Hello, I want to find the sequences in tmp01 which are containing in tmp02, then print all of them out. Tab seperated tmp02 file. Thanks in advance!

 tmp01

ATCCCACCGCTGCCACCA
ACCCTGCTCGCTGCGCCA
TCCCCGGCACCTCCACCA
TCCCCGGCATCTCCACCA
ATCCTGCCGACTACGCCA
TCGATTCCCGGCCCATGCACCA
TCGATTCCCGGCCAACGCACCA
GTCCCACCAGAGTCGCCA
ACCCCACTCCTGGTACCA
GTCCCTTCGTGGTCGCCA

tmp02

AACCCCATCCCACCGCTGCCACCA    1
AACCCCATCCTCGTCGCC    1
AACCCCATGAAATAAGAG    2
AACCCCATGATCAGGACAAG    1
AACCCCATTAAAAAATGG    1
AACTGGATTCTCTGAAATCCCACCGCTGCCACCA    1
AACTGGATTGTCTGTTTGT    1
AACTGGCAAGTTCAGGCATG    1
AACTGGCACACACAACC    1
AACTGGCACACACAACCT    1

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open(IN1,"tmp01") || die "Cannot open this file";

@lines1 = <IN1>;

open(IN2,"tmp02") || die "Cannot open this file";

@lines2 = <IN2>;


open(OUT,">tmp03") || die "Cannot open this file";

for $item1(@lines1){

    chomp $item1;


    #print OUT $item1,"\t";

@tmp1=split(/\t+/, $item1);


for $item2(@lines2){

    chomp $item2;

@tmp2=split(/\t+/, $item2);

        if ($tmp1[0] =~m/ *$tmp2[0]*){

            print OUT $item1,"\t",$item2;

            #last;    

        }

    $i++
}


print OUT "\n";


}


close(IN1);

close(IN2);

close(OUT);

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Is it also possible to use this mechanism to disable my own debug messages for a scope?

(I'm aware about the possibility to manipulate $SIG{"__WARN__"} handler, but trying not to reinvent the wheel².)

use strict;
use warnings;
my $x;

{
    no warnings;
#    no warnings 'uninitialized';
    print "$x";
    warn "inside";
}
print "$x";
warn "outside";
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inside at d:/Users/lanx/pm/no_warn.pl line 9.
Use of uninitialized value $x in string at d:/Users/lanx/pm/no_warn.pl
+ line 11.
outside at d:/Users/lanx/pm/no_warn.pl line 12.
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²) and overusing Pad::Walker

I am on macOS (HighSierra) using Perlbrew. I have problems to install PAR::Packer, as it fails with this error:

--> Working on PAR::Packer
Fetching http://www.cpan.org/authors/id/R/RS/RSCHUPP/PAR-Packer-1.045.
+tar.gz ... OK
==> Found dependencies: DynaLoader
skipping N/NW/NWCLARK/perl-5.8.6.tar.gz
! Installing the dependencies failed: Module 'DynaLoader' is not insta
+lled
! Bailing out the installation for PAR-Packer-1.045.
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I have on the same machine several Perl installation. Never had a problem to install this module. However, I noticed that if I use

I get a rather short list of cperl. This was not the case until a couple of months ago, where I got a list of perl. I have PAR::Packer installed with perl-5.24.4, however on both cperl-5.27.2 and cperl-5.26.2 it fails with me message above. Any idea?

Hi, I am trying to get the response from using SOAP API and results in parsing error. I am using SOAP LITE module to pull response. Is there a way we can get rid of error responses (￿￿) and process the rest of the data? or Are there any conversions available for SOAP responses? Below are code. Appreciate your reply

