Read file in array 1

mama12 · Oct 22, 2005

Hi all,
what is the beste script in Perl to read a file (DNA Sequence)in array and mutate this file between 7% and 10 %

KevinADC · Oct 22, 2005

there are a number of DNA related modules on cpan but I have no idea if any of them does what you want.

http://search.cpan.org/search?query=DNA&mode=all

mama12 · Oct 23, 2005

Hi again

how to read something ( file)in array in %

I appreciate any help

regards

TrojanWarBlade · Oct 23, 2005

If you show us some sample data and sample output that yuo would like I'm sure we can help.

Trojan.

mama12 · Oct 23, 2005

Hi again

DNA File like AAAACCCCTTTTGGGG

AAAACCCCTTTTGGGG mutate 7% and 10 % in this file

If it C it has to be A or T or G
If it is T it has to be A or C or G

uitput can be like that

AAAACCtCTaTTGGGG

I appreciate any help

regards

TrojanWarBlade · Oct 23, 2005

I'm sorry, I don't really understand genetic research so if you want some help I would appreciate a more detailed explanation.
Do you just want 7% of the characters to be swapped for another random character of the set "ACTG"?
I will assume that is the case and look at creating something that does this for you.
If I have misunderstood then I apologise and ask that you offer a more detailed explanation.
I will post when I have a little code for you.

Trojan.

mama12 · Oct 23, 2005

thanx for ur reply,

first read the file in array and from this array mutate 7% and 10 %.
yes ,I want 7% and 10% of the characters to be swapped for another random character of the set "ACTG" but not the same as 7% and 10% is has te be another character.
like this

If it C it has to be A or T or G
If it is T it has to be A or C or G

I appreciate ur work

regards

fishiface · Oct 23, 2005

Can I suggest that you read the first two FAQs on this forum, faq219-2884 and faq219-2889?

Understanding them will enable you to get more useful answers faster.

Yours,

fish

["]As soon as we started programming, we found to our surprise that it wasn't as easy to get programs right as we had thought. Debugging had to be discovered. I can remember the exact instant when I realized that a large part of my life from then on was going to be spent in finding mistakes in my own programs.["]
--Maur

TrojanWarBlade · Oct 23, 2005

Try this and see if it does what you want:

Code:

#!/usr/bin/perl -w
use strict;
my $ratio           = 7;  # Percentage error to apply
my $swapped_total   = 0;
my $characters_seen = 0;
my $charset         = "ACGT";
while(<DATA>) {
  chomp;
  # The line below calculates the number of characters to swap in this line
  my $this_line_todo = int(($characters_seen + length($_)) * $ratio / 100)
                     - $swapped_total;
  # Now we need to find the positions of the characters to change
  my %indexes = ();  # Place to store indexes
  $indexes{int(rand(length))}++
    while(scalar(keys %indexes) < $this_line_todo *2);
  foreach my $index (keys %indexes) {
    my $char = substr($_,$index,1);
    my $newchar;
    do {
      $newchar = substr($charset, rand(4), 1);
    } while ($char eq $newchar);
    substr($_,$index,1) = lc $newchar;
  }
  $characters_seen += length;
  $swapped_total   += $this_line_todo;
  print $_,"\n";
}
print "Total characters seen is $characters_seen\n";
print "Total characters swapped is $swapped_total\n";
__DATA__
GAATATCCCCATGATCTTTCCCTCAATCGCCCGCTGATAAGTGGGAAGACATCG
GTCGCGCCACACTCGATACCCTGCTCATGGTGGCGCTTGGTCTTCCCTTGGGAAT
GAATATCCCCATGATCTTCCCCTCAATCGACCTGGACGCTGATAAGTGGAAAGACATCG
GTCGCGCCACACTCGATACCCTGCTCACCCGCATTGGCGCTTGGTCTTCCCTTGGGAAT
GAATATCCCCATGATCTTCCCCTCAAACCTGGACGTTGATAAGTGGAAAGACATCG
GAATATCCCCATGATCTTTCCCTCAATCGACGCTGATAAGTGGGAAGACAT
GTCGCGCCACACTCGATACCCTGCTCGGCGCTTGGTCTTCCCTTGGGAATC
GGTTGGCGGTGCCGCCCTCGTGCAACCAATCAAGTTTGGTGGCGATGTTG
CACCAACGCTTAGTGTCACCTACTACATCACTAAAAAGTTGAGTTAT
GGTTGGCGGCGCCGCCCTCGTGCAACCAACAAGTTTGGTGGCGATGTTG
CACCAACGCTAAGTGTAACCTACTACATCAAGGGGCATTACTAAAAAGTT
AAAATGCAGCACAGAATACTGTCAAGTTTGGTGGCGATGTTG
GGTTGGCGGCGCTGCCCTCGTGCAACCAAAGAAAAGTTTGGTGGCGATGTTG
CACCAACGCTTAGTGTCACCTACTACATCAACGGGTATTACTAAAAAGTTGAG
AATGACCGAAATCAAGGAAGCTTTTGTCCCCCCCAGTGATTGAAGTGCTAGTCG
TTGGCGATACCGTCTCCAAGGGCCAAAGTTTCAACCATGGAAGTACCTTCGTCA
AATGACCGAAATCAAGGAAGCTTTTGTCCCCCCCAGTGATTGAAGTGCTAG
TTGGCGATACCGTCTCCAAGGGCCAAACAACCATGGAAGTACCCTCGTCA
AATGACCGAAATCAAGGAAGCTTTTGTCGTCCCAGTGATTGAAGTGCTAGTC
TTGGCGATACCGTCTCCAAGGGCCAAAGCAACCATGGAAGTACCCTCGTCA

