[Bioperl-l] parsing only the summary part of a blast report
Zhao, David [PRI]
DZhao1@prius.jnj.com
Tue, 10 Oct 2000 21:31:34 -0400
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Hi there,
How can I parse the summary part of a blast report using bioperl =
modules?
such as:
TBLASTN 2.0.10 [Aug-26-1999]
Reference:
Altschul, Stephen F., Thomas L. Madden, Alejandro A. Sch=E4ffer,=20
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),=20
"Gapped BLAST and PSI-BLAST: a new generation of protein database =
search
programs", Nucleic Acids Res. 25:3389-3402.
Query=3D GPC-R_HUMAN_TL217
(403 letters)
Database:
/home/dzhao1/new_download_test/testdir/gbDAILY/blastdb/gbcu.fasta
709,769 sequences; 2,255,827,756 total letters
Searching............................................................don=
e
=
Score
E
Sequences producing significant alignments: =
(bits)
Value
emb|AB041228.1|AB041228 Homo sapiens mRNA for G protein-cou... 305 =
2e-81
emb|AF292402.1|AF292402 Homo sapiens neuromedin U receptor-... 305 =
2e-81
emb|AB041229.1|AB041229 Rattus norvegicus mRNA for G protei... 304 =
7e-81
emb|BE751626.1|BE751626 203809 MARC 2BOV Bos taurus cDNA 5'... 146 =
2e-33
I've been played with blast.pm a little, such as display(), table(), =
etc,
but couldn't just get the summary only.
Thanks
David
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<TITLE>parsing only the summary part of a blast report</TITLE>
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<P><FONT COLOR=3D"#000080" FACE=3D"Comic Sans MS">Hi there,</FONT>
<BR><FONT COLOR=3D"#000080" FACE=3D"Comic Sans MS">How can I parse the =
summary part of a blast report using bioperl modules? such as:</FONT>
</P>
<P><FONT COLOR=3D"#000080" SIZE=3D2 FACE=3D"Courier">TBLASTN 2.0.10 =
[Aug-26-1999]</FONT>
</P>
<BR>
<P><FONT COLOR=3D"#000080" SIZE=3D2 FACE=3D"Courier">Reference:</FONT>
<BR><FONT COLOR=3D"#000080" SIZE=3D2 FACE=3D"Courier">Altschul, Stephen =
F., Thomas L. Madden, Alejandro A. Sch=E4ffer, </FONT>
<BR><FONT COLOR=3D"#000080" SIZE=3D2 FACE=3D"Courier">Jinghui Zhang, =
Zheng Zhang, Webb Miller, and David J. Lipman (1997), </FONT>
<BR><FONT COLOR=3D"#000080" SIZE=3D2 FACE=3D"Courier">"Gapped =
BLAST and PSI-BLAST: a new generation of protein database search</FONT>
<BR><FONT COLOR=3D"#000080" SIZE=3D2 =
FACE=3D"Courier">programs", Nucleic Acids Res. =
25:3389-3402.</FONT>
</P>
<P><FONT COLOR=3D"#000080" SIZE=3D2 FACE=3D"Courier">Query=3D =
GPC-R_HUMAN_TL217</FONT>
<BR><FONT COLOR=3D"#000080" SIZE=3D2 =
FACE=3D"Courier"> (403 =
letters)</FONT>
</P>
<P><FONT COLOR=3D"#000080" SIZE=3D2 FACE=3D"Courier">Database:</FONT>
<BR><FONT COLOR=3D"#000080" SIZE=3D2 =
FACE=3D"Courier">/home/dzhao1/new_download_test/testdir/gbDAILY/blastdb/=
gbcu.fasta</FONT>
<BR><FONT COLOR=3D"#000080" SIZE=3D2 =
FACE=3D"Courier"> &=
nbsp; 709,769 sequences; 2,255,827,756 total letters</FONT>
</P>
<P><FONT COLOR=3D"#000080" SIZE=3D2 =
FACE=3D"Courier">Searching..............................................=
..............done</FONT>
</P>
<P><FONT COLOR=3D"#000080" SIZE=3D2 =
FACE=3D"Courier"> &=
nbsp; &=
nbsp; &=
nbsp; &=
nbsp; &=
nbsp; =
Score E</FONT>
<BR><FONT COLOR=3D"#000080" SIZE=3D2 FACE=3D"Courier">Sequences =
producing significant =
alignments: &=
nbsp; &=
nbsp; (bits) Value</FONT>
</P>
<P><FONT COLOR=3D"#000080" SIZE=3D2 =
FACE=3D"Courier">emb|AB041228.1|AB041228 Homo sapiens mRNA for G =
protein-cou... 305 2e-81</FONT>
<BR><FONT COLOR=3D"#000080" SIZE=3D2 =
FACE=3D"Courier">emb|AF292402.1|AF292402 Homo sapiens neuromedin =
U receptor-... 305 2e-81</FONT>
<BR><FONT COLOR=3D"#000080" SIZE=3D2 =
FACE=3D"Courier">emb|AB041229.1|AB041229 Rattus norvegicus mRNA =
for G protei... 304 7e-81</FONT>
<BR><FONT COLOR=3D"#000080" SIZE=3D2 =
FACE=3D"Courier">emb|BE751626.1|BE751626 203809 MARC 2BOV Bos =
taurus cDNA 5'... 146 2e-33</FONT>
</P>
<P><FONT COLOR=3D"#000080" FACE=3D"Comic Sans MS">I've been played with =
blast.pm a little, such as display(), table(), etc, but couldn't just =
get the summary only.</FONT>
<BR><FONT COLOR=3D"#000080" FACE=3D"Comic Sans MS">Thanks</FONT>
<BR><FONT COLOR=3D"#000080" FACE=3D"Comic Sans MS">David</FONT>
</P>
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