Reading and writing files

Reading and writing files

Reading files 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 <STDIN>:my $line = <IN>;my @inputLines = <IN>;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") ordie "can't open file $file";

no comma here Writing to files Open a file for writing, and link it to a filehandle: open(OUT, ">EHD.analysis") ordie... 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") ordie... Print to a file:print OUT "The mutation is in exon $exonNumber\n";

File Test Operators 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).

Working with paths 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");

Command line parameters 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 myargumentlist

Command line parameters 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" my argument list

Command line parameters 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; > perl -w findProtein.pl D:\perl\input.fasta D:\perl\output.txt

Command line parameters in PerlExpress

Reading files - example Reminder: the class exercise of 3 days ago. 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

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 Reading files: example $line = <STDIN>; 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 = <STDIN>; 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 Reading files: example my ($inFileName) = @ARGV; open(IN, "<$inFileName") or die "can't open $inFileName"; $line = <IN>; 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 = <IN>; 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 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 = <IN>; 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 = <IN>; 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 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 = <IN>; 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 = <IN>; 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 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 = <IN>; # 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 = <IN>; } close(IN); close(OUT);

Pesach exercise The 3rd exercise is due on April 20th

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

Reading directories You can interpolate variables in the glob, as in double-quoted strings: @files = <D:\\scripts\\class_ex$lesson*.pl>; If $lesson is 4 then we may get these files in @files: class_ex4.pl class_ex4.1.pl class_ex4.2.pl

Manipulating files 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 <fred\\*.txt> 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";

Calling system commands 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"; }

Reading and writing files