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Bio::Tree:Statistics parsimony question
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Bio::Tree:Statistics parsimony question
by Chris-754
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Hello,
I have been able to use the ps() method in Bio::Tree::Statistics to calulate the parsimony for tag values from a tree if they are strings. This is the way I have been implementing the method: my $obj = Bio::Tree::Statistics->new(); my $pars = $obj->ps($tree,'seq'); print "Parsimony = $pars \n"; Is it possible to do so if they are an array? say I have an array @seq = qw(A,A,C,G), I can add these as values to a leaf node of a tree using; foreach my $char (@seq){ $node->add_tag_value('seq',$char); } Does anybody have a suggestion to get the parsimony for each label of the array of labels for such a tree ? Thanks in advance, Chris. _______________________________________________ Bioperl-l mailing list Bioperl-l@... http://lists.open-bio.org/mailman/listinfo/bioperl-l |
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Re: Bio::Tree:Statistics parsimony question
by Chris-754
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Hi Mark,
I might be missing something, but I cant see how that will work. ps() takes as input a tree with the tags already in the leaf nodes and the key for those tags. I think your suggested solution places the tags from the @seq array into ps() which throws an exception error. Maybe another explanaition; I would like to calculate the parsimony score at each position of an alignment. Consider 1 block with only 1 character in for each species; species1 A species 2 G species 3 G species 4 G I can do this for 1 position, by adding the tag (which Ive named 'seq') value pair to each leaf node of the phylogeny tree for the 4 species, where the tag is a single character. Then calculating the parsimony for that column is simply my $obj = Bio::Tree::Statistics->new(); my $pars = $obj->ps($tree,'seq'); print "Parsimony = $pars \n"; Now consider an alignment block with more than 1 character species1 ACG species 2 GCT species 3 GGG species 4 GGT I see it is possible to add an array of values as a tag, now, instead of a single character as a tag on each leaf node, I have an array of nucleotides as tags at each leaf node. I was hoping for a way to calculate the parsimony given a tree with such tag value pairs. Regards, Chris. On Fri, Oct 23, 2009 at 11:12 PM, Mark A. Jensen <maj@...> wrote: > up to list... > ----- Original Message ----- From: "Mark A. Jensen" <maj@...> > To: "Chris" <coldmeadow@...> > Sent: Friday, October 23, 2009 8:14 AM > Subject: Re: [Bioperl-l] Bio::Tree:Statistics parsimony question > > > > Hi Chris, >> looks like you could simply do >> >> @ps = map { $obj->ps($tree, $_) } @seq; >> >> or into a hash %ps with tags as keys: >> >> @ps{@seq} = map { $obj->ps($tree,$_) } @seq; >> >> cheers MAJ >> ----- Original Message ----- From: "Chris" <coldmeadow@...> >> To: <bioperl-l@...> >> Sent: Friday, October 23, 2009 1:10 AM >> Subject: [Bioperl-l] Bio::Tree:Statistics parsimony question >> >> >> Hello, >>> I have been able to use the ps() method in Bio::Tree::Statistics to >>> calulate >>> the parsimony for tag values from a tree if they are strings. >>> >>> This is the way I have been implementing the method: >>> >>> my $obj = Bio::Tree::Statistics->new(); >>> my $pars = $obj->ps($tree,'seq'); >>> print "Parsimony = $pars \n"; >>> >>> Is it possible to do so if they are an array? >>> >>> say I have an array @seq = qw(A,A,C,G), I can add these as values to a >>> leaf >>> node of a tree using; >>> >>> foreach my $char (@seq){ >>> $node->add_tag_value('seq',$char); >>> } >>> >>> Does anybody have a suggestion to get the parsimony for each label of the >>> array of labels for such a tree ? >>> >>> Thanks in advance, >>> Chris. >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l@... >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >>> >>> _______________________________________________ > Bioperl-l mailing list > Bioperl-l@... > http://lists.open-bio.org/mailman/listinfo/bioperl-l > Bioperl-l mailing list Bioperl-l@... http://lists.open-bio.org/mailman/listinfo/bioperl-l |
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Re: Bio::Tree:Statistics parsimony question
by Mark A. Jensen
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I see.