not well-formed (invalid token) at line 15, column 314, byte 3846 at C:/Perl64/lib/XML/Parser.pm line 187. <?xml version="1.0" encoding="UTF-8"?> <soapenv:Envelope xmlns:soapenv="http://schemas.xmlsoap.org/soap/envelope/"> <soapenv:Body> <GetRelevanceResultResponse xmlns="http://schemas.bigfix.com/Relevance"> ..... 1sys234&~&15802503&~&Adobe Creative Suite&~& &~& &~& C:\Users\boundsjr\Adobe &~& &~& &~& C:\PROGRA~2\INSTAL~1\{0134A~1\setup.exe /relaunched/rootloc=c:\users\boundsjr\desktop\creative suite 2 - standard\adobe creative suite 2.0/lang=0409￿￿嘸ņ椺倝 鈀牔湡潳瑦匠汯瑵潩獮䌠癩汩㌠⁄牆浡睥牯⸱‰縦…⸱‰縦…牔湡潳瑦匠汯瑵潩獮☠♾䌠尺牐杯慲楆敬⁳砨㘸尩牔湡潳瑦匠汯瑵潩獮䌠癩汩㌠⁄牆浡睥牯縦…☠♾†縦…䌢尺楗摮睯屳牔湡潳瑦匠汯瑵潩獮䌠癩汩㌠⁄牆浡睥牯屫湵湩瑳污⹬硥≥∠唯䌺尺楗摮睯屳牔湡潳瑦匠汯瑵潩獮䌠癩汩㌠⁄牆浡睥牯屫湕湩瑳污屬湵湩瑳污⹬浸≬" ..... </GetRelevanceResultResponse> </soapenv:Body> </soapenv:Envelope> at C:\Users\User1\Desktop\rep\SW\SoftwareInventoryFull_v5.pl line 74.

use SOAP::Lite;
my $configfile="Config.txt";
my $host;
my $cusername;
my $cpassword;
my $cexpr1;

my $offset = 0;
while ($offset < $loop) 
 {
    my $username = SOAP::Data->name('username' => $cusername );
    my $password = SOAP::Data->name('password' => $cpassword );
    my $service = SOAP::Lite -> uri( 'https://' . $host . '/reports?ws
+dl' )
                 -> proxy( 'https://' . $host );    
    $timestamp = localtime(time);
    
    #Retrieve the records
    my $expr = SOAP::Data->name('relevanceExpr' => $cexpr1 );
     my $result = $service -> GetRelevanceResult( $expr, $username, $p
+assword );
    if( $result->fault )
    {
        print " [".$timestamp. "] ---- faultcode: " . $result->faultco
+de . "\n";
        print " [".$timestamp. "] ---- faultstring: " . $result->fault
+string . "\n";
    }
    else
    {  
        # Insert the data in to Temp table from API
                   foreach my $answer ( $result->valueof( "//GetRelava
+nceResultResponse/a" ) )
                  {
                    
                    Insert in to the table.

                  }

    }
 }
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What is wrong in this command for pp and the filter option on Windows?

pp -u -g -o MyExe -F Bleach='^(GUI_|AA_|myMainScript)' myMainScript.pl
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the regex should pass to the bleach routines all modules starting with GUI_, AA_. etc.

I sometimes use (and suggest) this to slurp a file in a single line:

my $data = do { open my $fh, '<', $file or die $!; local $/; <$fh> };
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The lexical filehandle should be automatically closed at the end of the block. Can anyone think of any downsides to the above? Like perhaps some subtle scoping issue, or it's bad style to rely on the implicit close, etc. ... or am I just being paranoid?

Update: Typo fix, $/ not $\, thanks Corion!

Hello everyone, I am trying to write a script in perl which will do the following

it will read a pdb file that contains only Ca atoms as the following

1         2   3   4  5  6   
ATOM      1  CA  PRO A 889      84.370  72.820  26.830  1.00  0.00    
+        
ATOM      2  CA  THR A 890      87.370  73.900  28.080  1.00  0.00    
+        
ATOM      3  CA  VAL A 891      90.920  72.490  27.750  1.00  0.00    
+        
ATOM      4  CA  PHE A 892      93.640  74.890  28.970  1.00  0.00    
+        
ATOM      5  CA  HIS B 893      97.060  74.200  27.360  1.00  0.00    
+        
ATOM      6  CA  LYS B 894      99.880  73.920  29.990  1.00  0.00 
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it will read a second pdb that contains every atom

1         2  3    4  5  6 
     
ATOM      1  N   PRO A 889      16.220  12.185   1.804  1.00 71.54    
+       N  
ATOM      2  CA  PRO A 889      16.101  12.990   3.034  1.00 70.89    
+       C  
ATOM      3  C   PRO A 889      15.432  14.346   2.803  1.00 72.31    
+       C  
ATOM      4  O   PRO A 889      14.743  14.852   3.703  1.00 72.20    
+       O  
ATOM      5  CB  PRO A 889      17.553  13.151   3.502  1.00 72.96    
+       C  
ATOM      6  CG  PRO A 889      18.315  12.067   2.782  1.00 78.00    
+       C  
ATOM      7  CD  PRO A 889      17.626  11.907   1.465  1.00 73.35    
+       C  
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(The files refer to the same molecule but have different number of lines)

