1. Teaching Materials by Ivan Ovcharenko <IVOvcharenko@lbl
Teaching Materials by Ivan Ovcharenko
part 3

2. part 2
File management:
How to deal with files?
Read data from a file?
Write to a file?
Regular expressions:
How to compare strings?
Extract substrings?
Substitute characters?
Practical example: reverse complement of a DNA sequence

3. Windows Graphical User Interface
part 2
File management
Windows Graphical User Interface
1. Open
2. Edit
3. Save

4. Edit Read or Write part 2 Perl file management structure is simplier
1. Open file
2. READ or WRITE data
(line by line)
3. Close file

5. part 2
How to open and close a file “data.txt” from a perl program?
# open data.txt file for READING open (FILE, “ < data.txt”);
Direction of file data flow
File handler. This name will be used everywhere later in the program, when we will deal with this file.
<
- READ from a file
>
- WRITE to a file
# close a file specified by FILE file handler close (FILE);

6. part 2
Writing “Hello everyone” to the “tmp.txt” file:
#!/usr/local/bin/perl
open (FILE, “ > tmp.txt”);
print FILE “Hello everyone\n”;
close (FILE);

7. part 2
Reading data from a file
#!/usr/local/bin/perl
# open file data.txt for reading open (FILE, “ < data.txt”);
# read file line by line and print it out to the screen
while ($line = <FILE>) {
print “$line”; }
#close file
close(FILE);
while loop is analogous to the for loop.
All the body statements of it are executed until the condition in parenthesis is correct (true).
$line = <FILE>
- read next line from a file specified by the file handler FILE

8. part 2
Example. Calculating a sum of numbers in the file data.txt 1 18 23 2
chomp command removes
“\n” (new line) symbol from
the string
#!/usr/local/bin/perl
$sum = 0; open (FILE, “ < data.txt”);
while ($line = <FILE>) {
chomp($line);
$sum = $sum + $line; }
close(FILE);
print “Sum of the numbers in data.txt file is $sum\n”;
Sum of the numbers in data.txt file is 44

9. part 2
Operations with strings
$string = “Hello everybody\n”;
# concatenating strings $strA = “Hello “; $strB = “everybody\n”; $string = $strA . $strB;
# length of the string -> number of characters inside $strLen = length ($strA); # $strLen = 6;
# extracting a part of a string $strA = “Hello everybody\n”; $strB = substr ($strA, 2, 5); print “$strB”;
llo e
substr
substr ( $string, $offset, $n)
-- extracts $n characters from the string
$string, starting at the position $offset
(first position in a string is 0, not 1!)

10. part 2
Calculate a length of every string in a file named a.txt
#!/usr/local/bin/perl
# open the a.txt file
open (INP, “<a.txt”);
# read the file line by line
while ($line = <FILE>) {
chomp($line);
$lineLength = length($line);
print “$lineLength\n”; }
# close the file
close (INP);

11. ? ? part 2 Comparing strings $strA = “AAA”; $strB = “BBB”;
$strC = “bbb”
if ($strA eq $strB) { print “true\n”; }
if ($strB ne $strC) {
print “true\n”; ?
$strA = “AAAbbb”;
$strC = “bbb”
if ($strC eq substr($strA,3,3)) { print “true\n”; } ?

12. part 2
Modifying strings
$strA = “AAAxCTT”;
# substitute ‘x’ symbol by ‘N’ symbol in string $strA
$strA =~ s/x/N/;
# substitute all ‘A’ symbols by ‘G’ symbols
$strA =~ s/A/G/g;
global substitution
# substitute all ‘A’s by ‘G’s, all ‘T’s by ‘A’s
$strA =~ tr/AT/GA/;
print “$strA \n”;
GGGxCAA
Note: tr/// substitutes only symbols, while s/// substitutes strings
$strA =~ s/AAA/123/;
123xCTT

13. part 2
Example
Convert string “Robert has 2 brothers and 2 sisters” to “John has 3 brothers and 3 sisters”
$string = “Robert has 2 brothers and 2 sisters”;
# 2 --> 3
$string =~ tr/2/3/;
# Robert --> John
$string =~ s/Robert/John/;

14. part 2
Reverse complement of a DNA sequence. Input file “seq1.fasta”. Output file “RCseq1.fasta”.
#!/usr/local/bin/perl
# open file seq1.fasta for reading & RCseq1.fasta for # writing open (INP, “ < seq1.fasta”); open (OUT, “ > RCseq1.fasta”);
# read the sequence and store it into the string # variable $seq, skip the header line $seq = “”; <INP>; # reading a header line and losing the data while ($line = <FILE>) { chomp($line); $seq = $seq . $line; }
# reverse complement the sequence $seq = reverse($seq); $seq =~ tr/ACTGactg/TGACtgac/;
# output the $seq sequence in fasta format $offset = 0; while ($offset < length($seq)) { $subSeq = substr ($seq, $offset, 50); $offset = $offset + 50; print OUT “$subSeq\n”; }
#close files close (INP); close (OUT);