[Bioperl-guts-l] bioperl-run/Bio/Tools/Run FootPrinter.pm, 1.20, 1.21

Brian Osborne bosborne at dev.open-bio.org
Wed Feb 21 12:10:41 EST 2007


Update of /home/repository/bioperl/bioperl-run/Bio/Tools/Run
In directory dev.open-bio.org:/tmp/cvs-serv12637/Bio/Tools/Run

Modified Files:
	FootPrinter.pm 
Log Message:
Correct address, minor edits

Index: FootPrinter.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-run/Bio/Tools/Run/FootPrinter.pm,v
retrieving revision 1.20
retrieving revision 1.21
diff -C2 -d -r1.20 -r1.21
*** FootPrinter.pm	16 Feb 2007 19:18:42 -0000	1.20
--- FootPrinter.pm	21 Feb 2007 17:10:39 -0000	1.21
***************
*** 30,34 ****
    my $fp = Bio::Tools::Run::FootPrinter->new(@params, -verbose => 1);
  
!   my $sio = Bio::SeqIO->new(-file=>"seq.fa", -format => "fasta");
  
    while (my $seq = $sio->next_seq){
--- 30,34 ----
    my $fp = Bio::Tools::Run::FootPrinter->new(@params, -verbose => 1);
  
!   my $sio = Bio::SeqIO->new(-file => "seq.fa", -format => "fasta");
  
    while (my $seq = $sio->next_seq){
***************
*** 49,56 ****
  
  FootPrinter is a program that performs phylogenetic footprinting. 
! It takes as input a set of unaligned orthologous sequences from various species, 
! together with a phylogenetic tree relating these species. 
  It then searches for short regions of the sequences that are highly conserved, 
  according to a parsimony criterion. 
  The regions identified are good candidates for regulatory elements. 
  By default, the program searches for regions that are well conserved across 
--- 49,57 ----
  
  FootPrinter is a program that performs phylogenetic footprinting. 
! It takes as input a set of unaligned orthologous sequences from various 
! species, together with a phylogenetic tree relating these species. 
  It then searches for short regions of the sequences that are highly conserved, 
  according to a parsimony criterion. 
+ 
  The regions identified are good candidates for regulatory elements. 
  By default, the program searches for regions that are well conserved across 
***************
*** 60,121 ****
  =head2 About Footprinter
  
! Written by Mathieu Blanchette and Martin Tompa. Available at:
  
- L<http://abstract.cs.washington.edu/~blanchem/FootPrinterWeb/FootPrinterInput.pl>
  
  =head2 Running Footprinter
  
! To run FootPrinter, you will NEED to set the enviroment variable
  FOOTPRINTER_DIR to where the binary is located (even if the executable is in
  your path). For example:
  
!  setenv FOOTPRINTER_DIR=/usr/local/bin/FootPrinter2.0/
  
  =head2 Available Parameters
  
!   PARAM         VALUES        DESCRIPTION
!   ----------------------------------------
!   tree                      <file>        REQUIRED, Tree in Newick Format
!                                           to evaluate parsimony score 
!                                           REQUIRED unless tree_of_life
!                                           exists in FOOTPRINTER_DIR
!   sequence_type             upstream      Default upstream
!                             downstream
!                             other
!   size                      4-16          Specifies the size of the motifs sought
!   max_mutations             0-20          maximum parsimony score allowed for the motifs
!   max_mutations_per_branch  0-20          Allows at most a fixed number of mutations per 
!                                           branch of the tree
!   losses                    <file>        files give span constraints so that the motifs
!                                           reported are statistically significant
!                                           Example files
!                                           universal([6-9]|1[0-2])(loose|tight)?.config
!                                           come with FootPrinter2.0.
!                                           Install these in FOOTPRINTER_DIR and use by
!                                           setting "losses" to "somewhat significant",
!                                           "significant", or "very significant". Do not
!                                           set loss_cost.
!   loss_cost                 0-20          a cost associated with losing a motif along some 
!                                           branch of the tre
!   subregion_size            1-infinity    penalize motifs whose position in the sequences 
!                                           varies too much
!   position_change_cost      0-20          Cost for changing subregion
  
