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You can print the matching lines with a regular expression that matches only the lines you're interested in:

while (<$fh>) { print if /^(.+?)\|(.+?)\| (.+?)\s+(\d+)\s+(\d+e[+-]\d+)$/; }

The above will also handle arbitrarily large files, as it reads one line at a time into memory.

There are many hits, but if I want the top ten only, what do i do?

I'm not sure what you mean by top ten, exactly (highest "Score"? "E Value"? Order within the file?), but a likely approach to this would be to modify the above while loop and instead of printing, place each line in a hash. My regular expression already does basic parsing of the input line into capture variables $1 through $5, so you can try something like this:

$hash{$2} = { col1 => $1, desc => $3, score => $4, E => $5 } if /.../; # Use regex above

Then, after the loop finishes, you can sort and display the results however you like. For example:

my $how_many = 10; for (sort { $hash{$b}->{score} <=> $hash{$a}->{score} } keys %hash +) { printf "%-4s %-55s %5s\n", $hash{$_}->{col1}, $hash{$_}->{desc}, $hash{$_}->{score}; last if --$how_many == 0; }

Outputs:

emb plasma membrane H+-ATPase [Oryza sativa Japonica... 213 gb hypothetical protein OsI_09609 [Oryza sativa Indi... 213 ref Os03g0100800 [Oryza sativa Japonica Group] >... 213 gb ATPase 11, plasma membrane-type [Aegilops tauschii] 208 ref PREDICTED: ATPase 7, plasma membrane-type is... 207 ref H(\+)-transporting atpase plant/fungi plasma... 207 ref PREDICTED: plasma membrane ATPase 1-like [Br... 207 ref PREDICTED: ATPase 7, plasma membrane-type is... 207 ref autoinhibited H+ ATPase [Populus trichocarpa... 206 ref PREDICTED: plasma membrane ATPase 1-like iso... 205

In reply to Re: how do i obtain blast result from the given file by rjt
in thread how do i obtain blast result from the given file by bingalee

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