1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31

#!/usr/bin/perl                                                                                      
#Perl_3-5.pl                                                                                       
#finds occurrences of Nobody and somebody within text using index                                                                       
 
use strict;
use warnings;
 
my $nobody_infile = 'perl_III_nobody.txt';
my $nobody_outfile = 'Nobody.txt';
my $somebody_outfile = 'Somebody.txt';
 
open (IN, '<', $nobody_infile) or die "Cannot open infile: $!\n";
open (OUT1, '>', $nobody_outfile) or die "Cannot open outfile1: $!\n";
open (OUT2, '>', $somebody_outfile) or die "Cannot write to outfile2: $!\n";
 
 
while (my $line = <IN>){
  my $substr1 = 'Nobody';
  my $substr2 = 'somebody';
 
  my $position_nobody = index ($line, $substr1);
  my $position_somebody = index ($line, $substr2);
  if ($position_somebody > -1){
    warn ("somebody is here");
  }
 
 
print OUT1 $position_nobody,"\n";
print OUT2 $position_somebody,"\n";
 
}

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26

 
 
#!/usr/bin/perl -w                                                                                           
#Perl_3-3.pl
#Find reverse complement sequence
 
use strict;
 
my $infile = 'perl_III.fasta';
my $outfile = 'fasta.out';
 
open IN, "<", $infile or die "Cannot read infile: $!\n";
open OUT, '>', $outfile or die "Cannot write to outfile $!\n";
 
 
while (my $line = <IN>){
  chomp $line;
  my $header = $line;
  my $sequence = <IN>;
  chomp $sequence;
  my $reverse_sequence = reverse ($sequence);
  my $complement = $reverse_sequence;
  $complement =~ tr/ACGTacgt/TGCAtgca/;
 
  print OUT "$header-reverse_complement\n$complement\n";
}

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26

 
#!/usr/bin/perl -w                                                                                           
#Perl_3-4.pl
#Find character and line totals within fasta file
 
use strict;
 
my $infile = 'perl_III.fastq';
my $outfile = 'fastq.out';
 
open IN, "<", $infile or die "Cannot read infile: $!\n";
open OUT, '>', $outfile or die "Cannot write to outfile $!\n";
 
my $number_of_lines = 0;
my $total_length = 0;
 
while (my $line = <IN>){
  chomp $line;
  $number_of_lines++;
  my $length = length ($line);
  $total_length += $length;
}
 
my $average_line_length = $total_length/$number_of_lines;
 
print OUT "Total number of lines = $number_of_lines\nAverage line length = $average_line_length\nTotal line length or number of characters = $total_length\n";

]]>
			review-session-scripts-perl-ii-iii/feed/
		0
		
		
		
		lecture-unix/
		lecture-unix/#comments
		Tue, 15 Oct 2013 01:45:33 +0000
		Sofia Robb
				

		?p=508
		
				UNIX – Command-Line Survival Guide]]>
			lecture-unix/feed/
		0
		
		
		
		problem-set-perl-iv/
		problem-set-perl-iv/#comments
		Tue, 15 Oct 2013 01:40:39 +0000
		Sofia Robb
				

		?p=502
		read more)]]>
				Perl IV Problem Set

Files for Perl IV Problem Set

	
Perl_IV.fasta





Perl IV Problem Set
==================
1. Iterate through each element of this array using a foreach loop: (101,2,15,22,95,33,2,27,72,15,52);
        - Print out only the values that are even (use modulus operator).
2. Iterate through each of the elements of the above array, but sort them numerically.
        - Print each element.
        - Create two cumulative sums, one of all the even values and one of all the odd values. 
        - Print the two sums.
3. Iterate through each element in the above array using a for loop.
        - Print only the values of the indices that are odd    
4. Create a shuffled sequence
	Turn a DNA string into an array with split()
	Use a for loop to perform the following procedure N times (N = length of seq)
		Select a random position A with rand()
		Select a random position B with rand()
		Exchange the letters at array indices A and B
	Print the now shuffled sequence
 
5a. Start with 2 very similar DNA sequences. 
	Align with ClustalW, TCoffee, or some other web alignment application. 
	Output should be in fasta format.
	Store (copy and paste) the sequence, including dashes, from each ClustalW fasta output in a separate string variable inside your script.
	Turn each string into an array with split()
	Use a for loop to compare each index for nucleotide differences.
	Report the nucleotide position of each difference.
 
5b. Do the same as above but instead of coping and pasting into string variables
import from a file.
 
6. Calculate GC content
	Turn a DNA string into an array with split()
	Use a foreach loop to look at each nucleotide in turn
	Calculate total length of the sequence
	Keep a running total of C's and G's
	Print the calculated GC content as a percent.
 
 
7.  Run this code. Is its output what you expect? Why?
                  for (my $i = 0; $i < 10; $i++) {
                   if ($i = 2) {
                       print "\$i = $i\n";
                   }
                  }


 ]]>
			problem-set-perl-iv/feed/
		0
		
		
		
		problem-set-perl-iii/
		problem-set-perl-iii/#comments
		Tue, 15 Oct 2013 01:18:34 +0000
		Sofia Robb
				

		?p=488
		read more)]]>
				Perl III Problem Set:

	
Perl_III.nobody.txt
	
Perl_III.fastq
	
Perl_III.fasta




Perl III Problem Set
====================
 
1.  Create a script that divides two numbers provided on the command line.
        Your script should have the following requirements:
	Two numbers are required.
	The numbers have to be positive.
	The divisor cannot be zero.
 
        You should take care of the following in your Perl script
        =========================================================
	Write the quotient to STDOUT
	Write any errors to STDERR
 
        You should take care of the following on the command line in UNIX
        ==================================================================
	Redirect STDOUT to an output file (out.txt)
	Redirect STDERR to an error file (err.txt)
 
2. Open a file using the open function.
        As you read in lines from the file, make all the letters in each line uppercase. (There's a built-in
	Perl function which will do this.)
 
        Open a new file for output using the open function.
	Write the output to this file 
 
3. Open the provided fasta file (File 3). Print the reverse complement of each
    sequence. Make sure to print the output in fasta format including
    the sequence name and a note in the description that this is the
    reverse complement. Print to STDOUT and capture the output into a file
    with a command line redirect '>'.
 
4. Open the provided fastq file (File 2). Go through each line of the file. Count
    the number of lines and the number of characters per line.
 
    Have your program report the:
         a. total number of lines
         b. total number of characters
         c. average line length 
 
5. Create a script that uses <> to read in the contents of the provided
    text file (File 1). Use the function index() to
 
      a. find the first position of 'Nobody' on every line
      b. find the first position of 'somebody' on every line
 
    Use the warn() function to warn the user that 'somebody is here'
 
** You can look up how to use the index() and warn() functions in your books, from
   the command line with the perldoc command, or on perldoc.org.


]]>
			problem-set-perl-iii/feed/
		0
		
		
		
		command-line-cheat-sheet/
		command-line-cheat-sheet/#comments
		Mon, 14 Oct 2013 20:44:53 +0000
		Sofia Robb
				

		?p=484
		
				fwunixref]]>
			command-line-cheat-sheet/feed/
		0