search

nmdp-bioinformatics / gfe-db

Graph database representing IPD-IMGT/HLA sequence data as GFE
https://gfe-db.readthedocs.io
GNU General Public License v3.0
9 stars 15 forks source link

Read from local KIR.dat file #21

Open mmaiers-nmdp opened 5 years ago

mmaiers-nmdp commented 5 years ago

The GFE system downloads HLA.dat and KIR.dat from IMGT/HLA and IPD/KIR. For some applications (e.g. mapping PiNG reads) it is preferred to have imputed full gene sequence for all alleles. Steve Mack has prepared a KIR.dat file. The process for loading this file should be defined as an option in the GFE database load process

mmaiers-nmdp commented 4 years ago

Need to address things like image

mmaiers-nmdp commented 4 years ago

Another issue is that the :HAS_FEATURE edges are duplicated in the graph image

mmaiers-nmdp commented 4 years ago

Also GFEs have different lengths KIR3DL3w0-4-0-7-0-47-0-17-0-46-0-0-0-6-0-5-0-1-0-0 is GFE for KIR3DL3*00401 KIR3DL3w8-4-7-7-13-48-29-17-25-46-41-0-0-6-6-5-2-1-0-7 is GFE for KIR3DL3*0040202

pbashyal-nmdp commented 4 years ago

All the KIRs with 5/6 exons:

SV   KIR00077.1
FT                   /number="5/6"
--
SV   KIR00222.1
FT                   /number="5/6"
--
SV   KIR00078.1
FT                   /number="5/6"
--
SV   KIR00079.4
FT                   /number="5/6"
--
SV   KIR00218.1
FT                   /number="5/6"
--
SV   KIR00080.1
FT                   /number="5/6"
--
SV   KIR00303.1
FT                   /number="5/6"
--
SV   KIR00482.1
FT                   /number="5/6"
--
SV   KIR00642.1
FT                   /number="5/6"
--
SV   KIR00138.1
FT                   /number="5/6"
--
SV   KIR00486.1
FT                   /number="5/6"
--
SV   KIR00139.3
FT                   /number="5/6"
--
SV   KIR00140.3
FT                   /number="5/6"
--
SV   KIR00141.2
FT                   /number="5/6"
--
SV   KIR00142.1
FT                   /number="5/6"
--
SV   KIR00143.1
FT                   /number="5/6"
--
SV   KIR00175.1
FT                   /number="5/6"
--
SV   KIR00481.1
FT                   /number="5/6"
--
SV   KIR00484.1
FT                   /number="5/6"
--
SV   KIR00181.1
FT                   /number="5/6"
--
SV   KIR00179.1
FT                   /number="5/6"
--
SV   KIR00186.2
FT                   /number="5/6"
--
SV   KIR00485.1
FT                   /number="5/6"
--
SV   KIR00626.1
FT                   /number="5/6"
--
SV   KIR01042.1
FT                   /number="5/6"
--
SV   KIR00194.2
FT                   /number="5/6"
--
SV   KIR00483.1
FT                   /number="5/6"
--
SV   KIR00641.1
FT                   /number="5/6"