perl fix code (Help :) )

Question

[Elza Chotza]

i have got a big list with proteins like this below:

ID   140U_DROME              Reviewed;         261 AA.
AC   P81928; Q9VFM8;
FT   CHAIN         1    261       RPII140-upstream gene protein.
FT                                /FTId=PRO_0000064352.
FT   TRANSMEM     67     87       Potential.
FT   TRANSMEM    131    151       Potential.
FT   TRANSMEM    183    203       Potential.
FT   CONFLICT     64     64       S -> F (in Ref. 1).
SQ   SEQUENCE   261 AA;  29182 MW;  5DB78CF6CFC4435A CRC64;
     MNFLWKGRRF LIAGILPTFE GAADEIVDKE NKTYKAFLAS KPPEETGLER LKQMFTIDEF
     GSISSELNSV YQAGFLGFLI GAIYGGVTQS RVAYMNFMEN NQATAFKSHF DAKKKLQDQF
     TVNFAKGGFK WGWRVGLFTT SYFGIITCMS VYRGKSSIYE YLAAGSITGS LYKVSLGLRG
     MAAGGIIGGF LGGVAGVTSL LLMKASGTSM EEVRYWQYKW RLDRDENIQQ AFKKLTEDEN
     PELFKAHDEK TSEHVSLDTI K

and the format i want to receive is:

 >ADBR2_HUMAN|P07550|413aa
MGQPGNGSAFLLAPNGSHAPDHDVTQERDEVWVVGMGIVMSLIVLAIVFGNVLVITAIAKFERLQTVTN
----------------------------------MMMMMMMMMMMMMMMMMMMMMMMM-----------
//

can sοmeone fix my code please?

#!/usr/bin/perl 
use strict;

use warnings;  

open(IN, "<transmem_proteins.swiss") or die "i can not open the transmem_proteins.swiss, $!";
open (OUT, ">askisi1.txt");


while (<IN>)
{   

if ($_=~m/^ID\s{3} (\w+_\w+)\s / )
    $id=$1;
    print OUT "$id ID\n";


if ($_=~m/^AC\s{3} (\w+)\w{1} and $ac==0)
    $ac=$$1;
    $ac++;

if ($_=~m/^SQ\s{3} SEQ\s{3}(\w+)\s{1}AA)
    $aa = $1;
    print OUT "$aa aa\n";

if ($_=~m/^\s{5}(.*)\n/)
{
    seq = $seq.$1;
    }
if ($_=~m/^FT\s{3}TRANSMEM\s+(\w+)\s+(\w+)/)
    if($start[0] == NULL){
    shift (@start);
    }
    if ($end[0] == NULL){

    shift (@end);
    }
    push @start, $s1;
    push @end, $s2;
    $number_of_transmem++;

    $seq = ~s/\s//g;
    if ($_=~m/\/\//;

if ($tr_table[0]=NULL){
shift (@tr_table);
}   
for ($a=0; $a<$aa; $a++){
$tr_table[$a]='-';
}
for ($tr=0; $tr<$number_of_transmem; $tr++)
    for ($a=0; $a,aa; $a++)
    if (($a+1)>= $start[$tr] and ($a+1)<=$end[$tr]){
    $tr_table[$a]='M';
}
print OUT @tr_table;
print OUT "\n";
print OUT "//\n";

$ac=0;
$number_of_transmem=0;
$seq=~s/.*//;
@start=NULL;
@end=NULL;
@tr_table=NULL;
}

Answer 1

[AK]

Hi Elza Chotza,

Although 93% of Paint Splatters are Valid Perl Programs, you still have too many typos in your codes (and other things such as missing braces of if statements and a right slash in regular expression...), and $seq = ~s/\s//g should be written as $seq =~ s/\s//g. A quick check by PerlTidy returned:

PerlTidy: Errors reported by perltidy during last run
=====================================================

14: $id=$1;
    ^
found Scalar where operator expected

Missing ';' above?

30: if ($_=~m/^FT\s{3}TRANSMEM\s+(\w+)\s+(\w+)/)
                               ----------^
found ( where operator expected (previous token underlined)

11: {
    ^
43: if ($_=~m/\/\//;
       ^
66: }
    ^
Found 1 extra '(' between '{' on line 11 and '}' on line 66
    The most recent un-matched '(' is on line 43
67: final indentation level: 1

Final nesting depth of '('s is 1
The most recent un-matched '(' is on line 43
43: if ($_=~m/\/\//;
       ^
67: To save a full .LOG file rerun with -g

After fixing the typos and making use of $transmem_str = "-" x $aa; to create the transmembrane string, followed by substr( $transmem_str, $start, $length, "M" x $length ); to replace - with M according to the start and end locations, your codes can be modifed to (tested with example from https://www.uniprot.org/uniprot/P81928.txt):

#!/usr/bin/perl
use strict;
use warnings;

open( IN, "<P81928.txt" ) or die "i can not open the transmem_proteins.swiss, $!";
open( OUT, ">askisi1.txt" );

my ( $id, $ac, $aa, $seq, $transmem_str ) = ( "", "", "", "", "" );
my @tr_table = ();
while (<IN>) {
    if ( $_ =~ m/^ID\s{3}(.+?)\s+/ ) {
        $id = $1;
    }

    if ( $_ =~ m/^AC\s{3}(.+?);/ ) {
        $ac = $1;
    }

    if ( $_ =~ m/^FT\s{3}TRANSMEM\s+(\d+)\s+(\d+)\s+/ ) {
        my ( $start, $end ) = ( $1 - 1, $2 - 1 );
        my $length = $end - $start + 1;
        push @tr_table, [ $start, $length ];
    }

    if ( $_ =~ m/^SQ\s{3}SEQUENCE\s{3}(\d+)\sAA;/ ) {
        $aa           = $1;
        $transmem_str = "-" x $aa;
    }

    if ( $_ =~ m/^\s{5}(.*)\n/ ) {
        $seq = $seq . $1;
        $seq =~ s/\s//g;
    }

    if ( $_ =~ /^\/\// ) {
        foreach my $tr (@tr_table) {
            my ( $start, $length ) = ( $tr->[0], $tr->[1] );
            substr( $transmem_str, $start, $length, "M" x $length );
        }

        print OUT ">$id\|$ac\|$aa" . "aa\n";
        print OUT "$seq\n";
        print OUT "$transmem_str\n";
        print OUT "//\n";

        ( $id, $ac, $aa, $seq, $transmem_str ) = ( "", "", "", "", "" );
        @tr_table = ();
    }
}

It returns:

$ cat askisi1.txt
>140U_DROME|P81928|261aa
MNFLWKGRRFLIAGILPTFEGAADEIVDKENKTYKAFLASKPPEETGLERLKQMFTIDEFGSISSELNSVYQAGFLGFLIGAIYGGVTQSRVAYMNFMENNQATAFKSHFDAKKKLQDQFTVNFAKGGFKWGWRVGLFTTSYFGIITCMSVYRGKSSIYEYLAAGSITGSLYKVSLGLRGMAAGGIIGGFLGGVAGVTSLLLMKASGTSMEEVRYWQYKWRLDRDENIQQAFKKLTEDENPELFKAHDEKTSEHVSLDTIK
------------------------------------------------------------------MMMMMMMMMMMMMMMMMMMMM-------------------------------------------MMMMMMMMMMMMMMMMMMMMM-------------------------------MMMMMMMMMMMMMMMMMMMMM----------------------------------------------------------
//

[Elza Chotza]

Thank you so much! You saved my day :D. I am trying to learn Perl, but it's all greek to me.