1. 4.1 Reading and writing files

2. 4.2 Open a file for reading, and link it to a filehandle: open(IN, "<EHD.fasta"); And then read lines from the filehandle, exactly like you would from : my $line = ; my @inputLines = ; foreach $line (@inputLines)... Every filehandle opened should be closed: close(IN); Always check the open didn’t fail (e.g. if a file by that name doesn’t exists): open(IN, "<$file") or die "can't open file $file"; Reading files

3. 4.3 Open a file for writing, and link it to a filehandle: open(OUT, ">EHD.analysis") or die... NOTE: If a file by that name already exists it will be overwriten! Or, you can add lines at the end of an existing file (append): open(OUT, ">>EHD.analysis") or die... Print to a file: print OUT "The mutation is in exon $exonNumber\n"; Writing to files no comma here

4. 4.4 You can ask questions about a file or a directory name (not filehandle): if (-e $name) { print "The file $name exists!\n"; } -e$name exists -r$name is readable -w$name is writable by you -z$name has zero size -s$name has non-zero size (returns size) -f$name is a file -d$name is a directory -l$name is a symbolic link -T$name is a text file -B$name is a binary file (opposite of -T). File Test Operators

5. 4.5 open(IN, '<D:\workspace\Perl\p53.fasta'); Always use a full path name, it is safer and clearer to read Remember to use \\ in double quotes open(IN, "<D:\\workspace\\Perl\\$name.fasta"); (usually) you can also use / open(IN, "<D:/workspace/Perl/$name.fasta"); Working with paths

6. 4.6 It is common to give parameters within the command-line for a program or a script: They will be stored in the array @ARGV : @ARGV contains: ("my","argument","list"); foreach my $arg (@ARGV){ print "$arg\n"; } Command line parameters > perl -w findProtein.pl my argument list my argument list

7. 4.7 It is common to give parameters within the command-line for a program or a script: They will be stored in the array @ARGV : @ARGV contains: ("my argument list"); foreach my $arg (@ARGV){ print "$arg\n"; } > perl -w findProtein.pl "my argument list" Command line parameters my argument list

8. 4.8 It is common to give parameters within the command-line for a program or a script: They will be stored in the array @ARGV : my $inFile = $ARGV[0]; my $outFile = $ARGV[1]; Or more simply: my ($inFile,$outFile) = @ARGV; Command line parameters > perl -w findProtein.pl D:\perl\input.fasta D:\perl\output.txt

9. 4.9 Command line parameters in PerlExpress

10. 4.10 Reminder: the class exercise of 3 days ago. Reading files - example Input: Yossi 6.10,16.50,5.00 Dana 21.00,6.00 Refael 24.00,7.00,8.00 END Output: Yossi 27.6 Dana 27 Refael 45.1

11. 4.11 Reading files: example $line = ; chomp $line; # loop processes one input line and print output for line while ($line ne "END") { # Separate name and numbers @nameAndNums = split(" ", $line); $name = $nameAndNums[0]; @nums = split(",", $nameAndNums[1]); $sum = 0; # Sum numbers foreach $num (@nums) { $sum = $sum + $num; } print "$name $sum\n"; # Read next line $line = ; chomp $line; } Input: Yossi 6.10,16.50,5.00 Dana 21.00,6.00 Refael 24.00,7.00,8.00 END Output: Yossi 27.6 Dana 27 Refael 45.1

12. 4.12 Reading files: example my ($inFileName) = @ARGV; open(IN, "<$inFileName") or die "can't open $inFileName"; $line = ; chomp $line; # loop processes one input line and print output for line while ($line ne "END") { # Separate name and numbers @nameAndNums = split(" ", $line); $name = $nameAndNums[0]; @nums = split(",", $nameAndNums[1]); $sum = 0; # Sum numbers foreach $num (@nums) { $sum = $sum + $num; } print "$name $sum\n"; # Read next line $line = ; chomp $line; } close(IN); Input: Yossi 6.10,16.50,5.00 Dana 21.00,6.00 Refael 24.00,7.00,8.00 END Output: Yossi 27.6 Dana 27 Refael 45.1

