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Re^14: Help with pushing into a hash

by jemswira (Novice)
on Sep 03, 2012 at 06:27 UTC ( #991362=note: print w/ replies, xml ) Need Help??


in reply to Re^13: Help with pushing into a hash
in thread Help with pushing into a hash

well i ran the code and it returned this:

E7F888 Name=arid5b ;PF01388

which is correct. Well I selected the number cause it was in both files ( I manually ctrl-f ed the notepad file.

Well a lot of lines are missing from the final output. The $activ is 512 kb large and the out put is 3kb. And also @activline is missing alot when I did print @activline;. I randomly selected E7F888 from $activin and checked to make sure it was in $uniprot, so it may be another offending line of data. If I did this:

print $activ{E7F888},"\n"; for ( read_file $uniprot ) { next unless /(E7F888)\s+.+=([^\s]+)/; say; push @activline, "$1 | $2 | $activ{$1} \n" if $activ{$1}; } print @activline; } print @activline;

I got this:

PF01388 E7F888 Name=arid5b ;PF01388 E7F888 | arid5b | PF01388

which showed that it was in %activ and that it was found in the file. But when I run through the normal code, it is not in @activ anymore.

UPDATE,

I ran the following code to check something, and not all the data is printed, I.E. A lot of lines are not pushed into the array.

#!/usr/bin/perl use Modern::Perl; use File::Slurp qw/read_file write_file/; my $uniprot = 'uniprot-sfinal.txt'; my $activin = 'Activator-PFAM.txt'; my %activ = map { s/\.\d+//g; /(.+)\s+\|\s+(.+)/ and $1=>$2; } grep/\| +\s+\S+/,read_file $activin; for ( read_file $uniprot ) { next unless /(.{6})\s+.+=([^\s]+)/; print $1,"\n" if $activ{$1}; } print "done";

I am sure that there are more lines that are supposed to be printed. E.G.

$uniprot: Q801F8 Q90XZ5; Q90XZ8;Name=dmrt1 B7ZS42 A4PBN7; B7ZS44;Name=dmrt1-b ;PF00751;PF12374 Q157S1 Name=Crtc1 Synonyms=Mect1, $activ: Q801F8 | PF00751.13 PF12374.3 PF12374.3 B7ZS42 | PF00751.13 PF12374.3 PF12374.3 Q157S1 | PF12886.2 PF12885.2 PF12884.2

I shall try to reverse the order, I.E, make a hash out of $uniprot instead of $activ and run it again.


Comment on Re^14: Help with pushing into a hash
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Re^15: Help with pushing into a hash
by Kenosis (Priest) on Sep 03, 2012 at 16:29 UTC

    Perhaps your data is more complex than first thought. You listed the following:

    $uniprot Q801F8 Q90XZ5; Q90XZ8;Name=dmrt1 B7ZS42 A4PBN7; B7ZS44;Name=dmrt1-b ;PF00751;PF12374 Q157S1 Name=Crtc1 Synonyms=Mect1, $activ: Q801F8 | PF00751.13 PF12374.3 PF12374.3 B7ZS42 | PF00751.13 PF12374.3 PF12374.3 Q157S1 | PF12886.2 PF12885.2 PF12884.2

    Give the above listing, are you (potentially) expecting the following (keys/values)?

    Q801F8 -> PF00751 PF12374 PF12374 B7ZS42 -> PF00751 PF12374 PF12374 Q157S1 -> PF12886 PF12885 PF12884 ... Q801F8 -> dmrt1 PF00751 PF12374 PF12374 Q90XZ5 -> dmrt1 PF00751 PF12374 PF12374 Q90XZ8 -> dmrt1 PF00751 PF12374 PF12374 B7ZS42 -> dmrt1-b PF00751 PF12374 PF12374 A4PBN7 -> dmrt1-b PF00751 PF12374 PF12374 B7ZS44 -> dmrt1-b PF00751 PF12374 PF12374 Q157S1 -> Crtc1 PF12886 PF12885 PF12884

    It looks like there are multiple keys on a single $uniprot line:

    Q801F8 Q90XZ5; Q90XZ8;Name=dmrt1 ^^^^^^ ^^^^^^ ^^^^^^ | | | +-------+-------+--- keys to be captured?

    If this is the case, the current regex operating on the $uniprot lines would fail.

    Let me know if the script needs to capture potentially multiple keys on a single $uniprot line...

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