FarTech has asked for the wisdom of the Perl Monks concerning the following question:

Hi guys

i have the following xyz file which contains 

GTM1_MOUSE GLUTATHIONE S-TRANSFERASE GT8.7 (EC 2.5.1.1  (217 aa) 
 WFAGDKVTYVDFLAYDILDQYRMFEPKCLDAFPNLRDFLARFEGLKKISAYMKS-SRYIA 
 TPIFSKMAHWSNK                                                

GTM1_RAT GLUTATHIONE S-TRANSFERASE YB1 (EC 2.5.1.18) (  (217 aa) 
 WFAGDKVTYVDFLAYDILDQYHIFEPKCLDAFPNLKDFLARFEGLKKISAYMKSSRYLST 
 PIFSKLAQWSNK                                                 

GTMU_CRILO GLUTATHIONE S-TRANSFERASE Y1 (EC 2.5.1.18)   (217 aa) 
 FAGDKVTLCGFLAYDVLDQYQMFEPKCLDPFPNLKDFLARFEGLKKISAYMKTSRFLRRP 
 IFSKMAQWSNK                                                  

GTMU_RABIT GLUTATHIONE S-TRANSFERASE MU 1 (EC 2.5.1.18  (217 aa) 
               PMTLGYWDVRGLALPIRMLLEY--TDTSYEEKKYTMGDAPNYDQSK 
 WLSEKFTLGL----DFPN-LPYLID-GTHKLTQSNAILRYLARKHGLCGETEEERIRVDI 
 LENQLMDNRFQLVNVCYSPDFEKLKPEYLKGLPEKLQLYSQFLGSLPWFAGDKITFADFL 

GTM1_HUMAN GLUTATHIONE S-TRANSFERASE MU 1 (EC 2.5.1.18  (217 aa) 
 LPEKLKLYSEFLGKRPWFAGNKITFVDFLVYDVLDLHRIFEPKCLDAFPNLKDFISRFEG 
 LEKISAYMKSSRFLPRPVFSKMAVWGNK                                 

GLNA_ANASP GLUTAMINE SYNTHETASE (EC 6.3.1.2) (GLUTAMAT  (473 aa) 
 SLELALEALENDHAFLTDTGVFTEDFIQNWIDYKLANEVKQMQLRPH-PYEFSIYYDV   

GTM4_HUMAN GLUTATHIONE S-TRANSFERASE MU 4 (EC 2.5.1.18  (218 aa) 
 LPTMMQHFSQFLGKRPWFVGDKITFVDFLAYDVLDLHRIFEPNCLDAFPNLKDFISRFEG 
 LEKISAYMKSSRFLPKPLYTRVAVWGNK

[download]

i have to extract one sequence at a time from xyz file which can be either 2 or 3 lines and store it in a abc file which can be used as a input to fasta34.exe application

how should proceed

should i store the xyz file in a array and then extract lines till it come across a blank line or is there any other method to do so

Replies are listed 'Best First'.
Re: Arrays and Files
by borisz (Canon) on Jan 31, 2005 at 23:53 UTC 
    local $/ = "\n\n";
open my $fh, "<","xyz" or die $!;
while (<$fh>){
  # $_ contains one entry here
}

    [download]
    Boris
[reply]
[d/l]
Re: Arrays and Files
by gube (Parson) on Feb 01, 2005 at 04:23 UTC

    Hi, Try this the first sequence u will get u can write it to abc file 

    undef $/;
open(IN, "d:\\xyz.txt")    ||    die "Cannot open file\n";
$str = <IN>;
if ($str =~ m#(.*?)\n\n#gsi) {
    $a=$1;    
    
}

print $a;

    [download]
    o/p: GTM1_MOUSE GLUTATHIONE S-TRANSFERASE GT8.7 (EC 2.5.1.1 (217 aa) WFAGDKVTYVDFLAYDILDQYRMFEPKCLDAFPNLRDFLARFEGLKKISAYMKS-SRYIA TPIFSKMAHWSNK


    Regards,
    Gubendran.L

[reply]
[d/l]
Re: Arrays and Files
by sh1tn (Priest) on Jan 31, 2005 at 23:55 UTC
    Is it possible to be just hash structure?
    Thus You can r/w in pairs (keys-source/values-dest):

    use IO::File;

my $files = {
  'x', 'a',
  'y', 'b',
  'z', 'c'
};

for( keys %{$files} ){

  $read  = new IO::File "< $_";
  die "can't open_r $read: $!" unless defined($read);
  $write = new IO::File "> $files->{$_}";
  die "can't open_w $write: $!" unless defined($write);

  print $write $_ while <$read>;
  
  $read->close;
  $write->close;
}

    [download]
[reply]
[d/l]
Re: Arrays and Files
by Grundle (Scribe) on Feb 01, 2005 at 00:23 UTC
    What exactly counts as a sequence?? Is it the lines underneath

    GTM1_MOUSE etc.. etc..

    or is it the whole entry? I am going to assume it is the whole entry. 

    $file = "xyz";

if(!open(READ_FILE, "$file")){
    die "Cannot open file [$file]\n";
}

my $sequence = "";
while(my $line = <READ_FILE>){
    if($line =~ m/^G.*\(EC/){
        if($sequence){
            #write sequence here.
            print "seq: $sequence\n";
            $sequence = "";
        }
        $sequence .= $line;
        
        
    }else{
        $sequence .= $line;
    }
}
#write last sequence here
print "last: $sequence\n";

    [download]
    That regex is somewhat hardcoded, if you are nervous about it, you can always change it to look for the empty line. I sort of assumed that every sequence would start with

    G<something>

    and would have

    (EC <more-stuff>
[reply]
[d/l]
Re: Arrays and Files
by Mago (Parson) on Feb 01, 2005 at 13:16 UTC 

    #!/usr/local/bin/perl -w
use strict;

my (@seq, $x);
open (F, "< xyz") || die "Cannot open file\n";

while (<F>) { 
    chomp($_); 
    if (length($_) > 0) { 
        $seq[$x] .= $_; 
    } else { 
        $x++; 
    } 
}

    [download]


    Mago
    mago@rio.pm.org


[reply]
[d/l]

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