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1 parent feece49 commit c64217bd365fc3856fc7494a7532cabedbac3150 Chris Fields committed Mar 21, 2012
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2 lib/Bio/Coordinate/Result/Gap.pm
@@ -37,7 +37,7 @@ of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
-=head2 Support
+=head2 Support
Please direct usage questions or support issues to the mailing list:
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4 t/Coordinate/CoordinateBoundaryTest.t
@@ -7,9 +7,9 @@ use Data::Dumper;
BEGIN {
use lib '.';
use Bio::Root::Test;
-
+
test_begin( -tests => 174 );
-
+
use_ok('Bio::Location::Simple');
use_ok('Bio::Coordinate::Pair');
}
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6 t/Coordinate/CoordinateGraph.t
@@ -3,12 +3,12 @@
use strict;
-BEGIN {
+BEGIN {
use lib '.';
use Bio::Root::Test;
-
+
test_begin(-tests => 7);
-
+
use_ok('Bio::Coordinate::Graph');
}
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28 t/Coordinate/CoordinateMapper.t
@@ -3,12 +3,12 @@
use strict;
-BEGIN {
+BEGIN {
use lib '.';
use Bio::Root::Test;
-
+
test_begin(-tests => 175);
-
+
use_ok('Bio::Location::Simple');
use_ok('Bio::Coordinate::Pair');
use_ok('Bio::Coordinate::Result::Match');
@@ -23,7 +23,7 @@ ok $c = Bio::Coordinate::Result::Match-> new;
ok $c = Bio::Coordinate::Result::Gap-> new;
# propepide
-my $match1 = Bio::Location::Simple->new
+my $match1 = Bio::Location::Simple->new
(-seq_id => 'propeptide', -start => 21, -end => 40, -strand=>1 );
# peptide
my $match2 = Bio::Location::Simple->new
@@ -45,7 +45,7 @@ my ($count, $pos, $pos2, $res, $match, $res2);
#
# match within
#
-$pos = Bio::Location::Simple->new
+$pos = Bio::Location::Simple->new
(-start => 25, -end => 25, -strand=> -1 );
# results are in Bio::Coordinate::Result
@@ -232,7 +232,7 @@ is $res->match->end, 11;
is $res->match->strand, 1;
#
-# partial match2 = match & gap
+# partial match2 = match & gap
#
$pos = Bio::Location::Simple->new
@@ -271,7 +271,7 @@ is $gap2->strand, -1;
#
# propepide
-$match1 = Bio::Location::Simple->new
+$match1 = Bio::Location::Simple->new
(-seq_id => 'propeptide', -start => 5, -end => 40, -strand=>1 );
# peptide
$match2 = Bio::Location::Simple->new
@@ -310,7 +310,7 @@ is $match->strand, 1;
# pair1 pair2
# gene
-$match1 = Bio::Location::Simple->new
+$match1 = Bio::Location::Simple->new
(-seq_id => 'gene', -start => 5, -end => 9, -strand=>1 );
# exon2
$match2 = Bio::Location::Simple->new
@@ -320,7 +320,7 @@ ok my $pair1 = Bio::Coordinate::Pair->new(-in => $match1,
-out => $match2,
);
# gene
-my $match3 = Bio::Location::Simple->new
+my $match3 = Bio::Location::Simple->new
(-seq_id => 'gene', -start => 15, -end => 19, -strand=>1 );
# exon
my $match4 = Bio::Location::Simple->new
@@ -377,7 +377,7 @@ is $res->each_match, 2;
#
# create the third pair
# gene
-my $match5 = Bio::Location::Simple->new
+my $match5 = Bio::Location::Simple->new
(-seq_id => 'gene', -start => 25, -end => 29, -strand=>1 );
# exon
my $match6 = Bio::Location::Simple->new
@@ -444,7 +444,7 @@ compare (shift @res, shift @testres);
compare (shift @res, shift @testres);
ok $mapper->swap;
-$pos = Bio::Location::Simple->new
+$pos = Bio::Location::Simple->new
(-start => 2, -end => 5, -strand => -1, -seq_id => '627012');
$res = $mapper->map($pos);
is $res->match->start, 2;
@@ -457,7 +457,7 @@ is $res->match->seq_id, 'chr1';
#
# testing a simple pair
-$match1 = Bio::Location::Simple->new
+$match1 = Bio::Location::Simple->new
(-seq_id => 'a', -start => 5, -end => 17, -strand=>1 );
$match2 = Bio::Location::Simple->new
(-seq_id => 'b', -start => 1, -end => 13, -strand=>-1 );
@@ -526,7 +526,7 @@ is $mapper->return_match, 1;
is $mapper->return_match(1), 1;
-$pos = Bio::Location::Simple->new
+$pos = Bio::Location::Simple->new
(-start => 4, -end => 8, -strand => 1);
$res = $mapper->map($pos);
#print Dumper $res;
@@ -664,7 +664,7 @@ chr1 625357 1189804 1213915 1 24112 1
chr1 625359 1214016 1216330 1 2315 1
} );
# test the auto-sorting feature
- # @sgp_dump = reverse (@sgp_dump) if defined $reverse;
+ # @sgp_dump = reverse (@sgp_dump) if defined $reverse;
my $first = 1;
for my $line ( @sgp_dump ) {
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42 t/Coordinate/GeneCoordinateMapper.t
@@ -3,12 +3,12 @@
use strict;
-BEGIN {
+BEGIN {
