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Subject: Fix spelling errors
Author: Olivier Salllou <olivier.sallou@irisa.fr>
Description: fix spelling errors in man pages
Last-Updated: 09/11/11
--- a/lib/Bio/GMOD/DB/Adapter.pm
+++ b/lib/Bio/GMOD/DB/Adapter.pm
@@ -868,7 +868,7 @@
=item Returns
-On create, void. With an arguement, returns the requested file handle
+On create, void. With an argument, returns the requested file handle
=item Arguments
@@ -968,7 +968,7 @@
=item Returns
-See Arguements.
+See Arguments.
=item Arguments
@@ -3476,7 +3476,7 @@
-- short identifier that can help people find an analysis they
-- want. for instance "tRNAscan", "cDNA", "FlyPep", "SwissProt"
-- it should not be assumed to be unique. for instance, there may
--- be lots of seperate analyses done against a cDNA database.
+-- be lots of separate analyses done against a cDNA database.
--
-- program: not NULL (and programversion is NOT NULL...)
-- e.g. blastx, blastp, sim4, genscan
--- a/lib/Bio/GMOD/Config2.pm
+++ b/lib/Bio/GMOD/Config2.pm
@@ -81,7 +81,7 @@
Takes one optional argument that is the path to the root of the GMOD
installation. If that argument is not provided, Bio::GMOD::Config will
-fall back to the enviroment variable GMOD_ROOT, which should be defined
+fall back to the environment variable GMOD_ROOT, which should be defined
for any GMOD installation.
=cut
@@ -267,7 +267,7 @@
=head2 appendHash($tohash, $addhash, $replace)
-add keys to hash without replacing existing .. prefered behavior ?
+add keys to hash without replacing existing .. preferred behavior ?
unless $replace is flagged
=cut
--- a/lib/Bio/GMOD/Config.pm
+++ b/lib/Bio/GMOD/Config.pm
@@ -41,7 +41,7 @@
Takes one optional argument that is the path to the root of the GMOD
installation. If that argument is not provided, Bio::GMOD::Config will
-fall back to the enviroment variable GMOD_ROOT, which should be defined
+fall back to the environment variable GMOD_ROOT, which should be defined
for any GMOD installation.
=cut
--- a/lib/Bio/GMOD/Bulkfiles/GenbankSubmitWriter.pm
+++ b/lib/Bio/GMOD/Bulkfiles/GenbankSubmitWriter.pm
@@ -640,7 +640,7 @@
full of match: analysis types (messy names, types, etc.)
-- no feats written to fff in many hours !? - due to holding BAC and cytoband features
-- try dropping gffForwards; maybe better (gff written) but still memuse balloons
- -- added clearFinishedObs() - no apparent help; dont see what else is holding objects here
+ -- added clearFinishedObs() - no apparent help; don't see what else is holding objects here
-- ok now, added min base loc to keep in oidobs, delete all before
runs fast - chr 3L in 10 min. instead of >2hr.
@@ -775,8 +775,8 @@
if (!$type && $DEBUG && !/NULL|repeatmask/) { print STDERR "missing type: $_\n"; } ##<< repeatmasker kid objs
if ($type eq 'skip' || !$type) { # or what? undef? got some bad feats w/ no type??
- ## dont keep old oid: ($l_arm,$l_oid,$l_fmin)= ($arm,$oid,$fmin);
- ##dont save arm for skip !? if changed here, cant miss below openout..
+ ## don't keep old oid: ($l_arm,$l_oid,$l_fmin)= ($arm,$oid,$fmin);
+ ##don't save arm for skip !? if changed here, cant miss below openout..
($l_oid,$l_fmin)= (-1,$fmin);
next;
}
@@ -827,7 +827,7 @@
else {
## FIXME - bad if fob not in @fobs
## .. e.g. repeat region - many locs over arm, few oid's
- ## most of these we dont want to join - too far apart; need max_max setting below to keep small ranges together?
+ ## most of these we don't want to join - too far apart; need max_max setting below to keep small ranges together?
# print STDERR "missed join to last $type,$name,$oid\n" if $DEBUG;
}
}
@@ -875,7 +875,7 @@
if ($flushok) {
if ($self->hasObForwards(\@fobs, \%oidobs)) {
$flushok = 0;
- $min_max= $fmin + 2000; ##smaller step so we dont miss chance to flush
+ $min_max= $fmin + 2000; ##smaller step so we don't miss chance to flush
}
warn "hasObForwards no=$flushok at $fmin $type:$name $oid\n" if ($DEBUG>1);
}
@@ -908,7 +908,7 @@
$fob= $newob;
foreach my $fk (keys %addfob) { $fob->{$fk}= $addfob{$fk}; } %addfob=();
- #?? dont add here if it is simple feature; wait till know if it is parent or kid?
