print, number of character from a file

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Join Date: Oct 2007

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mank

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print, number of character from a file

Mar 25th, 2008

HI

I am trying to print a certain number of sequences from a file.
So if the sequence is like
LKSAJDLSAJDLSAJDLKSJD.
then I want to write from 10th character to 20th character.
please help. Here is my code

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

use warnings;

my ($fileName, $firstSequence, $lastSequence) = @ARGV;

open IN, "< $fileName" || die "Can't open $fileName";

while(<IN>) {
  chomp;
  my @line = split(/\t/, $_); 
#  print $line[0];
  print $line[$firstSequence..$lastSequence];
#  print $line[$lastsequence]; 
}

close(IN);
exit;

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Join Date: Oct 2007

Posts: 41

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Re: print, number of character from a file

Mar 25th, 2008

This only checks in a line, but what if the sequence is multiline

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#!/usr/bin/perl -w

use strict;
use warnings;

my ($fileName, $firstSequence, $lastSequence) = @ARGV;

open (IN, "<$fileName") || die "Can't open $fileName";

while(<IN>) { 
 chomp;
  my @line = split(//, $_);  

  print @line[$firstSequence..$lastSequence];

 print "\n";
}

close(IN);
exit;

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katharnakh katharnakh is offline

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Re: print, number of character from a file

Mar 25th, 2008

Hi, im just modifying your code, use substr() method to get substring from a string.

Syntax: substr EXPR,OFFSET,LENGTH

 Help with Code Tags 
 Perl Syntax (Toggle Plain Text) 
#!/usr/bin/perl -w
use strict;
 
use warnings;
 
my ($fileName, $firstSequence, $lastSequence) = @ARGV;
 
open (IN, "< $fileName") || die "Can't open $fileName";
 
while(<IN>) {
  chomp;
  print "\n",substr($_, $firstSequence, $lastSequence);
}
 
close(IN);
exit;
#!/usr/bin/perl -w
use strict;

use warnings;

my ($fileName, $firstSequence, $lastSequence) = @ARGV;

open (IN, "< $fileName") || die "Can't open $fileName";

while(<IN>) {
  chomp;
  print "\n",substr($_, $firstSequence, $lastSequence);
}

close(IN);
exit;

print $line[$firstSequence..$lastSequence]; this line will get you element at index 10 till element at index 20 from @line array, not sub string of an element.

katharnakh.

Last edited by katharnakh : Mar 25th, 2008 at 6:34 am.

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Re: print, number of character from a file

Mar 25th, 2008

•

Originally Posted by mank

This only checks in a line, but what if the sequence is multiline
Help with Code Tags

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#!/usr/bin/perl -w

use strict;
use warnings;

my ($fileName, $firstSequence, $lastSequence) = @ARGV;

open (IN, "<$fileName") || die "Can't open $fileName";

while(<IN>) { 
 chomp;
  my @line = split(//, $_);  

  print @line[$firstSequence..$lastSequence];

 print "\n";
}

close(IN);
exit;
#!/usr/bin/perl -w use strict; use warnings; my ($fileName, $firstSequence, $lastSequence) = @ARGV; open (IN, "<$fileName") || die "Can't open $fileName"; while(<IN>) { chomp; my @line = split(//, $_); print @line[$firstSequence..$lastSequence]; print "\n"; } close(IN); exit;

While loop in your code, will loop through lines of input file. What's question, explain clearly.

katharnakh.

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Re: print, number of character from a file

Mar 25th, 2008

this code only reads line by line
so if there is a single sequene like (distributed over 2 lines)

LASJDLKAJSDKJSADJLKSADLJLSAKJDK
AKSJDKLJSAKDJJSAD

so my code only prints character in the first and 2nd line seperately.
I want to add these two lines to a single line and print out the character sequence of that line.

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Re: print, number of character from a file

Mar 25th, 2008

•

Originally Posted by mank

this code only reads line by line
so if there is a single sequene like (distributed over 2 lines)

LASJDLKAJSDKJSADJLKSADLJLSAKJDK
AKSJDKLJSAKDJJSAD

so my code only prints character in the first and 2nd line seperately.
I want to add these two lines to a single line and print out the character sequence of that line.

Then you must go with concatenation.

 Help with Code Tags 
 Perl Syntax (Toggle Plain Text) 
...
my $line = '';
while my $l(<IN>){
    $line .= $l; # entire file in a line
}
...
...
my $line = '';
while my $l(<IN>){
    $line .= $l; # entire file in a line
}
...

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Re: print, number of character from a file

Mar 25th, 2008

You probably want to remove the newlines though.

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Re: print, number of character from a file

Mar 25th, 2008

its showing errors when I try to run that code

Help with Code Tags

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#!/usr/bin/perl -w

open (IN, "<$fileName") || die "Cant open $fileName";

my $line = '';

while my $1(<IN>){
chomp;
$line .= $1;
}

print $line;

exit;

Help with Code Tags

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./test.pl abc.txt
syntax error at ./test.pl line 7, near "while my "
syntax error at ./test.pl line 10, near "}"
Execution of ./test.pl aborted due to compilation errors.

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Re: print, number of character from a file

Mar 26th, 2008

ok, so the file contains data as

output.txt

>name1
lsdflsjdfljdsfsjdlfjlksdjfsdf
ksjdfjdsf
ksjdflkjsflksdf
>name2
ksajdasjd
aksjdalksjd
kajlkdjasd

I am trying to print from character #x to character #y for each name
so that it becomes

>name1
char#x....char#y
>name2
char#x....char#y

Here is my code

Help with Code Tags

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#!/usr/bin/perl -w

use strict;

use warnings;

my ($fileName, $firstSequence, $lastSequence) = @ARGV;

open (IN, "<$fileName") || die "Can't open $fileName";

my @line=();
my @line1=();

OUTER: while(<IN>) {
@line=(); 
 chomp;
   if (/>/) { 
     
       print "$_\n";
       next;
       @line1=();
    }
 @line = split(//, $_);

 push(@line1,@line);

}
print @line1;
print @line1[$firstSequence-1..$lastSequence-1];

close(IN);
exit;

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Re: print, number of character from a file

#10

Mar 26th, 2008

•

Originally Posted by mank

its showing errors when I try to run that code
Help with Code Tags

(Toggle Plain Text)
#!/usr/bin/perl -w

open (IN, "<$fileName") || die "Cant open $fileName";

my $line = '';

while my $1(<IN>){
chomp;
$line .= $1;
}

print $line;

exit;
#!/usr/bin/perl -w open (IN, "<$fileName") || die "Cant open $fileName"; my $line = ''; while my $1(<IN>){ chomp; $line .= $1; } print $line; exit;
Help with Code Tags

(Toggle Plain Text)
./test.pl abc.txt
syntax error at ./test.pl line 7, near "while my "
syntax error at ./test.pl line 10, near "}"
Execution of ./test.pl aborted due to compilation errors.
./test.pl abc.txt syntax error at ./test.pl line 7, near "while my " syntax error at ./test.pl line 10, near "}" Execution of ./test.pl aborted due to compilation errors.

sorry for that incomplete code. it should be like,

 Help with Code Tags 
 Perl Syntax (Toggle Plain Text) 
open(F, 'f1.txt') or die "$!";
my $line;
while (my $l = <F>){
		chomp($l); # get rid of newline at the end of line
		$line .= $l;
}
print $line;
close(F);
open(F, 'f1.txt') or die "$!";
my $line;
while (my $l = <F>){
		chomp($l); # get rid of newline at the end of line
		$line .= $l;
}
print $line;
close(F);