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speelink fixes, patch courtesy Charles Plessy, fixes #3256

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1 parent 20d2c48 commit 42649c5308b51c1b87d442ac35e82b8ccfa6545d Chris Fields committed Jul 6, 2011
@@ -205,7 +205,7 @@ clustalw program have not yet been implemented. If you would like
that a specific clustalw feature be added to this perl contact
bioperl-l@bioperl.org.
-These can be specified as paramters when instantiating a new Clustalw
+These can be specified as parameters when instantiating a new Clustalw
object, or through get/set methods of the same name (lowercase).
=head1 PARAMETER FOR ALIGNMENT COMPUTATION
@@ -192,7 +192,7 @@ sub new {
Args : The first argument represents a protein alignment, the second
argument a set of nucleotide sequences.
The alignment can be provided as an alignment file readable by
- Bio::AlignIO, or a Bio::Align::AlignI complient object (eg. a
+ Bio::AlignIO, or a Bio::Align::AlignI compliant object (eg. a
Bio::SimpleAlign).
The nucleotide sequences can be provided as a single filename of a
fasta file containing multiple nucleotide sequences, or an array ref
@@ -117,7 +117,7 @@ Email tqzhang1973@yahoo.com
=head1 Appendix
The rest of the documendation details each of the object
-methods. Internal methods are preceeded with a underscore
+methods. Internal methods are preceded with a underscore
=cut
@@ -865,7 +865,7 @@ sub parameters_changed {
Usage : @params = $pobj->available_parameters()
Function: Returns a list of the available parameters
Returns : Array of parameters
- Args : 'params' for settable program paramters
+ Args : 'params' for settable program parameters
'switches' for boolean program switches
default: all
@@ -67,7 +67,7 @@ Written by Mathieu Blanchette and Martin Tompa. Available here:
=head2 Running Footprinter
-To run FootPrinter, you will need to set the enviroment variable
+To run FootPrinter, you will need to set the environment variable
FOOTPRINTER_DIR to where the binary is located (even if the executable
is in your path). For example:
@@ -172,7 +172,7 @@ our @UNSUPPORTED = qw(h verbose a compat pvm);
-o is synonymous with -outfile
# may be specified here, allowing run() to be used, or
- # it can be ommitted and the corresponding method (eg.
+ # it can be omitted and the corresponding method (eg.
# hmmalign()) used later.
-program => hmmalign|hmmbuild|hmmcalibrate|hmmemit|hmmpfam|hmmsearch
View
@@ -216,7 +216,7 @@ sub new {
third argument represents annotation of the exons in the alignment.
The alignment can be provided as a multi-fasta format alignment
- filename, or a Bio::Align::AlignI complient object (eg. a
+ filename, or a Bio::Align::AlignI compliant object (eg. a
Bio::SimpleAlign).
The position in the genome can be provided as a Bio::Location::Atomic
@@ -211,10 +211,10 @@ sub new {
Args : The first argument represents an alignment, the second argument
a phylogenetic tree with branch lengths.
The alignment can be provided as a MAF format alignment
- filename, or a Bio::Align::AlignI complient object (eg. a
+ filename, or a Bio::Align::AlignI compliant object (eg. a
Bio::SimpleAlign).
The species tree can be provided as a newick format tree filename
- or a Bio::Tree::TreeI complient object.
+ or a Bio::Tree::TreeI compliant object.
In all cases, the alignment sequence names must correspond to node
ids in the tree. Multi-word species names should have the
@@ -284,10 +284,10 @@ sub annots {
Args : The first argument represents an alignment, the second argument
a species tree.
The alignment can be provided as a multi-fasta format alignment
- filename, or a Bio::Align::AlignI complient object (eg. a
+ filename, or a Bio::Align::AlignI compliant object (eg. a
Bio::SimpleAlign).
The species tree can be provided as a newick format tree filename
- or a Bio::Tree::TreeI complient object. Alternatively a
+ or a Bio::Tree::TreeI compliant object. Alternatively a
Bio::DB::Taxonomy object can be supplied, in which case the species
tree will be generated by using the alignment sequence names as
species names and looking for those in the supplied database.
@@ -554,7 +554,7 @@ sub set_parameter{
Returns : none
Args : boolean: keep existing parameter values
NB : using this isn't an especially good idea! You don't need to do
- anything to end up using default paramters: hence 'default'!
+ anything to end up using default parameters: hence 'default'!
=cut
@@ -331,13 +331,13 @@ sub rho {
('footprinting').
