96-Summer生物資訊程式設計實習(二 )

Bioinformatics with Perl

8/13~8/22 蘇中才8/24~8/29 張天豪

8/31 曾宇鳯

ScheduleDate Time Subject Spea

ker

8/13 一

13:30~17:30 Perl Basics 蘇中才

8/15 三

13:30~17:30 Programming Basics 蘇中才

8/17 五

13:30~17:30 Regular expression 蘇中才

8/20 一

13:30~17:30 Retrieving Data from Protein Sequence Database

蘇中才

8/22 三

13:30~17:30 Perl combines with BLAST and ClustalW 蘇中才

8/24 五

13:30~17:30 PDB database and structure files 張天豪

8/27 一

8:30~12:30 Extracting ATOM information 張天豪

8/27 一

13:30~17:30 Mapping of Protein Sequence IDs and Structure IDs

張天豪

8/31五 13:30~17:30 Final and Examination 曾宇鳳

Process Management

Introduction

Introduction

systemsystem(“date”);

` ``date`;

execexec(“date”);

Introduction - system

system (“ … ”);

Examplesystem “date”;system 'ls', "-al", '/home/course1/';system ‘for i in *; do echo == $i ==; cat $i; done’;system “~/course5/output.pl”;

Return 0 if success

Execute ‘date’ by system

#!/usr/bin/perl -w

# date1.pl : execute a shell command - date

my $ret = system "date";

print "return = $ret\n";

Execute ‘date’ by system without message

#!/usr/bin/perl -w

# date2.pl : execute a shell command - date

my $ret = system "date > /dev/null";

print "return = $ret\n";

Introduction - ` `

` … `

Example$now = `date`;$result = `ls –al /home/course1/`;$result = `for i in *; do echo == $i ==; cat $i; do

ne`;`~/course5/output.pl`;

Execute ‘date’ by system without message

#!/usr/bin/perl -w

# date3.pl : execute a shell command - date

my $ret = `date`;

print "return = [$ret]\n";

Print message to STDOUT and STDERR

#!/usr/bin/perl -w

# output.pl : output a message to STDOUT and STDERR

print STDOUT "print to STDOUT\n";

print STDERR "print to STDERR\n";

Print message to STDOUT and STDERR

[course5]$ ./output.pl

print to STDOUT

print to STDERR

[course5]$ ./output.pl > log

print to STDERR

[course5]$ cat log

print to STDOUT

[course5]$ (./output.pl 2>&1) > log

[course5]$ cat log

print to STDOUT

print to STDERR

Execute ‘date’ by system without message

#!/usr/bin/perl -w

# redirect.pl : STDOUT and STDERR

my $ret = system "./output.pl";

print "redirect nothing ($ret)\n";

$ret = system "./output.pl 1>/dev/null";

print "redirect STDOUT to /dev/null ($ret)\n";

$ret = system "./output.pl 1>/dev/null 2>&1";

print "redirect STDOUT and STDERR to /dev/null ($ret)\n";

Print message to STDOUT and STDERR

#!/usr/bin/perl -w

# exec_output1.pl : execute output.pl

my $ret = `./output.pl`;chomp($ret);print "return = [$ret]\n";

Print message to STDOUT and STDERR

#!/usr/bin/perl -w

# exec_output2.pl : execute output.pl

my $ret = `./output.pl 2>&1`;chomp($ret);print "return = [$ret]\n";

%ENV

Shell commandenv

Example$ENV{‘PATH’}$ENV{‘HOME’}$ENV{‘HOSTNAME’}$ENV{‘USER’}

%ENV#!/usr/bin/perl -w

# env.pl : execute a shell command - env

my @ret = `env`;foreach (@ret) { chomp; if (/PATH/) { print "$_\n"; }}

print "PATH=$ENV{'PATH'}\n";

Process Management

Arguments, Here-document

Arguments parsinguse Getopt::Std;getopts( "hvf:", \%opt ) or usage();usage() if $opt{h};usage() if (!defined{$opt{f});

sub usage(){ print STDERR << "EOF";usage: $0 [-hv] [-f file] -h : this (help) message -v : verbose output -f file : file containing usersnames, one per line

example: $0 -v -f fileEOF exit;}

Here-document

print <<EOF;print me!!!!print you!!!!print us!!!!EOF

print << x 3;print me!!!!

Exercise

system and ` `

Quiz – system & ` `

Are they workable ?system ‘for i in *; do echo == $i ==; cat $i; done’;

$result = `for i in *; do echo == $i ==; cat $i; done`;

Why ?

Quiz – sleep10.pl

#!/usr/bin/perl -w

# sleep10.pl : sleep 10 seconds

foreach (1..10) { print "$_\n"; sleep 1;}

Quiz – system & ` `

Do they execute by background mode?system ‘./sleep10.pl &’;

$result = `./sleep10.pl &`;

Why ?

Project

BLAST, ClustalW

Project1 - BLAST

TodoGet the result from BlastExtract its homology (evalue <= 10^-1)

Input A protein sequence (FASTA format)

Output All homologous sequences of the query sequence

BLAST

Get BLAST packages ftp://ftp.ncbi.nih.gov/blast/

Get nr database ftp://ftp.ncbi.nih.gov/blast/db/

Command ~/tools/PSSM/BLAST/blastall -p blastp -i P53_HUMAN.fa

-o output.txt -d /home/sbb/tools/PSSM/BLAST/db/SwissProt.v50.fa –m 9

Project2 - ClustalW

Tododo multiple sequence alignment by ClustalW

Input A protein sequence with its homology (FASTA format)

Output The conserved score of each residue in the query sequen

ce

ClustalW

Get ClustalW package ftp://ftp.ebi.ac.uk/pub/software/unix/clustalw/

Command ./clustalW <fasta sequences>