examples/tools/psw.pl

   1 #!/usr/bin/perl
   2
   3 # PROGRAM  : psw.pl
   4 # PURPOSE  : Simple driver for Bio::Tools::pSW
   5 # AUTHOR   : Ewan Birney birney@sanger.ac.uk
   6 # CREATED  : Tue Oct 27 1998
   7 # REVISION : $Id$
   8 #
   9 # INSTALLATION
  10 #
  11 # you almost certainly have to have installed bioperl
  12 # from the makefile system for this to work. This is
  13 # because this module use XS extensions (C source code
  14 # 'compiled into' perl)
  15 #
  16 # The lib system below is just so that I (ewan) can test it
  17 # on site...
  18 #
  19
  20 use lib "/nfs/disk100/pubseq/wise/PerlMod/";
  21
  22 #
  23 # This is a simple example script. We are going
  24 # to make 3 sequences directly from memory and
  25 # then align them once using blosum matrix and once
  26 # using a gonnet matrix. These matrices should
  27 # in the examples directory.
  28 #
  29
  30 use Bio::Tools::pSW;
  31
  32 # redundant, as Bio::Tools::pSW uses them, but useful to say
  33 # precisely what we are using ;)
  34
  35 use Bio::Seq;
  36 use Bio::SimpleAlign;
  37 use Bio::AlignIO;
  38
  39 # for legibility - write with newlines and then strip them!
  40
  41 $tseq = 'SKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVT
  42 YATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHL
  43 RDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKAL
  44 SKQEMASASSSQRGRSGSGNFGGGRGGGFGGNDNFGRGGNFSGRGGFGGSRGGGGYGGSG
  45 DGYNGFGNDGGYGGGGPGYSGGSRGYGSGGQGYGNQGSGYGGSGSYDSYNNGGGRGFGGG
  46 SGSNFGGGGSYNDFGNYNNQSSNFGPMKGGNFGGRSSGPYGGGGQYFAKPRNQGGYGGSS
  47 SSSSYGSGRRF';
  48
  49 $tseq =~ s/[^A-Z]//g;
  50
  51 $seq1 = Bio::Seq->new(-id=>'roa1_human',-seq=>$tseq);
  52
  53 $tseq = 'MVNSNQNQNGNSNGHDDDFPQDSITEPEHMRKLFIGGLDYRTTDENLKAHFEKWGNIVDV
  54 VVMKDPRTKRSRGFGFITYSHSSMIDEAQKSRPHKIDGRVVEPKRAVPRQDIDSPNAGAT
  55 VKKLFVGALKDDHDEQSIRDYFQHFGNIVDINIVIDKETGKKRGFAFVEFDDYDPVDKVV
  56 LQKQHQLNGKMVDVKKALPKQNDQQGGGGGRGGPGGRAGGNRGNMGGGNYGNQNGGGNWN
  57 NGGNNWGNNRGGNDNWGNNSFGGGGGGGGGYGGGNNSWGNNNPWDNGNGGGNFGGGGNNW
  58 NNGGNDFGGYQQNYGGGPQRGGGNFNNNRMQPYQGGGGFKAGGGNQGNYGGNNQGFNNGG
  59 NNRRY';
  60
  61 $tseq =~ s/[^A-Z]//g;
  62
  63 $seq2 = Bio::Seq->new(-id=>'roa1_drome',-seq=>$tseq);
  64
  65 $tseq = 'MHKSEAPNEPEQLRKLFIGGLSFETTDESLREHFEQWGTLTDCVVMRDPNSKRSRGFGFV
  66 TYLSTDEVDAAMTARPHKVDGRVVEPKRAVSREDSSRPGAHLTVKKIFVGGIKEDTEEDH
  67 LREYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFEDHDSVDKIVIQKYHTVNNHNSQVRKA
  68 LSKQEMASVSGSQRERGGSGNYGSRGGFGNDNFGGRGGNFGGNRGGGGGFGNRGYGGDGY
  69 NGDGQLWWQPSLLGWNRGYGAGQGGGYGAGQGGGYGGGGQGGGYGGNGGYDGYNGGGSGF
  70 SGSGGNFGSSGGYNDFGNYNSQSSSNFGPMKGGNYGGGRNSGPYGGGYGGGSASSSSGYG
  71 GGRRF';
  72
  73 $tseq =~ s/[^A-Z]//g;
  74 $seq3 = Bio::Seq->new(-id=>'roa1_xenla',-seq=>$tseq);
  75
  76
  77 #
  78 # Now make an Alignment Factory with blosum62 as a matrix
  79 # gap -12 and ext -2
  80 #
  81
  82 $fac = Bio::Tools::pSW->new(-matrix => 'blosum62.bla',-gap => 12, -ext => 2);
  83
  84
  85 #
  86 # run seq1 vs seq2 and seq1 vs seq3 and write the output direct
  87 # to stdout using the 'pretty' method
  88 #
  89
  90 $fac->align_and_show($seq1,$seq2,STDOUT);
  91 print "Next alignment\n";
  92 $fac->align_and_show($seq1,$seq3,STDOUT);
  93
  94
  95 #
  96 # a different factory, using gonnet, and now make a simple align and
  97 # provide MSF format
  98 #
  99
 100 $fac = Bio::Tools::pSW->new(-matrix => 'gon250.bla',-gap => 12, -ext => 2);
 101
 102
 103 # switch on reporting this time and change the amount of memory it is allowed
 104
 105 print STDOUT "Doing the next calculation in limited memory, with a progress report\n";
 106
 107 $fac->report(1);
 108 $fac->kbyte(100);
 109
 110 $al = $fac->pairwise_alignment($seq1,$seq2);
 111
 112
 113 # write out a MSF file
 114 my $out = Bio::AlignIO->newFh('-fh'=> \*STDOUT,  '-format' => 'msf');
 115 my $status = print $out $al;
 116 #$al->write_MSF(\*STDOUT);
 117
 118
 119