So if the residue number (column num 5) is the same it will take the chain letter (column num 4) from the first file and replace all the chain letters that have the same residue number in the second file. So far i've got this disaster :/

print "\nEnter the network pdb file file: ";
$inputFile = <STDIN>;
chomp $inputFile;

unless (open(INPUTFILE, $inputFile)) {
    print "Cannot read from '$inputFile'";
    <STDIN>;
    exit;
}
# load the file into an array
chomp(@networkpdb = <INPUTFILE>);

# close the file
close(INPUTFILE);

print "\nEnter the pdb output file: ";
$inputFile2 = <STDIN>;
chomp $inputFile2;

unless (open(INPUTFILE, $inputFile2)) {
    print "Cannot read from '$inputFile2'";
    <STDIN>;
    exit;
}

chomp(@pdb = <INPUTFILE>);


close(INPUTFILE);


            
for ($line1 = 0; $line1 < scalar @networkpdb; $line1++) {
    if ($networkpdb[$line1] =~ m/ATOM\s+\d+\s+\w+\s+\w{3}\s*(\w+)\s*(\
+d*)\s+\S+\.\S+\s+\S+\.\S+\s+\S+\.\S+\s+.+\..+\..*/ig) {
               my  $resnum=$2;
               my  $chain=$1;
for ($line = 0; $line < scalar @pdb; $line++) {
     if ($pdb[$line]=~ m/(ATOM\s+\d+\s+\w+\s+\w{3}\s*)(\w+)\s*(\d*)(\s
++\S+\.\S+\s+\S+\.\S+\s+\S+\.\S+\s+.+\..+\..*)/ig) {
                my $begining=$1;
                my  $resnum1=$3;
                my  $chain1=$2;
                my $end=$4;
 if ($resnum1=$resnum)
                 {$chain1=$chain;
 $parsedData{$line} = $begining.$chain1."\s".$resnum1.$end;
        
    
}}}}}

# create the output file name
$outputFile = "WithNetwork_".$inputFile;

# open the output file
open (OUTFILE, ">$outputFile");
# print the data lines
foreach $line (sort {$a <=> $b} keys %parsedData) {
    print OUTFILE $parsedData{$line}."\n";
}

# close the output file
close (OUTFILE);
[download]

thank you very much in advance

for ($foo) {
  when (/blah/) {...}
  when (/xyz/)  {...}
 ...
 }
[download]

Hi Perl Monks,

I am interested in converting the Gene ID of NCBI to GenBank ID. In NCBI Gene database, when I write 7157 as Gene ID in search box, the page opens with the heading "TP53 tumor protein p53 Homo sapiens (human)". Almost at the bottom of that page the sub-heading appears as "mRNA and Protein(s)" which shows the GenBank ID as "NM_000546.5" (first entry) with a hyperlink. When clicked, the GenBank page opens up and shows the details. This is a cumbersome process when one has to get the GenBank ID of many genes. I searched in the web for a perl script which can convert Gene ID to GenBank ID using internet directly. But I did not get such a script. However, the link http://biodb.jp/ can perform this task of conversion in a very lengthy procedure. Then, I tried to get the sequence of Gene ID 7157 using a script:

Here goes the script for sequence:

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

use Bio::DB::GenBank;
use Bio::SeqIO;  
use Text::Wrap; 

my $gb= new Bio::DB::GenBank; 

my $id='7157'; 

my $seq = $gb->get_Seq_by_gi($id); 

print "\n seq: $seq\n"; 

exit; 
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But I got the wrong result and not the sequence in cmd as follows: Here goes the result in cmd:

 C:\Users\x>cd d*

C:\Users\x\Desktop>g2.pl

 seq: Bio::Seq::RichSeq=HASH(0x780b234)

C:\Users\x\Desktop> 
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I need suggestions from PerlMonks to solve this problem of ID conversion so that I can get the results of Gene IDs: 7157, 7422 as follows in cmd:

I expect results in the following format:

 
GenBank ID
NM_000546.5
NM_001025366.2 
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Hello to all! I am new to perl-cgi, just trying to execute my first program and stored it as mytest.pl in my home directory. I am working on a shared unix based server so I don't have access to var/www/cgi-bin folder of my directory and there is not any webserver package installed. So how should i run this type of files. Please provide step by step procedure for running this file such that on browser Hello World! should display.

#!/usr/local/bin/perl
print "Content-Type: text/html\n\n";
print "<html> <head>\n";
print "<title>Hello, world!</title>";
print "</head>\n";
print "<body>\n";
print "<h1>Hello, world!</h1>\n";
print "</body> </html>\n";
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