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CHANGES  view on Meta::CPAN

	file parent directory instead of the current directory.

v.1.10.2 (svn 591)
	- Added a new option of position when adjusting coordinates of retrieved
	features using the script get_features.pl. Coordinates may be adjusted
	at the 5 prime, 3 prime, or both ends of stranded features. This also 
	fixes bugs where collected features on the reverse strand with adjusted
	coordinates were not reported properly.
	- Improved automatic recognition of the name, score, and other columns
	in the convertor scripts data2bed.pl, data2gff.pl, and data2wig.pl. 
	- Improved the Cluster and Treeview export function in script
	manipulate_datasets.pl. The CDT files generated now include separate ID
	and NAME columns per the specification, and new manipulations are
	included prior to exporting, including percentile rank and log2.
	- The convert null function now also converts zero values if requested
	in script manipulate_datasets.pl.
	- Added new option of a minimum size when trimming windows in the script
	find_enriched_regions.pl.
	- Increased the radius from 35 bp to 50 bp when verifying a putative
	mapped nucleosome in script map_nucleosomes.pl, leading to fewer
	overlapping or offset nucleosomes.

CHANGES  view on Meta::CPAN

	requesting database feature types. By default, all database features are
	presented to the user as a list when selecting database features to
	collect data. The source_exclude parameter in the biotoolbox.cfg
	configuration file is now deprecated.
	- Upgraded script get_intersecting_features.pl to automatically
	recognize input file columns and search for more than 1 feature type
	- Fixed bug in script get_datasets.pl where the program will not
	continue when only a data database was provided
	- Fixed bug of requesting index when using a .kgg file as a gene list in
	script pull_features.pl
	- Fixed bug in generating file name for Treeview export function in
	script manipulate_datasets.pl
	- Fixed behavior when reading files to prevent adding the current
	program name to the metadata when the input file does not have this
	metadata
	- Minor updates to script novo_wrapper.pl
	
v.1.9.0 (svn 493)
	- Added new script get_features.pl which generates a list of features
	for one or more feature types from a database. Information about the
	features may be returned, including name, type, and coordinates. Sub

lib/Bio/ToolBox/Data/file.pm  view on Meta::CPAN

gene prediction, and known Gene tables. The Bin column may or may not be present.

=item Peak files

These include file extensions F<.narrowPeak> and F<.broadPeak>. 
These are special "BED6+4" file formats. 

=item CDT

These include file extension F<.cdt>. 
Cluster data files used with Cluster 3.0 and Treeview.

=item SGR

Rare file format of chromosome, position, score. File extension F<.sgr>.

=item TEXT

Almost any tab-delimited text file with a F<.txt> or F<.tsv> extension
can be loaded.