[Bioperl-l] 0.6.2 and /examples

[Ewan Birney]

On Mon, 2 Oct 2000, Clay Shirky wrote:

> I've installed 0.6.2pre3 on both Linux (Caldera 2.3) and Solaris (2.4)
> with no problems (though I think the README should reference
> IO-stringy as a possible external dependency, at least according to
> /examples/blast/blast_seq.pl).
> 
> However, having installed it (and trying to teach myself bioperl as I
> go), I have run into some warnings and exceptions in /examples.
> 
> I am happy to fix these scripts (and add some comments to help other
> newcomers) if anyone can give me some pointers on how to re-write
> around these error conditions.

Geez. I was *convinced* I had squashed these bugs. Oh vey! 

many thanks...


> 
> With "examples/rev_and_trans.pl" I get
> 
>   -------------------- WARNING --------------------
>   MSG: ./rev_and_trans.pl:35 Seq::str - deprecated method. You should
>   use $obj->seq in preference
>   -------------------------------------------------
> 
> and
> 
>   -------------------- WARNING --------------------
>   MSG: ./rev_and_trans.pl:41 Seq::out_fasta - deprecated method. You
>   should use the SeqIO package in preference
>   -------------------------------------------------
> 
> and with "examples/psw.pl" in the blosum alignment I get
> 
>   -------------------- WARNING --------------------
>   MSG: /usr/local/lib/perl5/site_perl/5.005/Bio/Tools/pSW.pm:199
>   Seq::str - deprecated method. You should use $obj->seq in preference
>   -------------------------------------------------
> 
> and with gonnet I get
> 
>   -------------------- EXCEPTION --------------------
>   MSG: Unable to process non locatable sequences
>   CONTEXT: Error in uNKNOWN CONTEXT
>   SCRIPT: ./psw.pl
>   STACK:
>   Bio::SimpleAlign::addSeq(177)
>   Bio::Tools::pSW::pairwise_alignment(265)
>   main::./psw.pl(122)
>   ---------------------------------------------------
> 
> -clay
> 
> --
> Clay Shirky                 |    shirky.com - Essays on the Internet:
> http://www.shirky.com/      |        Culture, Economics, Globalization
> 
> 
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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
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