You can use the add_trait method on the tree object; to this, you provide a file containing a table of nodes X traits. The following code works; it creates a trait table on the fly, according to seq data given in the DATA section (after __END__). Then in a loop, add_traits is used to add each position and calculate the ps. There's probably a better way, but this could get you started. use Bio::Tree::Statistics; use Bio::TreeIO; use strict; use warnings; # tree file can be found in t/data... my $in = Bio::TreeIO->new(-format => 'nexus', -file => 'traittree.nexus'); my $obj = Bio::Tree::Statistics->new(); my $tree = $in->next_tree; # make a trait table from the sequences open(my $tmpf, ">seq.dat"); my $len = <DATA>; chomp $len; print $tmpf join("\t", "id", map { "pos".$_ } (1..$len)), "\n"; while (<DATA>) { chomp; my ($id, $seq) = split /\s+/; print $tmpf join( "\t", $id, split('', $seq) ), "\n"; } close($tmpf); # cycle through my @pars; for (1..$len) { my $key = $tree->add_trait('seq.dat', $_); push @pars, $obj->ps($tree, $key); } print join("\n", @pars); __END__ 3 1 ACG 2 GCT 3 GGG 4 GGT 5 ACG 6 GCT 7 GGG 8 GGT 9 ACG 10 GCT 11 GGG 12 GGT 13 ACG 14 GCT 15 GGG 16 GGT ----- Original Message ----- From: Chris To: Mark A. Jensen Cc: bioperl List Sent: Friday, October 23, 2009 5:00 PM Subject: Re: [Bioperl-l] Bio::Tree:Statistics parsimony question Hi Mark, I might be missing something, but I cant see how that will work. ps() takes as input a tree with the tags already in the leaf nodes and the key for those tags. I think your suggested solution places the tags from the @seq array into ps() which throws an exception error. Maybe another explanaition; I would like to calculate the parsimony score at each position of an alignment. Consider 1 block with only 1 character in for each species; species1 A species 2 G species 3 G species 4 G I can do this for 1 position, by adding the tag (which Ive named 'seq') value pair to each leaf node of the phylogeny tree for the 4 species, where the tag is a single character. Then calculating the parsimony for that column is simply my $obj = Bio::Tree::Statistics->new(); my $pars = $obj->ps($tree,'seq'); print "Parsimony = $pars \n"; Now consider an alignment block with more than 1 character species1 ACG species 2 GCT species 3 GGG species 4 GGT I see it is possible to add an array of values as a tag, now, instead of a single character as a tag on each leaf node, I have an array of nucleotides as tags at each leaf node. I was hoping for a way to calculate the parsimony given a tree with such tag value pairs. Regards, Chris. On Fri, Oct 23, 2009 at 11:12 PM, Mark A. Jensen <maj@...> wrote: up to list... ----- Original Message ----- From: "Mark A. Jensen" <maj@...> To: "Chris" <coldmeadow@...> Sent: Friday, October 23, 2009 8:14 AM Subject: Re: [Bioperl-l] Bio::Tree:Statistics parsimony question Hi Chris, looks like you could simply do @ps = map { $obj->ps($tree, $_) } @seq; or into a hash %ps with tags as keys: @ps{@seq} = map { $obj->ps($tree,$_) } @seq; cheers MAJ ----- Original Message ----- From: "Chris" <coldmeadow@...> To: <bioperl-l@...> Sent: Friday, October 23, 2009 1:10 AM Subject: [Bioperl-l] Bio::Tree:Statistics parsimony question Hello, I have been able to use the ps() method in Bio::Tree::Statistics to calulate the parsimony for tag values from a tree if they are strings. This is the way I have been implementing the method: my $obj = Bio::Tree::Statistics->new(); my $pars = $obj->ps($tree,'seq'); print "Parsimony = $pars \n"; Is it possible to do so if they are an array? say I have an array @seq = qw(A,A,C,G), I can add these as values to a leaf node of a tree using; foreach my $char (@seq){ $node->add_tag_value('seq',$char); } Does anybody have a suggestion to get the parsimony for each label of the array of labels for such a tree ? Thanks in advance, Chris. _______________________________________________ Bioperl-l mailing list Bioperl-l@... http://lists.open-bio.org/mailman/listinfo/bioperl-l _______________________________________________ Bioperl-l mailing list Bioperl-l@... http://lists.open-bio.org/mailman/listinfo/bioperl-l _______________________________________________ Bioperl-l mailing list Bioperl-l@... http://lists.open-bio.org/mailman/listinfo/bioperl-l |
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