!   triplet_filtering         1/0           pre-filtering step that removes from consideration 
!                                           any substring that does not have a sufficiently good 
!                                           pair of matching substrings in some pair of the other 
!                                           input sequences
!   pair_filtering            1/0           Same as triplet filtering, but looks only for one match 
!                                           per other sequence
!   post_filtering            1/0           when used in conjunction with the triplet filtering 
!                                           option, this often significantly speeds up the program, 
!                                           while still garanteeing optimal results
!   indel_cost                1-5           insertions and deletions will be allowed in the motifs 
!                                           sought, at the given cost
!   inversion_cost            1-5           This option allows for motifs to undergo inversions, 
!                                           at the given cost. An inversion reverse-complements the motif.
!   details                   1/0           Shows some of the details about the progress of the computation
!   html                      1/0           produce html output (never deleted)
!   ps                        1/0           produce postscript output (never deleted)
  
  =head1 FEEDBACK
--- 61,131 ----
  =head2 About Footprinter
  
! Written by Mathieu Blanchette and Martin Tompa. Available here:
! 
! http://www.mcb.mcgill.ca/~blanchem/FootPrinter2.1.tar.gz 
  
  
  =head2 Running Footprinter
  
! To run FootPrinter, you will need to set the enviroment variable
  FOOTPRINTER_DIR to where the binary is located (even if the executable is in
  your path). For example:
  
!  setenv FOOTPRINTER_DIR /usr/local/bin/FootPrinter2.0/
! 
  
  =head2 Available Parameters
  
! PARAM         VALUES        DESCRIPTION
! ------------------------------------------------------------------------
! tree                      <file>     REQUIRED, Tree in Newick Format
!                                      to evaluate parsimony score 
!                                      REQUIRED unless tree_of_life
!                                      exists in FOOTPRINTER_DIR
! sequence_type             upstream   Default upstream
!                           downstream
!                           other
  
! size                      4-16       Specifies the size of the motifs sought
! 
! max_mutations             0-20       maximum parsimony score allowed for the motifs
! 
! max_mutations_per_branch  0-20       Allows at most a fixed number of mutations per 
!                                      branch of the tree
! losses                    <file>     files give span constraints so that the motifs
!                                      reported are statistically significant
!                                      Example files
!                                      universal([6-9]|1[0-2])(loose|tight)?.config
!                                      come with FootPrinter2.0.
!                                      Install these in FOOTPRINTER_DIR and use by
!                                      setting "losses" to "somewhat significant",
!                                      "significant", or "very significant". Do not
!                                      set loss_cost.
! loss_cost                 0-20       a cost associated with losing a motif along some 
!                                      branch of the tre
! subregion_size            1-infinity penalize motifs whose position in the sequences 
!                                      varies too much
! position_change_cost      0-20       Cost for changing subregion
! 
! triplet_filtering         1/0        pre-filtering step that removes from consideration 
!                                      any substring that does not have a sufficiently good 
!                                      pair of matching substrings in some pair of the other 
!                                      input sequences
! pair_filtering            1/0        Same as triplet filtering, but looks only for one match 
!                                      per other sequence
! post_filtering            1/0        when used in conjunction with the triplet filtering 
!                                      option, this often significantly speeds up the program, 
!                                      while still garanteeing optimal results
! indel_cost                1-5        insertions and deletions will be allowed in the motifs 
!                                      sought, at the given cost
! inversion_cost            1-5        This option allows for motifs to undergo inversions, 
!                                      at the given cost. An inversion reverse-complements 
!                                      the motif.
! details                   1/0        Shows some of the details about the progress of the 
!                                      computation
! 
! html                      1/0        produce html output (never deleted)
! 
! ps                        1/0        produce postscript output (never deleted)
  
  =head1 FEEDBACK



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