[med-svn] [libtfbs-perl] 05/08: Refresh spelling error patch.
Charles Plessy
plessy at moszumanska.debian.org
Sat Oct 21 02:48:17 UTC 2017
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plessy pushed a commit to branch master
in repository libtfbs-perl.
commit fb6026da72aa281791ab49d67e1eae99b0895ff0
Author: Charles Plessy <plessy at debian.org>
Date: Sat Oct 21 11:19:05 2017 +0900
Refresh spelling error patch.
---
debian/patches/spelling-errors.patch | 141 ++++-------------------------------
1 file changed, 14 insertions(+), 127 deletions(-)
diff --git a/debian/patches/spelling-errors.patch b/debian/patches/spelling-errors.patch
index 2ba8a06..4c97ff4 100644
--- a/debian/patches/spelling-errors.patch
+++ b/debian/patches/spelling-errors.patch
@@ -1,102 +1,11 @@
Description: Fix spelling errors.
- classs -> class
hierachical -> hierarchical
- infromation -> information
occurence -> occurrence
- repective -> respective
- supresses -> suppresses
- taht -> that
Author: Bas Couwenberg <sebastic at debian.org>
---- a/TFBS/DB/JASPAR2.pm
-+++ b/TFBS/DB/JASPAR2.pm
-@@ -458,7 +458,7 @@ gives a set of PWMs whose (structural cl
- OR 'Mus musculus').
-
- The -min_ic filter is applied after the query in the sense that the
--matrices profiles with total infromation content less than specified
-+matrices profiles with total information content less than specified
- are not included in the set.
-
- =cut
---- a/TFBS/DB/JASPAR4.pm
-+++ b/TFBS/DB/JASPAR4.pm
-@@ -409,7 +409,7 @@ sub get_Matrix_by_name {
- database storage, any tag can be used for information retrieval.
- Additionally, arguments as 'name' and 'class' can be used (even though
- they are not tags.
-- As with get_Matrix methods, it is important to realize taht any matrix
-+ As with get_Matrix methods, it is important to realize that any matrix
- format can be stored in the database: the TFBS::MatrixSet might therefore
- consist of PFMs, ICMs and PWMS, depending on how matrices are stored,
-
-@@ -445,7 +445,7 @@ gives a set of TFBS::Matrix::PFM objects
- from is 'Homo sapiens'OR 'Mus musculus').
-
- The -min_ic filter is applied after the query in the sense that the
--matrices profiles with total infromation content less than specified
-+matrices profiles with total information content less than specified
- are not included in the set.
-
- =cut
---- a/TFBS/PatternGen.pm
-+++ b/TFBS/PatternGen.pm
-@@ -14,7 +14,7 @@ TFBS::PatternGen - a base class for patt
-
- =head1 DESCRIPTION
-
--TFBS::PatternGen is a base classs providing methods common to all pattern generating
-+TFBS::PatternGen is a base class providing methods common to all pattern generating
- modules. It is meant to be inherited by a concrete pattern generator, which must have its own
- constructor.
-
---- a/TFBS/Matrix/ICM.pm
-+++ b/TFBS/Matrix/ICM.pm
-@@ -98,7 +98,7 @@ following information content matrix:
- G:[0.00 0.89 2.00 0.00 0.00 0.00]
- T:[0.00 0.00 0.00 0.13 0.06 2.00]
-
--which contains the "weights" associated with the occurence of each
-+which contains the "weights" associated with the occurrence of each
- nucleotide at the given position in a pattern.
-
- A TFBS::Matrix::PWM object is equipped with methods to search nucleotide
---- a/TFBS/Matrix/PWM.pm
-+++ b/TFBS/Matrix/PWM.pm
-@@ -100,7 +100,7 @@ following position weight matrix:
- G:[-1.57 1.85 -2.57 -1.34 -1.57 1.14]
- T:[ 0.31 -3.16 -2.57 1.76 0.24 -0.83]
-
--which contains the "weights" associated with the occurence of each
-+which contains the "weights" associated with the occurrence of each
- nucleotide at the given position in a pattern.
