without a problem with several example scripts and =
a few I've written. However on switching to TBLASTN parsing, the =
programs halt and I get an ugly screen dump. I've found that this is =
due to the exclusion of "Identities =3D #, Positives =3D #, Gaps =3D #" =
from the TBLASTN file, so that when I copy/paste this line in from a =
BLASTP output (or delete this line from a BLASTP output), I get these =
error messages. I'm sure people haven't just been parsing BLASTP files, =
so there must be some easy workaround I've overlooked??
Thanks!
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<DIV><FONT face=3DArial size=3D2>This is a pretty basic problem I seem =
to have hit,=20
so I'm sure it's on the mail list somewhere but I haven't been able to =
dig it=20
up. I've been parsing BLASTP files without a problem with several =
example=20
scripts and a few I've written. However on switching to TBLASTN =
parsing,=20
the programs halt and I get an ugly screen dump. I've found that =
this is=20
due to the exclusion of "Identities =3D #, Positives =3D #, Gaps =3D #" =
from the=20
TBLASTN file, so that when I copy/paste this line in from a BLASTP =
output (or=20
delete this line from a BLASTP output), I get these error =
messages. I'm=20
sure people haven't just been parsing BLASTP files, so there must be =
some easy=20
workaround I've overlooked??</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>Thanks!</FONT></DIV>
<DIV> </DIV></BODY></HTML>
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