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Re: how to split the elements in an array of arrays ?

by ptum (Priest)
on Oct 31, 2006 at 18:28 UTC ( #581542=note: print w/ replies, xml ) Need Help??


in reply to how to split the elements in an array of arrays ?

I'm sure lots of us would be glad to help. What have you tried so far, heidi?

Hint: try split with an empty pattern //.


Comment on Re: how to split the elements in an array of arrays ?
Re^2: how to split the elements in an array of arrays ?
by heidi (Sexton) on Oct 31, 2006 at 18:38 UTC
    this is the program which i have done (which is a part of the whole program where i am doin other processings too)
    open (PIR,'file.txt'); while (<PIR>) { chomp; if( /^ENTRY/ ) { $entry = $_ } elsif ( /^(TITLE)\s+(\S.*)/ ) { $title = "$1\n\t $2" } elsif ( /^(ORGANISM)\s+(\S.*)/ ) { $org = "$1\n\t $2" } elsif ( /^ACCESSIONS/ ) { $acc = $_ } else { push @se, $_; }
    this is my file: now plz dont confuse with the query file ok...let me explain u.
    ENTRY CCHU #type complete TITLE cytochrome c [validated] - human ORGANISM #formal_name Homo sapiens #common_name man ACCESSIONS A31764; A05676; I55192; A00001 MGDVEKGKKIFIMKCSQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIWGEDTLMEYLE +NPKKYIPGTKMIFVGIKKKEERADLIAYLKKATNE ENTRY CCCZ #type complete TITLE cytochrome c - chimpanzee (tentative sequence) ORGANISM #formal_name Pan troglodytes #common_name chimpanzee ACCESSIONS A00002 GDVEKGKKIFIMKCSQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIWGEDTLMEYLEN +PKKYIPGTKMIFVGIKKKEERADLIAYLKKATNE ENTRY CCMQR #type complete TITLE cytochrome c - rhesus macaque (tentative sequence) ORGANISM #formal_name Macaca mulatta #common_name rhesus macaq +ue ACCESSIONS A00003 GDVEKGKKIFIMKCSQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKGITWGEDTLMEYLEN +PKKYIPGTKMIFVGIKKKEERADLIAYLKKATNE
    @se will collect all the sequence in an array.. and then my query proceeds...instead of hello hi and bye, there will be the alphabetical sequences. i just wanted to get an idea and thats why i used hello hi and bye. hope u dont mind. waiting for ur reply. thanks.

      Perhaps I am not understanding you correctly, but this seems to be a very different question than the one you asked first. In the example you gave, what happens to the values in $entry, $title, $org or $acc? You seem to drop them on the floor ...

      To solve this kind of a problem, I would probably establish a hash of array references, something like this (untested):

      use strict; my %filecontents = ('entries' => [], 'titles' => [], 'organisms' => [], 'accessions' => [], 'unknown' => [] ); my $filehandle; unless (open($filehandle,"<file.txt")) { die "Cannot open file.txt: $!"; } while (<$filehandle>) { chomp; if (/^ENTRY/) { push @{$filecontents{'entries'}}, $_; } elsif (/^TITLE/) { push @{$filecontents{'titles'}}, $_; } # and so on ... }

      Update: Notice, by the way, that I check for success in opening the filehandle, always a good thing to do.

      Update 2: Arrghh! I was duped! I didn't realize you'd asked this question before. Why not pay attention to the answers you've already received, as Fletch points out below?

      Huzzah, the crufty re-implementation of Bio::SeqIO continues unabashed by suggestions to the contrary and pointers to its documentation.

      Addendum: That perhaps sounds a bit cruel, but if you don't understand enough Perl to know how to split scalars into characters you really shouldn't be trying to re-invent wheels that other people have already solved. Use the off-the-shelf widgets for the parts you can, and get fancy once you know what you're doing. Something like Beginning Perl for Bioinformatics that's aimed at biology-types specifically should help you get going.

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