Bio-ViennaNGS

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Changes  view on Meta::CPAN

	- added Bio::ViennaNGS::Peak
	- make Bio::ViennaNGS::MinimalFeature subclass of
	  Bio::ViennaNGS::FeatureInterval
	- added scripts/rnaseq_peakfinder.pl
	- added scripts/bed2nt2aa.pl
	- updated POD and README

0.17 Fri Jun 09 2017
	- added Bio::ViennaNGS::FeatureIO
	- added Bio::ViennaNGS::Subtypes
	- refactored Bio::ViennaNGS::Fasta to transparently coerce input
	  data into a Bio::DB::Fasta object
	- refactored executables in scripts/ folder to new
	  Bio::ViennaNGS::Fasta interface
	- changed output format in scripts/bed2nt2aa.pl to csv
	- removed parse_bed6() and extend_chain() from Bio::ViennaNGS::Util
	  (bed I/O is now available in Bio::ViennaNGS::FeatureIO and chain
	   extension is available in bedtools)
	- added uniquify_bam2() in Bio::ViennaNGS::Bam
	- implemented correct handling of unmapped reads in
	  Bio::ViennaNGS::Bam

Doxyfile  view on Meta::CPAN

# Use this tag to change the font size of LaTeX formulas included as images in
# the HTML documentation. When you change the font size after a successful
# doxygen run you need to manually remove any form_*.png images from the HTML
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# This tag requires that the tag GENERATE_HTML is set to YES.

FORMULA_FONTSIZE       = 10

# Use the FORMULA_TRANPARENT tag to determine whether or not the images
# generated for formulas are transparent PNGs. Transparent PNGs are not
# supported properly for IE 6.0, but are supported on all modern browsers.
#
# Note that when changing this option you need to delete any form_*.png files in
# the HTML output directory before the changes have effect.
# The default value is: YES.
# This tag requires that the tag GENERATE_HTML is set to YES.

FORMULA_TRANSPARENT    = YES

# Enable the USE_MATHJAX option to render LaTeX formulas using MathJax (see

Doxyfile  view on Meta::CPAN

# root by following a path via at most 3 edges will be shown. Nodes that lay
# further from the root node will be omitted. Note that setting this option to 1
# or 2 may greatly reduce the computation time needed for large code bases. Also
# note that the size of a graph can be further restricted by
# DOT_GRAPH_MAX_NODES. Using a depth of 0 means no depth restriction.
# Minimum value: 0, maximum value: 1000, default value: 0.
# This tag requires that the tag HAVE_DOT is set to YES.

MAX_DOT_GRAPH_DEPTH    = 0

# Set the DOT_TRANSPARENT tag to YES to generate images with a transparent
# background. This is disabled by default, because dot on Windows does not seem
# to support this out of the box.
#
# Warning: Depending on the platform used, enabling this option may lead to
# badly anti-aliased labels on the edges of a graph (i.e. they become hard to
# read).
# The default value is: NO.
# This tag requires that the tag HAVE_DOT is set to YES.

DOT_TRANSPARENT        = NO

lib/Bio/ViennaNGS/Fasta.pm  view on Meta::CPAN

L<Bio::DB::Fasta>, spiced up with a few convenience methods for easy
sequence data retrieval.

=head2 ATTRIBUTES

=over 3

=item fasta (required)

Upcon object construction, this attribute expects an input fasta file,
which is transparently coerced into a L<Bio::DB::Fasta> object and
hitherto available via the C<fasta> attribute.

=item fastaids (auto-computed)

Arrary reference to the Fasta IDs found in the input file

=item primaryseqH (auto-computed)

Hash reference to L<Bio::PrimarySeq::Fasta> objects whose keys are the
Fasta IDs found in the input file

lib/Bio/ViennaNGS/UCSC.pm  view on Meta::CPAN

}

sub make_track{
  my ($tag, $track, $bigDataUrl, $shortLabel, $longLabel, $type, $autoScale, $bedNameLabel, $searchIndex, $colorByStrand, $visibility, $group, $priority) = @_;
  my $trackEntry ="#$tag\ntrack $track\nbigDataUrl $bigDataUrl\nshortLabel $shortLabel\nlongLabel $longLabel\ntype $type\nautoScale $autoScale\nbedNameLabel $bedNameLabel\nsearchIndex $searchIndex\ncolorByStrand $colorByStrand\nvisibility $visibility...
  return $trackEntry;
}

sub make_multi_bigwig_container_track{
  my ($tag, $track, $shortLabel, $longLabel, $type, $autoScale, $visibility, $priority) = @_;
  my $trackEntry ="#$tag\ntrack $track\ncontainer multiWig\nnoInherit on\nshortLabel $shortLabel\nlongLabel $longLabel\ntype $type\nconfigureable on\nvisibility $visibility\naggregate transparentOverlay\nshowSubtrackColorOnUi on\nautoScale $autoScale...
  return $trackEntry;
}

sub make_bigwig_container_track{
  my ($track, $bigDataUrl, $shortLabel, $longLabel, $type, $parent, $color) = @_;
  my $trackEntry = "track $track\nbigDataUrl $bigDataUrl\nshortLabel $shortLabel\nlongLabel $longLabel\ntype $type\nparent $parent\ncolor $color\n\n";
  return $trackEntry;
}

sub make_bigwig_track{

t/04-UCSC-TrackHub.t  view on Meta::CPAN

  my $expected =
"#hg19_highlyexpressed_bw
track hg19_highlyexpressed_bw
container multiWig
noInherit on
shortLabel hg19_highlyexpressed_bw
longLabel hg19_highlyexpressed_bw
type bigWig
configureable on
visibility full
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction maximum
priority 1500
alwaysZero on
yLineMark 0
yLineOnOff on
maxHeightPixels 125:125:11

";

t/04-UCSC-TrackHub.t  view on Meta::CPAN

  my $expected =
"#hg19_highlyexpressed_bw
track hg19_highlyexpressed_bw
container multiWig
noInherit on
shortLabel hg19_highlyexpressed_bw
longLabel hg19_highlyexpressed_bw
type bigWig
configureable on
visibility full
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction maximum
priority 1500
alwaysZero on
yLineMark 0
yLineOnOff on
maxHeightPixels 125:125:11

track hg19_highlyexpressed_bw_pos