Slide 1Slide 2Slide 3Slide 4Slide 5Slide 6Slide 7Slide 8Slide 9Slide 10Slide 11Slide 12Slide 13Slide 14Slide 15Slide 16Slide 17Slide 18Slide 19Scripting Language BasicsCSE/BENG/BIMM 182September 28, 2009Scripting Languages●Examples: Perl (Documentation: http://www.perl.org/docs.html) and Python (Documentation: http://docs.python.org/)●Advantages:●Easy to code●Tons of prewritten scripts/modules developed for the bioinformatics community (e.g. BioPerl & BioPython)●Not required for this class, but they are convenient for many applications discussed●The best way to learn any language is to write some small scripts in itPerl Basics: Command Line Input●To invoke a Perl script from command line, type the following:perl PATH/FILE_NAME [ARG1 ARG2 …]●ARGs are optional parameters which are fed as an array of inputs into the program (more later)Perl Basics: Syntax and Headers●All variables should start with identifiers●$ for scalars●@ for arrays●% for hashes●All lines should end with a semicolon (;)●A script should begin with:#!PATHwhere PATH is the location of the Perl interpreter files– This is usually /usr/bin/perl●To use premade modules, type use MODULE_NAMEPerl Basics: Variables●Variables can be assigned values using the assignment operator (=)●$i = 3;●$j = 4;●$str = “This is a Perl string”;●Standard operations can be performed on integers●$k = $i + $j; #$k = 7Perl Basics: Strings●Single quotes mean string is taken literally, double quotes mean string is interpreted●Useful functions●Size–length($str)●Substring–substr($str, 3, 5)#takes the substring starting at index 3 with length 5●Concatenation–$str = "con"."cat".”enate”; #$str = “concatenate”●Splitting a string up–my @line = split(/a/, $str);#@line is an array containing 3 parts: “conc”, “ten”, and “te”–Any regular expression can fit in between the slashes in the split functionPerl Basics: Arrays●Can be instantiated during use●Array labeled with '@', while elements in the array labeled with '$' (e.g. $row_line[$0] is the 1st element in @row_line, which is “conc”)●Maximum Index: $#array●Size: scalar(@array)Perl Basics: Conditionals and Loops●Conditional:if(BOOLEAN){STATEMENTS;}elsif(BOOLEAN){STATEMENTS;}else{STATEMENTS;}●For Loops:for($i = 1; $i <= $size; $i++){print “$i\n”;}ORfor $i (1 .. $size){print “$i\n”;}Other types of loops occur too (e.g. while)Perl Basics: File I/O●To open a stream:open(F0, STRING_LOCATION);●Start the STRING_LOCATION with '>' for write/overwrite, '>>' for write/append, or '<' for read (default – if nothing is placed before the file name)●To read all at once into an array:my(@lines) = <F0>;●To read line-by-line:●while(<F0>){$line = $_;chomp($line);#Process as requiredprint “$line\n”;}●To write to a file, simply insert the stream between print and the text(e.g. print F1 “$line\n”; #F1 is a write stream opened similarly to above)Sample ScriptCalled from command line with:perl ./PerlTest.pl TestArraySizes.txtPython Basics: Syntax and Headers●Spacing is important – off by one can throw off the whole program●Should begin with:#!<PATH>where <PATH> is the location of the Python interpreter files (usually /usr/bin/env python)●To use premade modules, type import <MODULE_NAME>Python Basics: Command Line Input●To invoke a Python script from command line, type the following:python <PATH/FILE_NAME> [ARG1 ARG2 …]●ARGs are optional parameters which are fed as an array of inputs into the program (more later)Python Basics: Variables●Variables can be assigned values using the assignment operator (=)●i = 3●j = k = 4●str = “This is a Python string”●Standard operations can be performed on integers●l = i + j; #l = 7Python Basics: Strings●Immutable (can't be changed directly, but can be modified and stored)●Useful functions●Size–len(str)●Substring–str[3:7] #takes the substring starting at index 3 with length 5●Concatenation–str = "con" + "cat" + ”enate” #str = “concatenate”●Splitting a string up–line = str.split(“a”);#line is an array containing 3 parts: “conc”, “ten”, and “te”Python Basics: Arrays●Should be instantiated prior to usage●Access: array[i] is the ith element in array●Size: len(array)Python Basics: Conditionals and Loops●Conditional:if(BOOLEAN):STATEMENTSelif(BOOLEAN):STATEMENTSelse:STATEMENTS●For Loops:for i in range(1, size):print '%d' % i●Other types of loops occur too (e.g. while)Python Basics: File I/O●To open a stream:F0 = open(STRING_LOCATION)●Have a second parameter with 'w' for write/overwrite, 'a' for write/append, or 'r' for read (default – if nothing is placed before the file name)●To read all at once into an array:lines = F0.readlines()●To read line-by-line:●line = F0.readline()●for line in F0:#Process as requiredprint line●To write to a file,print >>F1 “line” #F1 is a write stream opened similarly to aboveOR●F1.write(“line”)Sample ScriptCalled from command line with:python ./PythonTest.pl