[Bioperl-guts-l] [BioPerl - Feature #1881] implement Bio::PopGen::IO::haploview.pm

[redmine at redmine.open-bio.org]

Issue #1881 has been updated by Chris Fields.

Tracker changed from Bug to Feature


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Feature #1881: implement Bio::PopGen::IO::haploview.pm
http://redmine.open-bio.org/issues/1881

Author: Albert Vilella
Status: New
Priority: Low
Assignee: Bioperl Guts
Category: Unclassified
Target version: unspecified
URL: 


Haploview format is mostly similar to the already present (hapmap.org) Hapmap format, without a couple or three of the columns (that were added in hapmap).

snip

##date Fri Oct 14 08:27:50 2005
##population All
##sequence-region Chr21 21000001 21500000
##source gbrowse HaploviewDumper plugin
id	alleles	chrom	pos	strand	assembly#	center	NA17102	NA17103	NA17104	NA17105	NA17106	NA17107	NA17108	NA17109	NA17110	NA17111	NA17112	NA17113	NA17114	NA17115	NA17116	NA17133	NA17134	NA17135	NA17136	NA17137	NA17138	NA17139	NA17140	NA06990	NA07019	NA07348	NA07349	NA10830	NA10831	NA10842	NA10843	NA10844	NA10845	NA10848	NA10850	NA10851	NA10852	NA10853	NA10854	NA10857	NA10858	NA10860	NA10861	NA12547	NA12548	NA12560	NA17201	NA17733	NA17734	NA17735	NA17736	NA17737	NA17738	NA17739	NA17740	NA17741	NA17742	NA17743	NA17744	NA17745	NA17746	NA17747	NA17749	NA17752	NA17753	NA17754	NA17755	NA17756	NA17757	NA17759	NA17761
afd0023980	G/A	chr21	21000458	+	ncbi_b34	perlegen	AA	GA	GA	AA	NN	AA	AA	AA	AA	NN	AA	AA	AA	AA	AA	AA	AA	GG	AA	AA	AA	AA	AA	NN	AA	AA	AA	AA	NN	AA	GG	AA	AA	AA	AA	AA	AA	GA	AA	AA	AA	AA	GA	AA	AA	AA	AA	AA	GG	AA	AA	AA	AA	AA	AA	AA	AA	AA	GA	GA	AA	AA	AA	GA	AA	AA	AA	AA	AA	GA	AA
afd0023983	T/C	chr21	21002155	+	ncbi_b34	perlegen	TT	TC	TT	TT	TT	TT	TT	TT	TT	TT	TT	TT	TT	TT	TT	TT	TT	TT	TT	TT	TT	TT	TT	TT	TC	TT	TT	TT	TT	TT	TT	TC	TT	TT	TT	TT	TT	TT	TT	TT	TT	TT	TT	TT	TT	CC	TT	TT	TT	TT	TT	TT	TT	TT	TT	TT	TT	TT	TT	TT	TT	TT	TT	TT	TT	TT	TT	TT	TT	TT	TT


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