+ #?? don't add here if it is simple feature; wait till know if it is parent or kid?
# this is bad for 'gene' NOT? simple feat
unless( $simplefeat{$type} ) {
$oidobs{$oid}->{fob}= $newob;
@@ -1157,7 +1157,7 @@
}
}
}
- ## else { } # $iskid only - dont save
+ ## else { } # $iskid only - don't save
}
return \@cobs;
@@ -1256,7 +1256,7 @@
looks like chado pg reporting instance with CDS_exons is bad for transspliced mod(mdg4)
08may: change behavior for GenbankSubmit to offsetLocation:
- dont return Genbank style string location, but
+ don't return Genbank style string location, but
adjust @loc to CDS_exons by CDS span offset;
See also getCDSexons and makeCompound
@@ -1573,7 +1573,7 @@
## for each gene model part; should add locus_tag == gene ID
# if ($gff_keepoids) { $at{$k} .= ATTR_LISTCHAR if $at{$k}; $at{$k} .= $v; }
- next if $segmentfeats{$type}; # dont do parent for these ... ?
+ next if $segmentfeats{$type}; # don't do parent for these ... ?
$v =~ s/:.*$//;
$k= 'Parent';
--- a/lib/Bio/GMOD/Bulkfiles/SWISS_CRC64.pm
+++ b/lib/Bio/GMOD/Bulkfiles/SWISS_CRC64.pm
@@ -7,7 +7,7 @@
=head2 SYNOPSIS
-** dgg: rewrite for line-add so dont need to suck all into mem **
+** dgg: rewrite for line-add so don't need to suck all into mem **
use SWISS::CRC64;
--- a/bin/gmod_gff3_preprocessor.pl
+++ b/bin/gmod_gff3_preprocessor.pl
@@ -24,7 +24,7 @@
--gfffile The file containing GFF3 (optional, can read
from stdin)
--outfile The name kernel that will be used for naming result files
- --splitfile Split the files into more managable chunks, providing
+ --splitfile Split the files into more manageable chunks, providing
an argument to control splitting
--onlysplit Split the files and then quit (ie, don't sort)
--nosplit Don't split the files (ie, only sort)
@@ -61,7 +61,7 @@
=head2 FASTA sequence
If the GFF3 file contains FASTA sequence at the end, the sequence
-will be placed in a separate file with the extention '.fasta'. This
+will be placed in a separate file with the extension '.fasta'. This
fasta file can be loaded separately after the split and/or sorted
GFF3 files are loaded, using the command:
--- a/bin/gmod_make_gff_from_dbxref.pl
+++ b/bin/gmod_make_gff_from_dbxref.pl
@@ -21,7 +21,7 @@
=head1 DESCRIPTION
-This tool takes a list of tab seperated db identifiers and accessions on
+This tool takes a list of tab separated db identifiers and accessions on
the command line (like gmod_extract_dbxref_from_gff.pl would produce)
along with a directory containing fasta files and creates a GFF file.
The script tries several options for identifying the accession in the
--- a/bin/gmod_materialized_view_tool.pl
+++ b/bin/gmod_materialized_view_tool.pl
@@ -59,7 +59,7 @@
=item 1 Data syncronisity
When normal tables are updated with values that are reflected in a MV,
-there will be a delay (usually a very noticable one) between when
+there will be a delay (usually a very noticeable one) between when
the normal table is updated and when the MV is updated. This tool
provides the means of updating the MVs; see --automatic below.
--- a/load/bin/bulk_load_gff3.PLS
+++ b/load/bin/bulk_load_gff3.PLS
@@ -90,7 +90,7 @@
to use the current directory)
--no_target_syn By default, the loader adds the targetId in
the synonyms list of the feature. This flag
- desactivate this.
+ deactivate this.
--unique_target Trust the unicity of the target IDs. IDs are case
sensitive. By default, the uniquename of a new target
will be 'TargetId_PrimaryKey'. With this flag,
@@ -256,7 +256,7 @@
db_name must have an entry in the db table, with a value of
db.name equal to 'DB:db_name'; several database names were preinstalled
with the database when 'make prepdb' was run. Execute 'SELECT name
-FROM db' to find out what databases are already availble. New dbxref
+FROM db' to find out what databases are already available. New dbxref
entries are created in the dbxref table, and dbxrefs are linked to
features via the feature_dbxref table.
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