I recently ran the following command on linux:
*blastall -p blastn -d new_NotPatoDB.fa -i smallQuery.fasta -o textout.xml -m 7*
The results I received are in XML format , I'm trying to extract the sequences with minimum hits. I tried using the following script:
by running the following command:
perl ncbiblastparser.pl output.xml 5 parseout.txt
but I get the following error:
*Can't locate Bio/SearchIO.pm in @INC (you may need to install the Bio::SearchIO module) (@INC contains: /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.22.1 /usr/local/share/perl/5.22.1 /usr/lib/x86_64-linux-gnu/perl5/5.22 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.22 /usr/share/perl/5.22 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base .) at ncbiblastparser.pl line 6. BEGIN failed--compilation aborted at ncbiblastparser.pl line 6.*
I have downloaded the Bio/SearchIO.pm package a few times.
can anyone identify the problem? or have any other ideas or ways parse the results.