in reply to Re: how to remove duplicate strings?
in thread how to remove duplicate strings?

hi graff, thanks for the reply. but,all i want to process now is the SEQUENCE. that is the string(a continous stretch of alphabets)which is next to the accessions line. so when i grep it and store it in a seperate array, and when i print the array (inside the loop) i am getting the output something like this 
MGDVEKGKKIFIMKCSQCHTVEMGDVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIWGEDTL
+ +MEYLENPKKYIP MGDVEKGKKIFIMKCSQCHTVEMGDVEKGGKHKTGPNLHGLFGRKTGQAPGYSY
+TAANKNKGIIWGEDTL +MEYLENPKKYIP MGDVEKGKKIFIMKCSQCHTVEMGDVEKGGKHKTGPNL
+HGLFGRKTGQAPGYSYTAANKNKGIIWGEDTL +MEYLENPKKYIP MGDVEKGKKIFIMKCSQCHTVE
+MGDVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIWGEDTL +MEYLENPKKYIP MGDVEK
+GKKIFIMKCSQCHTVEMGDVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIWGEDTL +MEY
+LENPKKYIP GDVEKGKKIFIMKCSQCHTVEKGSSSKHKSSSTGPNLHGLFGRKTGQAPGYSYTAANKN
+KGIIWGED GDVEKGKKIFIMKCSQCHTVEKGSSSKHKSSSTGPNLHGLFGRKTGQAPGYSYTAANKNK
+GIIWGED GDVEKGKKIFIMKCSQCHTVEKGSSSKHKSSSTGPNLHGLFGRKTGQAPGYSYTAANKNKG
+IIWGED GDVEKGKKIFIMKCSQCHTVEKGSSSKHKSSSTGPNLHGLFGRKTGQAPGYSYTAANKNKGI
+IWGED GDVEKGKKIFIMKCSQCHTVEKGSSSKHKSSSTGPNLHGLFGRKTGQAPGYSYTAANKNKGII
+WGED GDVEKGKKIFIMKCSQCHTVEKGGSSSSKHKTGPNLHGLFGAAAAAAAARKTGQAPGYSYTAAN
+KSSSSN +KGITWGEDTLMEYLENPKKYIPGTKMIFVGIKKKEE GDVEKGKKIFIMKCSQCHTVEKGG
+SSSSKHKTGPNLHGLFGAAAAAAAARKTGQAPGYSYTAANKSSSSN +KGITWGEDTLMEYLENPKKYI
+PGTKMIFVGIKKKEE GDVEKGKKIFIMKCSQCHTVEKGGSSSSKHKTGPNLHGLFGAAAAAAAARKTG
+QAPGYSYTAANKSSSSN +KGITWGEDTLMEYLENPKKYIPGTKMIFVGIKKKEE GDVEKGKKIFIMK
+CSQCHTVEKGGSSSSKHKTGPNLHGLFGAAAAAAAARKTGQAPGYSYTAANKSSSSN +KGITWGEDTL
+MEYLENPKKYIPGTKMIFVGIKKKEE GDVEKGKKIFIMKCSQCHTVEKGGSSSSKHKTGPNLHGLFGA
+AAAAAAARKTGQAPGYSYTAANKSSSSN +KGITWGEDTLMEYLENPKKYIPGTKMIFVGIKKKEE GD
+VFKGKRIFIMKCSQCHTVESSSSKGGKHKTGPNLHGLFGSSSSSSSSSSR

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when i print the array outside the loop, either its printing the last string alone, or, removes the repeating alphabets from the string and printin a result like this. 
MGDVEKIFCSQHTPNLRAYW MGDVEKIFCSQHTPNLRAYW MGDVEKIFCSQHTPNLRAYW MGDVEKI
+FCSQHTPNLRAYW MGDVEKIFCSQHTPNLRAYW GDVEKIFMCSQHTPNLRAYW GDVEKIFMCSQHT
+PNLRAYW GDVEKIFMCSQHTPNLRAYW GDVEKIFMCSQHTPNLRAYW GDVEKIFMCSQHTPNLRAY
+W GDVEKIFMCSQHTPNLARYW GDVEKIFMCSQHTPNLARYW GDVEKIFMCSQHTPNLARYW GDVE
+KIFMCSQHTPNLARYW GDVEKIFMCSQHTPNLARYW GDVFKRIMCSQHTEPNL

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but the result which i need is: 
MGDVEKGKKIFIMKCSQCHTVEMGDVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIWGEDTL
+ +MEYLENPKKYIP GDVEKGKKIFIMKCSQCHTVEKGSSSKHKSSSTGPNLHGLFGRKTGQAPGYSYT
+AANKNKGIIWGED GDVEKGKKIFIMKCSQCHTVEKGGSSSSKHKTGPNLHGLFGAAAAAAAARKTGQA
+PGYSYTAANKSSSSN +KGITWGEDTLMEYLENPKKYIPGTKMIFVGIKKKEE GDVFKGKRIFIMKCS
+QCHTVESSSSKGGKHKTGPNLHGLFGSSSSSSSSSSR

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and i need all this as 4 elements in the same array. i hope u got it.

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Re^3: how to remove duplicate strings?
by graff (Chancellor) on Oct 30, 2006 at 06:39 UTC
    Well no, I'm not sure that I got it. What is clear is that you did not satisfy GrandFather's request in the first reply, as I hoped you would.

    So let me make another guess at what you really want. How about this: 

    my @arr = ();
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 @arr, $_;
    }
}

print "@arr\n";

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    Now, I would assume there should be more code than that, if you really need to do things with $acc, $entry, $org and $title. If you really just want to output an array with those long strings as the elements of the array, the code could be a lot simpler.

    If there's a chance that one of those long strings might appear more than once in the data file, use those long strings as hash keys instead of array values: 

    # simplified version: ignore header stuff:

my %hash;
while(<PIR>)
{
    chomp;
    $hash{$_} = undef unless /^(?:ENTRY|TITLE|ORGANISM|ACCESSIONS)\s/;
}

print join " ", keys %hash, "\n";

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    Using a hash like that might be a good idea for other reasons: maybe you would want the header values to be associated with each long string. (Hint: some people refer to hashes as "associative arrays".) If so, assign the header strings as the hash value.
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      hey graff, thank ya, u got my problem rite.i tried writting the code the way u said, and i got the answer, but the problem which i am facing now is, i had to save each element of that array in to a new array and split the characters. to make it clear, the program is now like this. 
      open (PIR,'/home/guest/sampir.txt');
my @arr = ();
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, $_;
    }
}

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      and i tried splitting it up like this 
      foreach $r(@se)
{
@y=split(//,$r);
}

      [download]
      but am not getting the answer. how to go abt it.?
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