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96-Summer 生物資訊程式設計實習 ( 二 )

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. Schedule. Process Management. Introduction. Introduction. system system(“date”); ` ` `date`; exec exec(“date”);. Introduction - system. system (“ … ”); Example system “date”;

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96-Summer 生物資訊程式設計實習 ( 二 )

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  1. 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

  2. Schedule

  3. Process Management Introduction

  4. Introduction • system • system(“date”); • ` ` • `date`; • exec • exec(“date”);

  5. Introduction - system • system (“ … ”); • Example • system “date”; • system 'ls', "-al", '/home/course1/'; • system ‘for i in *; do echo == $i ==; cat $i; done’; • system “~/course5/output.pl”; • Return 0 if success

  6. Execute ‘date’ by system #!/usr/bin/perl -w # date1.pl : execute a shell command - date my $ret = system "date"; print "return = $ret\n";

  7. 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";

  8. Introduction - ` ` • ` … ` • Example • $now = `date`; • $result = `ls –al /home/course1/`; • $result = `for i in *; do echo == $i ==; cat $i; done`; • `~/course5/output.pl`;

  9. Execute ‘date’ by system without message #!/usr/bin/perl -w # date3.pl : execute a shell command - date my $ret = `date`; print "return = [$ret]\n";

  10. 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";

  11. 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

  12. 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";

  13. 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";

  14. 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";

  15. %ENV • Shell command • env • Example • $ENV{‘PATH’} • $ENV{‘HOME’} • $ENV{‘HOSTNAME’} • $ENV{‘USER’}

  16. %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";

  17. Process Management Arguments, Here-document

  18. Arguments parsing use 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 file EOF exit; }

  19. Here-document print <<EOF; print me!!!! print you!!!! print us!!!! EOF print << x 3; print me!!!!

  20. Exercise system and ` `

  21. 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 ?

  22. Quiz – sleep10.pl #!/usr/bin/perl -w # sleep10.pl : sleep 10 seconds foreach (1..10) { print "$_\n"; sleep 1; }

  23. Quiz – system & ` ` • Do they execute by background mode? • system ‘./sleep10.pl &’; • $result = `./sleep10.pl &`; • Why ?

  24. Project BLAST, ClustalW

  25. Project1 - BLAST • Todo • Get the result from Blast • Extract its homology (evalue <= 10^-1) • Input • A protein sequence (FASTA format) • Output • All homologous sequences of the query sequence

  26. 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

  27. Project2 - ClustalW • Todo • do multiple sequence alignment by ClustalW • Input • A protein sequence with its homology (FASTA format) • Output • The conserved score of each residue in the query sequence

  28. ClustalW • Get ClustalW package • ftp://ftp.ebi.ac.uk/pub/software/unix/clustalw/ • Command • ./clustalW <fasta sequences>

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