use lib '.';
use Bio::Root::Test;
-
+
test_begin(-tests => 116);
-
+
use_ok('Bio::Location::Simple');
use_ok('Bio::Coordinate::Pair');
use_ok('Bio::Coordinate::ExtrapolatingPair');
@@ -32,7 +32,7 @@ ok my $pairr = Bio::Coordinate::ExtrapolatingPair->
-out => $outr
);
-my $posr = Bio::Location::Simple->new
+my $posr = Bio::Location::Simple->new
(-start => 3, -end => 4, -strand=> 1 );
my $resr = $pairr->map($posr);
is $resr->start, 11;
@@ -42,7 +42,7 @@ is $resr->strand, -1;
# propepide
-my $match1 = Bio::Location::Simple->new
+my $match1 = Bio::Location::Simple->new
(-seq_id => 'propeptide', -start => 21, -end => 40, -strand=>1 );
# peptide
my $match2 = Bio::Location::Simple->new
@@ -62,7 +62,7 @@ is $pair->strict(), 1;
my ($count, $pos, $pos2, $res, $match, $res2);
# match within
-$pos = Bio::Location::Simple->new
+$pos = Bio::Location::Simple->new
(-start => 25, -end => 25, -strand=> -1 );
$res = $pair->map($pos);
@@ -114,7 +114,7 @@ is $res->end, 20;
#
# chr
-$match1 = Bio::Location::Simple->new
+$match1 = Bio::Location::Simple->new
(-seq_id => 'chr', -start => 21, -end => 40, -strand=>1 );
# gene
$match2 = Bio::Location::Simple->new
@@ -127,14 +127,14 @@ $match2 = Bio::Location::Simple->new
-strict => 0
);
-$pos = Bio::Location::Simple->new
+$pos = Bio::Location::Simple->new
(-start => 38, -end => 40, -strand=> 1 );
$res = $pair->map($pos);
is $res->start, 1;
is $res->end, 3;
is $res->strand, -1;
-$pos = Bio::Location::Simple->new
+$pos = Bio::Location::Simple->new
(-start => 1, -end => 3, -strand=> 1 );
$res = $pair->map($pos);
is $res->start, 38;
@@ -156,7 +156,7 @@ is $m->peptide_offset(5), 5;
# match within
-$pos = Bio::Location::Simple->new
+$pos = Bio::Location::Simple->new
(-start => 25, -end => 25, -strand=> 1 );
$res = $m->map($pos);
@@ -171,7 +171,7 @@ is $res->seq_id, 'peptide';
#
# match within
-$pos = Bio::Location::Simple->new
+$pos = Bio::Location::Simple->new
(-start => 4, -end => 5, -strand=> 1 );
$res = $m->map($pos);
is $res->start, -1;
@@ -186,7 +186,7 @@ is $m->nozero(0), 0;
ok $m->swap;
-$pos = Bio::Location::Simple->new
+$pos = Bio::Location::Simple->new
(-start => 5, -end => 5, -strand=> 1 );
$res = $m->map($pos);
is $res->start, 10;
@@ -203,7 +203,7 @@ ok $res = $m->_reverse_translate($pos);
is $res->start, 13;
is $res->end, 15;
-$pos = Bio::Location::Simple->new
+$pos = Bio::Location::Simple->new
(-start => 26, -end => 26, -strand=> 1 );
$m->out('peptide');
$res = $m->map($pos);
@@ -214,7 +214,7 @@ is $res->start, 4;
# frame
#
-$pos = Bio::Location::Simple->new
+$pos = Bio::Location::Simple->new
(-start => 1, -end => 3, -strand=> 1 );
$res = $m->_frame($pos);
is $res->start, 1;
@@ -232,11 +232,11 @@ is $res->end, 3;
# pair1 pair2 pair3
# gene
-my $e1 = Bio::Location::Simple->new
+my $e1 = Bio::Location::Simple->new
(-seq_id => 'gene', -start => 5, -end => 9, -strand=>1 );
-my $e2 = Bio::Location::Simple->new
+my $e2 = Bio::Location::Simple->new
(-seq_id => 'gene', -start => 15, -end => 19, -strand=>1 );
-my $e3 = Bio::Location::Simple->new
+my $e3 = Bio::Location::Simple->new
(-seq_id => 'gene', -start => 25, -end => 29, -strand=>1 );
my @cexons = ($e1, $e2, $e3);
@@ -257,7 +257,7 @@ is $res->start, 2;
is $res->end, 3;
$m->out('negative_intron');
-$pos = Bio::Location::Simple->new
+$pos = Bio::Location::Simple->new
(-start => 12, -end => 14, -strand=> 1 );
$res = $m->map($pos);
is $res->start, -3;
@@ -427,7 +427,7 @@ $g2->exons(@exons);
#map_snps($g2, @snp_dump);
-$match1 = Bio::Location::Simple->new
+$match1 = Bio::Location::Simple->new
(-seq_id => 'a', -start => 5, -end => 17, -strand=>1 );
$match2 = Bio::Location::Simple->new
(-seq_id => 'b', -start => 1, -end => 13, -strand=>-1 );
@@ -472,7 +472,7 @@ is $sublocs[1]->end, 12;
# gene
$e1 = Bio::Location::Simple->new
(-seq_id => 'gene', -start => 5, -end => 9, -strand=>-1 );
-$e2 = Bio::Location::Simple->new
+$e2 = Bio::Location::Simple->new
(-seq_id => 'gene', -start => 15, -end => 19, -strand=>-1 );
@cexons = ($e1, $e2);
my $cds= Bio::Location::Simple->new
@@ -502,7 +502,7 @@ is $sublocs[1]->end, 16;
$m->in('gene');
$m->out('inex');
-$pos = Bio::Location::Simple->new
+$pos = Bio::Location::Simple->new
(-seq_id => 'gene', -start => 2, -end => 10, -strand=> 1 );
$res = $m->map($pos);

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