Trojan.

TrojanWarBlade · Oct 23, 2005

Just altered it slightly to take into account a little rounding error. As you can see, the ratio is set at the top to 7% so if you want to run at 10% then you just need to change that value.

Code:

#!/usr/bin/perl -w
use strict;
my $ratio           = 7;  # Percentage error to apply
my $swapped_total   = 0;
my $characters_seen = 0;
my $charset         = "ACGT";
while(<DATA>) {
  chomp;
  # The line below calculates the number of characters to swap in this line
  my $this_line_todo = int(($characters_seen + length($_)) * $ratio / 100 +0.5)
                     - $swapped_total;
  # Now we need to find the positions of the characters to change
  my %indexes = ();  # Place to store indexes
  $indexes{int(rand(length))}++
    while(scalar(keys %indexes) < $this_line_todo *2);
  foreach my $index (keys %indexes) {
    my $char = substr($_,$index,1);
    my $newchar;
    do {
      $newchar = substr($charset, rand(4), 1);
    } while ($char eq $newchar);
    substr($_,$index,1) = lc $newchar;
  }
  $characters_seen += length;
  $swapped_total   += $this_line_todo;
  print $_,"\n";
}
print "Total characters seen is $characters_seen\n";
print "Total characters swapped is $swapped_total\n";
__DATA__
GAATATCCCCATGATCTTTCCCTCAATCGCCCGCTGATAAGTGGGAAGACATCG
GTCGCGCCACACTCGATACCCTGCTCATGGTGGCGCTTGGTCTTCCCTTGGGAAT
GAATATCCCCATGATCTTCCCCTCAATCGACCTGGACGCTGATAAGTGGAAAGACATCG
GTCGCGCCACACTCGATACCCTGCTCACCCGCATTGGCGCTTGGTCTTCCCTTGGGAAT
GAATATCCCCATGATCTTCCCCTCAAACCTGGACGTTGATAAGTGGAAAGACATCG
GAATATCCCCATGATCTTTCCCTCAATCGACGCTGATAAGTGGGAAGACAT
GTCGCGCCACACTCGATACCCTGCTCGGCGCTTGGTCTTCCCTTGGGAATC
GGTTGGCGGTGCCGCCCTCGTGCAACCAATCAAGTTTGGTGGCGATGTTG
CACCAACGCTTAGTGTCACCTACTACATCACTAAAAAGTTGAGTTAT
GGTTGGCGGCGCCGCCCTCGTGCAACCAACAAGTTTGGTGGCGATGTTG
CACCAACGCTAAGTGTAACCTACTACATCAAGGGGCATTACTAAAAAGTT
AAAATGCAGCACAGAATACTGTCAAGTTTGGTGGCGATGTTG
GGTTGGCGGCGCTGCCCTCGTGCAACCAAAGAAAAGTTTGGTGGCGATGTTG
CACCAACGCTTAGTGTCACCTACTACATCAACGGGTATTACTAAAAAGTTGAG
AATGACCGAAATCAAGGAAGCTTTTGTCCCCCCCAGTGATTGAAGTGCTAGTCG
TTGGCGATACCGTCTCCAAGGGCCAAAGTTTCAACCATGGAAGTACCTTCGTCA
AATGACCGAAATCAAGGAAGCTTTTGTCCCCCCCAGTGATTGAAGTGCTAG
TTGGCGATACCGTCTCCAAGGGCCAAACAACCATGGAAGTACCCTCGTCA
AATGACCGAAATCAAGGAAGCTTTTGTCGTCCCAGTGATTGAAGTGCTAGTC
TTGGCGATACCGTCTCCAAGGGCCAAAGCAACCATGGAAGTACCCTCGTCA

