[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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