[Bioperl-l] Bioperl use question

Philip M Terry pterry2 at unlnotes.unl.edu
Tue Feb 28 13:53:11 EST 2006


Hello,

Is this an appropriate mailing list for this question?

I am trying Test 4 from the Tisdale book, p-299, "Mastering Perl for
Bioinformatics".

Comparing screen output from p-303 of the Tisdale book for bp1.pl with
mine:

philip-terrys-power-mac-g5:~/perl_prac/pgms/source mterry$ ./bp1.pl
Sequence name is AI129902
Sequence acc  is AI129902
First 5 bases is CTCCG

-------------------- WARNING ---------------------
MSG: acc (gb|3598416) does not exist
---------------------------------------------------
Submitted Blast for [ROA1_HUMAN]
philip-terrys-power-mac-g5:~/perl_prac/pgms/source mterry$

Two questions:
i. why the warning message in my screen output?
ii. my Blast fails, that is,
--I don't see "dots" on the output line on screen following "Submitted
Blast for [ROA1_HUMAN]"?
--my output file, blast.out has 0 KB in it?

My computer system:
Power Mac G5, OS X 10.4.5, installed "core" bioperl, that is,
sudo perl -MCPAN -e shell;
cpan> force install B/BI/BIRNEY/bioperl-1.4.tar.gz

Can you comment?

Thanks,
Philip M. Terry, Ph.D.
University of Nebraska-Lincoln



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