Find the next best hit

[bio_informatics]

Hi,
I am using blast+ for my blast.
I have created database from a fasta file and and I am blasting the same file against the database created.
I got the output in tabular format, with Query id, subject id and e-value.

Most of them would have e-value as 0, (as it is obvious)
other have output as:

Q1 Sub1 4e-08
Q1 Sub2 9e-45

can I compare 4e-08 and 9e-45 in perl?

Please help me.
how do I get the second best hit from this?

[atcghelix]

Perl should recognize those as numbers:

perl -e "if(4e-08 > 9e-45) {print 'Perl can handle scientific notation.'}"

Are you asking about how to parse the records themselves?

[bio_informatics]

@atcghelix
Thank you.
I didn't know that Perl can handle scientific notation.
I was afraid, that Perl might consider these as strings.

Perl should recognize those as numbers:

perl -e "if(4e-08 > 9e-45) {print 'Perl can handle scientific notation.'}"

Are you asking about how to parse the records themselves?

[rhinoceros]

Maybe:

Get best hits:

sort -k1,1 -k3,3g blastOutput | sort -u -k1,1 --merge > bestHits

Remove best hits from the output:

grep -v -f bestHits blastOutput > blastOutputBestHitsRemoved

Get the now best hits:

sort -k1,1 -k3,3g blastOutputBestHitsRemoved | sort -u -k1,1 --merge > secondBestHits