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comparison gmap/README @ 2:52da588232b0

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Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these.
author Jim Johnson <jj@umn.edu>
date Fri, 21 Oct 2011 11:38:55 -0500
parents d58d272914e7
children 72ab00e732c3
comparison
equal deleted inserted replaced
1:30d42bb409b8 2:52da588232b0
7 import gmap # added for gmap tools 7 import gmap # added for gmap tools
8 8
9 add to datatypes_conf.xml 9 add to datatypes_conf.xml
10 <!-- Start GMAP Datatypes --> 10 <!-- Start GMAP Datatypes -->
11 <datatype extension="gmapdb" type="galaxy.datatypes.gmap:GmapDB" display_in_upload="False"/> 11 <datatype extension="gmapdb" type="galaxy.datatypes.gmap:GmapDB" display_in_upload="False"/>
12 <!-- 12 <datatype extension="gmapsnpindex" type="galaxy.datatypes.gmap:GmapSnpIndex" display_in_upload="False"/>
13 13 <datatype extension="iit" type="galaxy.datatypes.gmap:IntervalIndexTree" display_in_upload="True"/>
14 14 <datatype extension="splicesites.iit" type="galaxy.datatypes.gmap:SpliceSitesIntervalIndexTree" display_in_upload="True"/>
15 <datatype extension="introns.iit" type="galaxy.datatypes.gmap:IntronsIntervalIndexTree" display_in_upload="True"/>
16 <datatype extension="snps.iit" type="galaxy.datatypes.gmap:SNPsIntervalIndexTree" display_in_upload="True"/>
17 <datatype extension="gmap_annotation" type="galaxy.datatypes.gmap:IntervalAnnotation" display_in_upload="False"/>
18 <datatype extension="gmap_splicesites" type="galaxy.datatypes.gmap:SpliceSiteAnnotation" display_in_upload="True"/>
19 <datatype extension="gmap_introns" type="galaxy.datatypes.gmap:IntronAnnotation" display_in_upload="True"/>
20 <datatype extension="gmap_snps" type="galaxy.datatypes.gmap:SNPAnnotation" display_in_upload="True"/>
21 <!-- End GMAP tools -->
15 22
16 Tools: 23 Tools:
17 GMAP_Build - create a GmapDB set of index files for a reference sequence and optional set of annotations 24 GMAP_Build - create a GmapDB set of index files for a reference sequence and optional set of annotations
18 GMAP - map sequences to a reference sequence GmapDB index 25 GMAP - map sequences to a reference sequence GmapDB index
19 GSNAP - align sequences to a reference and detect splicing 26 GSNAP - align sequences to a reference and detect splicing
20 27
21 Add to tool_conf.xml ( probably in the "NGS: Mapping" section ) 28 Add to tool_conf.xml ( probably in the "NGS: Mapping" section )
22 <tool file="gmap/gmap_build.xml" />
23 <tool file="gmap/gmap.xml" /> 29 <tool file="gmap/gmap.xml" />
24 <tool file="gmap/gsnap.xml" /> 30 <tool file="gmap/gsnap.xml" />
31 <tool file="gmap/gmap_build.xml" />
32 <tool file="gmap/snpindex.xml" />
33 <tool file="gmap/iit_store.xml" />
34
35 Admin built cached gmapdb indexes defined in tool-data/gmap_indices.loc
25 36
26 37
27 TODO: 38 TODO:
28 Add classes to gmap.py 39 Add classes to gmap.py
29 IntervalIndexTree - datatype for the iit_store result
30 IntervalAnnotation - generic class for gmap annotation formats
31 SpliceSiteAnnotation - class for gmap splicesite annotation format
32 IntronAnnotation - class for gmap introns annotation format
33 SNPAnnotation - class for gmap snp annotation format
34 GmapIndex - generic class for a gmap index
35 SnpIndex - an index created by snpindex
36 CmetIndex - an index created by cmetindex 40 CmetIndex - an index created by cmetindex
37 AtoiIndex - an index created by atoiindex 41 AtoiIndex - an index created by atoiindex
38 42
39 Possibly add Tools: 43 Possibly add Tools:
40 iit_store - creates a mapping index .iit from: gtf,gff3,gmapannotation, UCSC refGene table
41 iit_get - retrieves from .iit store
42 get_genome - retrieves from a gmapdb 44 get_genome - retrieves from a gmapdb
43 snpindex - create a SNPIndex
44 cmetindex - create methylcytosine index 45 cmetindex - create methylcytosine index
45 atoiindex - create A-to-I RNA editing index 46 atoiindex - create A-to-I RNA editing index
46 47
47 48
48 49