[Bioperl-l] how to input files named by variables to SearchIO?

Jason Stajich jason at bioperl.org
Wed Feb 4 12:42:41 EST 2009


Please ask your questions on the mailing list in the future.

You are using single quotes
> =>'/home/evolution/temp/$id1.out');
instead of double quotes which you need to interpolate a variable
> =>"/home/evolution/temp/$id1.out");

On Feb 4, 2009, at 9:21 AM, kevin fan wrote:

> Dear Dr. Jason,
>
> i am annotating 11000 ESTs using stand along blastx against the NCBI
> non-redundant protein database. I put  the blast results seperately  
> since it
> will be too large to see the raw results if i put all results into  
> one file.
> the blast results are named as the sequences name. my question is  
> how to
> input those files into to SearchIO?
>
> here are some of my codes:
>
>
> system("$formatdb -i /home/evolution/temp3/$id1.txt -p F");#$id1 is  
> variable
> for sequences.
>
> system("$blastx -i /home/evolution/temp/$id1.txt -d
> /home/evolution/blast-2.2.19/data/nr -p blastx -o
> /home/evolution/temp/$id1.out");
>
> my $in = new Bio::SearchIO(-format => 'blast',-file
> =>'/home/evolution/temp/$id1.out');
>
> the first two commands run well on my machine, but when i try to  
> iuput the
> file in SearchIO. it can not open the file named by variables.
>
> shaohua fan

Jason Stajich
jason at bioperl.org





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