13. 4.13 Reading files: example my ($inFileName, $outFileName) = @ARGV; open(IN, "<$inFileName") or die "can't open $inFileName"; open(OUT, ">$outFileName") or die "can't open $outFileName"; $line = ; chomp $line; # loop processes one input line and print output for line while ($line ne "END") { # Separate name and numbers @nameAndNums = split(" ", $line); $name = $nameAndNums[0]; @nums = split(",", $nameAndNums[1]); $sum = 0; # Sum numbers foreach $num (@nums) { $sum = $sum + $num; } print OUT "$name $sum\n"; # Read next line $line = ; chomp $line; } close(IN); close(OUT); Input: Yossi 6.10,16.50,5.00 Dana 21.00,6.00 Refael 24.00,7.00,8.00 END Output: Yossi 27.6 Dana 27 Refael 45.1

14. 4.14 Reading files: example my ($inFileName, $outFileName) = @ARGV; open(IN, "<$inFileName") or die "can't open $inFileName"; open(OUT, ">$outFileName") or die "can't open $outFileName"; $line = ; chomp $line; # loop processes one input line and print output for line while (defined $line) { # Separate name and numbers @nameAndNums = split(" ", $line); $name = $nameAndNums[0]; @nums = split(",", $nameAndNums[1]); $sum = 0; # Sum numbers foreach $num (@nums) { $sum = $sum + $num; } print OUT "$name $sum\n"; # Read next line $line = ; chomp $line; } close(IN); close(OUT); Input: Yossi 6.10,16.50,5.00 Dana 21.00,6.00 Refael 24.00,7.00,8.00 Output: Yossi 27.6 Dana 27 Refael 45.1

15. 4.15 Reading files: example my ($inFileName, $outFileName) = @ARGV; open(IN, "<$inFileName") or die "can't open $inFileName"; open(OUT, ">$outFileName") or die "can't open $outFileName"; $line = ; # loop processes one input line and print output for line while (defined $line) { chomp $line; # Separate name and numbers @nameAndNums = split(" ", $line); $name = $nameAndNums[0]; @nums = split(",", $nameAndNums[1]); $sum = 0; # Sum numbers foreach $num (@nums) { $sum = $sum + $num; } print OUT "$name $sum\n"; # Read next line $line = ; } close(IN); close(OUT); Input: Yossi 6.10,16.50,5.00 Dana 21.00,6.00 Refael 24.00,7.00,8.00 Output: Yossi 27.6 Dana 27 Refael 45.1

16. 4.16 Class exercise 5 1.Write a script that reads a file containing a Perl script, that is named by the first command-line parameter (from @ARGV). Print out the script without comment lines (lines that begin with #). 2.Now write the results to a file that is named by the second command- line parameter. 3.Now remove all other comments as well (that may not start at the beginning of a line).

17. 4.17 Perl allows easy access to the files in a directory by “globbing”: The * represents any string character. For example, *.fasta represents all filenames with the extension ".fasta" my @files = ; foreach $fileName (@files) { open(IN, $fileName) or die "can't open file $fileName"; foreach $line ( ) { do something... } } Note: the “glob” gives a list of the file names in the directory. Reading directories no " here

18. 4.18 You can interpolate variables in the glob, as in double-quoted strings: @files = ; If $chromosome is 4 then we may get these files in @files: chr4.fasta chr4_NT_003827.fasta chr4_NT_007222.fasta Reading directories

19. 4.19 Delete a file: unlink ("fred.txt") or die "can't delete fred.txt"; Delete all files in a directory whose name matches a certain “pattern”: unlink or die "can't delete files in fred"; (Here – all file names that end with “.txt”) Move/rename files: rename ("fred.txt", "friends\\bob.txt") or die "can't move fred.txt"; Manipulating files

20. 4.20 Generally, you can execute any command of the operating system: $systemReturn = system("delete fred.txt"); Or: $systemReturn = system("copy fred.txt george.txt"); When checking the value returned by a system call, usually 0 means no errors: if ($systemReturn != 0) { die "can't copy fred.txt"; } Calling system commands

21. 4.21 Class exercise 6 1.Write a script that prints a list of all Perl files (i.e. files with extension “.pl ” ) in a given directory, that is named by the first command-line parameter. 2.Change the script from class exercise 5.1 so that it will read all Perl files in a given directory, that is named by the first command-line parameter, and print them out to the screen without the comment lines. 3* Change the script so that each script will be written to a file named as the input file with an added extension “.noComments” e.g. input “class_ex.2.2.pl”  output “class_ex.2.2.pl.noComments”