Lecture 7

You’re on your own now..

More reading files

• Using regexes within while (): while () { />(.+)/; #regex acts on $_ by default push @anlines, $1; #keep annotation }

last and next while () { next if (/>/); last unless (/[ACGT]/); $sequence = chomp $_; push @anlines, $sequence; }

Confounding problems

• Windows, Mac and UNIX file endings: • Perl is looking for the UNIX file ending on UNIX, the Windows one on ActivePerl for Windows • So \n means different things depending on the computer

Reformatting in Perl

• Unix uses LF (carriage return,

\015

) • Windows line ending is CR LF

(\015\012)

• Need to remove LFs

(s/\012//g)

• Mac line ending (to OS9) is CR

(\012)

• Need to replace CR with LF

(s/\012/\015/g)

Reformatting in UNIX

• Can also be done on the UNIX command line: • dos2unix file.txt

• Linux has got quite good at dealing with dos files, but you will still have problems with other UNIXes (eg Solaris) • If there is a problem, the extra character (CR) will print as “^M”

System calls

• There are three commands that can be used to make

system calls

– i.e., to make UNIX commands from within Perl • exec • system • `` (“backticks”)

examples

exec “ls”; Tell UNIX “ls” then die. Results will be printed to the terminal system “ls”; Tell UNIX “ls”, wait for it to finish, then continue with the program. Results will be printed to the terminal my $ls = `ls`; Tell UNIX “ls”, but don’t print any output to the terminal. Wait until the command has finished, then capture the output in the variable $ls

Doing BLAST from within Perl

• So now we can operate BLAST, or any other command, from inside our Perl script: open FASTA, “>seq.fas”; print FASTA, “>seq\n$sequence”; close FASTA; my $res = `blastall –i seq.fas –p blastp –d nr`; if ($res =~/ Sequences producing significant/) { print “BLAST hits found!\n”;} else {print “No BLAST hits!\n”;}

Rules for successful programming

• Trust no-one (I mean, to write code for you. I am especially thinking of Bioperl! Often it is quicker to write it yourself in the long run) • Don’t get bogged down in complexity. There is probably a simpler way to do it.

• Try alternative approaches • Be vicariously lazy (Larry Wall)