Trojan.

mama12 · Oct 23, 2005

Hi again

thanks for ur help

I appreciate ur work Trojan

regards

TrojanWarBlade · Oct 23, 2005

mama12,
Does it do what you want?

Trojan.

mama12 · Oct 23, 2005

HI Torjan.

the script is working thanx for it,but I am searchting voor script that read a file like this

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

# Get the DNA sequence data
print "Please type the filename of the DNA sequence data: ";

$dna_filename = <STDIN>;

chomp $dna_filename;

and it will mutate the (AAAAAAAAAATTTTTTGGGGCCCCCC) in the file(filename) 7% and 10% only and save it in another file (filename)

that it what I am really searching for

I appreciate any help

regards

mama12

mama12 · Oct 23, 2005

HI Torjan.

the script is working thanx for it,but I am searchting voor script that read a file like this

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

# Get the DNA sequence data
print "Please type the filename of the DNA sequence data: ";

$dna_filename = <STDIN>;

chomp $dna_filename;

then read the file in array

and it will mutate the (AAAAAAAAAATTTTTTGGGGCCCCCC) in the file(filename) 7% and 10% only and save it in another file (filename)

that it what I am really searching for

I appreciate any help

regards

mama12

TrojanWarBlade · Oct 23, 2005

OK, try this then:

Code:

#!/usr/bin/perl -w
use strict;
my $charset = "ACGT";

# Get the DNA sequence data filename
print "Please type the filename of the DNA sequence data: ";
my $dna_filename = <>;
chomp ($dna_filename);

# Validate filename
$dna_filename =~ /^\w+(?:\.\w+)$/
  or die "Invalid filename format [$dna_filename]";

# Process once at 7% and once at 10%
foreach my $ratio (7,10) {
  my $swapped_total   = 0;
  my $characters_seen = 0;

  # Open file for reading
  open FH, "$dna_filename"
    or die "Failed to open file [$dna_filename]";

  open OUT, ">${dna_filename}_${ratio}percent"
    or die "Failed to create output file [${dna_filename}_${ratio}percent]";
  while(<FH>) {
    chomp;
    # The line below calculates the number of characters to swap in this line
    my $this_line_todo = int(($characters_seen + length($_)) * $ratio / 100 +0.5)
                       - $swapped_total;
    # Now we need to find the positions of the characters to change
    my %indexes = ();  # Place to store indexes
    $indexes{int(rand(length))}++
      while(scalar(keys %indexes) < $this_line_todo *2);
    foreach my $index (keys %indexes) {
      my $char = substr($_,$index,1);
      my $newchar;
      do {
        $newchar = substr($charset, rand(4), 1);
      } while ($char eq $newchar);
      substr($_,$index,1) = lc $newchar;
    }
    $characters_seen += length;
    $swapped_total   += $this_line_todo;
    print OUT $_,"\n";
  }
  print "Total characters seen is $characters_seen\n";
  print "Total characters swapped is $swapped_total\n";
  close OUT;
  close FH;
}

Trojan.

mama12 · Oct 23, 2005

HI again,

the script is working thanx for it, I appreciate ur work

how can I make a little change in this script the out put of this file will be saving ( the mutate 7% and 10%) in 1 file not in 2 files ,the name of the file is giving bij user.

regards

mama12

duncdude · Oct 23, 2005

blimey Trojan! you must have a halo...

Kind Regards
Duncan

TrojanWarBlade · Oct 23, 2005

mama12,
Can you understand anything that I have developed for you so far?
I've done 99% for you. I would be surprised if you cannot make the last little changes that you ask for.
The best way to learn is to try doing a little for yourself sometimes.
Give it a go and come back if you still have trouble.
Good Luck!

Trojan.

mama12 · Oct 23, 2005

thanx any way for u work

Kind Regards

mama12

KevinADC · Oct 23, 2005

hehehe.... now that's gratitude for ya! [dazed]

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