-
- A TFBS::Matrix::PWM object is equipped with methods to search nucleotide
---- a/TFBS/PatternGen/Elph.pm
-+++ b/TFBS/PatternGen/Elph.pm
-@@ -66,7 +66,7 @@ use Bio::SeqIO;
- Other arguments are:
- -binary # a fully qualified path to Gibbs executable
- # OPTIONAL: default 'Gibbs'
-- -nr_hits # a presumed number of pattern occurences in the
-+ -nr_hits # a presumed number of pattern occurrences in the
- # sequence set: it can be a single integer, e.g.
- # -nr_hits => 24 , or a reference to an array of
- # integers, e.g -nr_hits => [12, 24, 36]
---- a/TFBS/PatternGen/Gibbs.pm
-+++ b/TFBS/PatternGen/Gibbs.pm
-@@ -67,7 +67,7 @@ use Bio::SeqIO;
- Other arguments are:
- -binary # a fully qualified path to Gibbs executable
- # OPTIONAL: default 'Gibbs'
-- -nr_hits # a presumed number of pattern occurences in the
-+ -nr_hits # a presumed number of pattern occurrences in the
- # sequence set: it can be a single integer, e.g.
- # -nr_hits => 24 , or a reference to an array of
- # integers, e.g -nr_hits => [12, 24, 36]
--- a/TFBS/PatternGen/YMF.pm
+++ b/TFBS/PatternGen/YMF.pm
-@@ -177,7 +177,7 @@ sub _parse_stats_output{
+@@ -177,7 +177,7 @@
my $motif =TFBS::PatternGen::YMF::Motif->new
(-word=>$word,
-tags => {z_score=>$z_score,
@@ -105,49 +14,16 @@ Author: Bas Couwenberg <sebastic at debian.org>
'expectation value'=>$expect,
'variance'=>$var}
);
-@@ -190,4 +190,4 @@ sub _parse_stats_output{
+@@ -190,4 +190,4 @@
}
#
-1;
\ No newline at end of file
+1;
---- a/TFBS/Matrix/Alignment.pm
-+++ b/TFBS/Matrix/Alignment.pm
-@@ -239,7 +239,7 @@ sub new {
- Title : alignment
- Usage : my $alignment_string = $alignmentobject->alignment();
- Function: access a string describing the alignment
-- Returns : an string, where each number refers to a position in repective PFM.
-+ Returns : an string, where each number refers to a position in respective PFM.
- Position numbering is according to orientation: ie if the second profile is
- reversed, position 1 corresponds to the last position in the input profile.
- Gaps are denoted as - .
---- a/TFBS/DB/LocalTRANSFAC.pm
-+++ b/TFBS/DB/LocalTRANSFAC.pm
-@@ -70,7 +70,7 @@ use TFBS::Matrix::PFM;
- # have read and accepted the terms
- # of use of TRANSFAC at
- # http://transfac.gbf.de/TRANSFAC/disclaimer.htm;
-- # this also supresses the annoying
-+ # this also suppresses the annoying
- # message that is printed to STDERR
- # upon invoking the method
-
---- a/TFBS/DB/TRANSFAC.pm
-+++ b/TFBS/DB/TRANSFAC.pm
-@@ -69,7 +69,7 @@ use LWP::Simple qw($ua get);
- # have read and accepted the terms
- # of use of TRANSFAC at
- # http://transfac.gbf.de/TRANSFAC/disclaimer.htm;
-- # this also supresses the annoying
-+ # this also suppresses the annoying
- # message that is printed to STDERR
- # upon invoking the method
-
--- a/TFBS/MatrixSet.pm
+++ b/TFBS/MatrixSet.pm
-@@ -763,7 +763,7 @@ sub _build_cluster {
+@@ -763,7 +763,7 @@
Title : cluster
Usage : $matrixset->cluster(%args)
Function: Clusters the matrices in the set
@@ -156,3 +32,14 @@ Author: Bas Couwenberg <sebastic at debian.org>
An integer specifying the optimal number of clusters.
An array of TFBS::MatrixSets, one for each cluster.
Args : Many:
+--- a/TFBS/Matrix/PFM.pm
++++ b/TFBS/Matrix/PFM.pm
+@@ -366,7 +366,7 @@
+ # "pseudocounts" - standard pseudocount
+ # correction, more suitable for
+ # PFMs with large r column sums
+- # If the parameter is ommited, small
++ # If the parameter is omitted, small
+ # sample correction is not applied
+
+ -draw_error_bars # if true, adds error bars to each position
--
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