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Re^2: how do i obtain blast result from the given file

by bingalee (Acolyte)
on Jun 17, 2013 at 19:59 UTC ( #1039460=note: print w/replies, xml ) Need Help??


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

correction- I'm so sorry, I meant the first ten hits

  • Comment on Re^2: how do i obtain blast result from the given file

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Re^3: how do i obtain blast result from the given file
by rjt (Deacon) on Jun 17, 2013 at 20:15 UTC

    In that case, just modify the initial loop to stop after ten hits:

    my $how_many = 10; while (<$fh>) { if (/^(.+?)\|(.+?)\| (.+?)\s+(\d+)\s+(\d+e[+-]\d+)$/) { print; last if --$how_many == 0; } }

    If that's all you want to do, you don't need the hash. Note that you can still format the output with printf: printf "%-4s %-55s %5s\n", $1, $3, $4;

    You could still use the hash, as well, if you need to do further processing on the results. In that case, to preserve the order, either add an index to the hash ref for use with sort, or, simpler, push each key to an array as you find them:

    my @hits; # Keys in order my $how_many = 10; while (<$fh>) { if (/^(.+?)\|(.+?)\| (.+?)\s+(\d+)\s+(\d+e[+-]\d+)$/) { $hash{$2} = { col1 => $1, desc => $3, score => $4, E => $5, key => $2 }; push @hits, $2; last if --$how_many == 0; } } # Go through the first ten hits, in order for (map { $hash{$_} } @hits) { # $_ contains the hash ref for each record printf "%-5s %-55s %5s\n", $_->{col1}, $_->{desc}, $_->{score}; }

      thank you :)

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[ambrus]: Corion: I think I parsed a HTTP header from a string with LWP once. You can definitely use that to create a HTTP message too. The problme is
[ambrus]: that if you do that, you'd have to find where each HTTP response ends, which is nontrivial if you want persistent connections (essential for performance if you have small requests).
[Corion]: ambrus: Yes, ideally an API that I feed the incoming data piece by piece and that I can ask "is that response done" and "what should I do next" and "please construct the appropriate redirect for me"
[Corion]: ambrus: Yes, ideally the module would do all that nasty stuff for me and give me a way to ask it what the current situation is
[ambrus]: Corion: you could also consider using some wrapper over the multi interface of curl, I think Net::Curl might be a good one, since implementing enough of what it expects from the event loop might be easier than a full AnyEvent interface.
[ambrus]: Corion: you could also consider using IO::Async and its POE driver and some HTTP module for it, but I don't know if that would solve your problems with AnyEvent+POE
[ambrus]: Corion: wait, you didn't say POE. You said Prima, let me look up what that is.
[ambrus]: Corion: have you considered just writing an AnyEvent integration for that thing?
[ambrus]: Or perhaps pushing schmorp to write one?
[ambrus]: Also, searching for an existing one on CPAN obviously

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