Returns : array of Bio::SeqFeature::Annotated (one feature per alignment
sequence and prediction)
- Args : The first arguement represents an alignment, the second arguement
+ Args : The first argument represents an alignment, the second argument
a species tree.
The alignment can be provided as a multi-fasta format alignment
- filename, or a Bio::Align::AlignI complient object (eg. a
+ filename, or a Bio::Align::AlignI compliant object (eg. a
Bio::SimpleAlign).
The species tree can be provided as a newick format tree filename
- or a Bio::Tree::TreeI complient object. Alternatively a
+ or a Bio::Tree::TreeI compliant object. Alternatively a
Bio::DB::Taxonomy object can be supplied, in which case the species
tree will be generated by using the alignment sequence names as
species names and looking for those in the supplied database.
@@ -241,10 +241,10 @@ sub new {
Args : The first argument represents an alignment, the second argument
a species tree.
The alignment can be provided as a multi-fasta format alignment
- filename, or a Bio::Align::AlignI complient object (eg. a
+ filename, or a Bio::Align::AlignI compliant object (eg. a
Bio::SimpleAlign).
The species tree can be provided as a newick format tree filename
- or a Bio::Tree::TreeI complient object. Alternatively a
+ or a Bio::Tree::TreeI compliant object. Alternatively a
Bio::DB::Taxonomy object can be supplied, in which case the species
tree will be generated by using the alignment sequence names as
species names and looking for those in the supplied database.
@@ -97,7 +97,7 @@ this is still experimental as v3.6 is still under alpha release and not all func
Title : TYPE
Description : (optional)
- Only avaliable in phylip v3.6
+ Only available in phylip v3.6
This program supports 3 types of consensus generation
@@ -315,7 +315,7 @@ sub version {
Returns : Bio::Tree::Tree object
Args : file name for your input alignment in a format
recognised by AlignIO, OR Bio::Align::AlignI
- complient object (eg. Bio::SimpleAlign).
+ compliant object (eg. Bio::SimpleAlign).
=cut
@@ -358,7 +358,7 @@ sub stats {
Title : tree_string
Usage : $factory->tree_string;
$factory->run($align_object);
- Function: Returns the contents of the phyml '_phyml_tree.txt' ouput file
+ Function: Returns the contents of the phyml '_phyml_tree.txt' output file
Returns : string with tree in Newick format, undef before run()
Args : none
@@ -240,7 +240,7 @@ sub boot {
Function: Runs QuickTree to generate a tree
Returns : Bio::Tree::Tree object
Args : file name for your input alignment in stockholm format, OR
- Bio::Align::AlignI complient object (eg. Bio::SimpleAlign).
+ Bio::Align::AlignI compliant object (eg. Bio::SimpleAlign).
=cut
@@ -252,10 +252,10 @@ sub new {
argument a species tree (to set an initial tree: normally the -t
option to Semphy).
The alignment can be provided as a multi-fasta format alignment
- filename, or a Bio::Align::AlignI complient object (eg. a
+ filename, or a Bio::Align::AlignI compliant object (eg. a
Bio::SimpleAlign).
The species tree can be provided as a newick format tree filename
- or a Bio::Tree::TreeI complient object. Alternatively a
+ or a Bio::Tree::TreeI compliant object. Alternatively a
Bio::DB::Taxonomy object can be supplied, in which case the species
tree will be generated by using the alignment sequence names as
species names and looking for those in the supplied database.
@@ -210,7 +210,7 @@ To get the tempfile basename, do:
=item * Specify data post-construction
-Use the explict attribute setters:
+Use the explicit attribute setters:
$fac = Bio::Tools::Run::StandAloneBlastPlus->new(
-create => 1
@@ -179,7 +179,7 @@ TIGR Assembler options available in this module:
ignore_tandem_32mers: a flag which causes tandem 32mers (a tandem 32mer is a
32mer which occurs more than once in at least one sequence read) to be
ignored (this is now the default behavior and this flag is for backward
- compatability)
+ compatibility)
use_tandem_32mers: a flag which causes tandem 32mers to be used for pairwise
comparison opposite of the -t flag which is now the default).
safe_merging_stop: a flag which causes merging to stop when only sequences
@@ -323,7 +323,7 @@ will function normally and cause success/errors for B<Test::Harness>.
sub test_test
{
- # decode the arguements as described in the pod
+ # decode the arguments as described in the pod
my $mess;
my %args;
if (@_ == 1)

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