1. Computer Programming for Biologists Class 10 Dec 5 th, 2014 Karsten Hokamp http://bioinf.gen.tcd.ie/GE30M25/programming

2. Computer Programming for Biologists system calls one-liners Overview

3. Computer Programming for Biologists - integrate other programs - Perl acts as wrapper - three possible ways: system "command"; exec "command"; $output = `command`; - only backticks option allows to capture output - exec option quits the Perl script System calls backticks

4. Computer Programming for Biologists # shut down the computer: exec "shutdown -h now"; # run an alignment program system "clustalw multi.fa"; # check the load of the computer $load = `uptime`; System calls - examples

5. Computer Programming for Biologists http://bioinf.gen.tcd.ie/GE3M25/programming/class10 Practial

6. Computer Programming for Biologists - quick way of programming - no need for editor - handy for testing pieces of code - bioinformatics examples online One-liners

7. Computer Programming for Biologists A very simple example: One-liners $ perl –w -e 'print "Hello world!\n";' use warnings Perl codeexecute code

8. Computer Programming for Biologists Squash short Perl scripts into one line: One-liners $ perl –w -e 'while (<>) { print ++$count." $_";}' input.txt #!/usr/bin/perl use warnings; # add numbers to each input line while (<>) { print ++$count." $_"; }

9. Computer Programming for Biologists One-liners $ perl -e 'while (<>) {print ++$i. " $_";}' X62493_embl.txt 1 ID X62493; SV 1; linear; genomic RNA; STD; VRL; 4789 BP. 2 XX 3 AC X62493; 4 XX 5 DT 29-MAY-1992 (Rel. 32, Created) 6 DT 18-APR-2005 (Rel. 83, Last updated, Version 7) … argument to script Perl code Perl flag $ perl -e 'while (<>) {print ++$i. " $_";}' X62493_embl.txt > out.txt Alternatively, redirect output into a new file:

10. Computer Programming for Biologists Useful switches: One-liners -a turns on autosplit mode (@F = split / /, $_;), used with -n, -p -d starts perl in debugging mode -e specify perl code to be executed -i[extension] edit file(s) in-place (create backup copy with extension) -l strips newlines on input, and adds them on output -n loops through each line of input file -p loops through each line of input file and prints it -F[pattern] specifies the pattern to split on if -a is also in effect -M[module] use module with program -v prints version of Perl executable -w prints warnings about dubious constructs more detailed info through man perlrun

11. Computer Programming for Biologists One-liners -l strips newlines on input, and adds them on output No more 'chomp' and "\n" ! -l strips newlines on input, and adds them on output No more 'chomp' and "\n" ! -n loops through each line of input file Does the following internally: while (<>) { … # the code after –e flag goes here } -n loops through each line of input file Does the following internally: while (<>) { … # the code after –e flag goes here }

12. Computer Programming for Biologists Useful switch combinations: One-liners -p -i -e 's/pattern1/pattern2/g' file(s) loops through each line and prints it, replaces some text, changes files in-place perl -p -i.bak -e 's/^/sprintf("%-5s", ++$i)/e if (/\S/)' seq.fa -p -i -e 's/pattern1/pattern2/g' file(s) loops through each line and prints it, replaces some text, changes files in-place perl -p -i.bak -e 's/^/sprintf("%-5s", ++$i)/e if (/\S/)' seq.fa -lane 'do something with @F' file(s) process line ending, splits line on spaces into @F, cycles through each line and lets you do something with @F -F"\t" -lane 'do something with @F' file(s) same as above but on tab-delimited files perl -F"\t" -lane 'print(join "\t", @F[0,2,1,3..$#F])' in > out -lane 'do something with @F' file(s) process line ending, splits line on spaces into @F, cycles through each line and lets you do something with @F -F"\t" -lane 'do something with @F' file(s) same as above but on tab-delimited files perl -F"\t" -lane 'print(join "\t", @F[0,2,1,3..$#F])' in > out

13. Computer Programming for Biologists Useful switch combinations: One-liners -p -i -e 's/pattern1/pattern2/g' file(s) loops through each line and prints it, replaces some text, changes files in-place perl -p -i.bak -e 's/^/sprintf("%-5s", ++$i)/e if (/\S/)' seq.fa -p -i -e 's/pattern1/pattern2/g' file(s) loops through each line and prints it, replaces some text, changes files in-place perl -p -i.bak -e 's/^/sprintf("%-5s", ++$i)/e if (/\S/)' seq.fa -lane 'do something with @F' file(s) process line ending, splits line on spaces into @F, cycles through each line and lets you do something with @F -F"\t" -lane 'do something with @F' file(s) same as above but on tab-delimited files perl -F"\t" -lane 'print(join "\t", @F[0,2,1,3..$#F])' in > out -lane 'do something with @F' file(s) process line ending, splits line on spaces into @F, cycles through each line and lets you do something with @F -F"\t" -lane 'do something with @F' file(s) same as above but on tab-delimited files perl -F"\t" -lane 'print(join "\t", @F[0,2,1,3..$#F])' in > out replace start of line increment counter variable and pad it with whitespace treat replacement string as an expression only work on lines that are not empty create backup with.bak ending modify file in-place

14. Computer Programming for Biologists Useful switch combinations: One-liners -p -i -e 's/pattern1/pattern2/g' file(s) loops through each line and prints it, replaces some text, changes files in-place perl -p -i.bak -e 's/^/sprintf("%-5s", ++$i)/e if (/\S/)' seq.fa -p -i -e 's/pattern1/pattern2/g' file(s) loops through each line and prints it, replaces some text, changes files in-place perl -p -i.bak -e 's/^/sprintf("%-5s", ++$i)/e if (/\S/)' seq.fa -lane 'do something with @F' file(s) process line ending, splits line on spaces into @F, cycles through each line and lets you do something with @F -F"\t" -lane 'do something with @F' file(s) same as above but on tab-delimited files perl -F"\t" -lane 'print(join "\t", @F[0,2,1,3..$#F])' in > out -lane 'do something with @F' file(s) process line ending, splits line on spaces into @F, cycles through each line and lets you do something with @F -F"\t" -lane 'do something with @F' file(s) same as above but on tab-delimited files perl -F"\t" -lane 'print(join "\t", @F[0,2,1,3..$#F])' in > out split at tabs process each line, elements in @F print in tab-delimited format change order of elements

15. Computer Programming for Biologists One-liners for bioinformatics: One-liners The Scriptome - Protocols for Manipulating Biological Data http://sysbio.harvard.edu/csb/resources/computational/scriptome In-house collection (includes Perl primer): http://bioinf.gen.tcd.ie/pol

16. Computer Programming for Biologists http://bioinf.gen.tcd.ie/GE3M25/programming/class10 Practial

17. Computer Programming for Biologists loads of great recipes: Where to go from here? loads of useful extensions: BioPerl http://www.bioperl.org

18. Computer Programming for Biologists Exam Programming Exam: Thu, Dec 11 th, 11 -1 pm Bioinformatics Exam: Tue, Dec 9 th, 11 -1 pm