Generating and querying .g3d file
Project description
g3dtools
A tool for operating .g3d (genome 3D structure) format.
Require: Python 3 and above. (Note: not work with Python 2)
example input
columns are:
- chromosome
- start position
- end position
- X
- Y
- Z
- haplotype, m for maternal, p for paternal, . for unknown
python g3dtools.py dump test -g hg19 -s GM12878 -o GM12878_chr1_chr2
let the tool calculate resolutions:
python g3dtools.py 3dg test/GSM3271347_gm12878_01.impute3.round4.clean.3dg.txt.gz -o testOut/GSM3271347_gm12878_01.impute3.round4.clean -s 2,3,4,5,6,7,8,9,10
or prepare resolutions in advance:
Query:
python g3dtools.py query testOut/GSM3271347_gm12878_01.impute3.round4.clean.g3d -c chr7 -s 27053397 -e 27373765
change resolution: python g3dtools.py query testOut/GSM3271347_gm12878_01.impute3.round4.clean.g3d -c chr7 -s 27053397 -e 27373765 -r 100000
when resolution not exists: python g3dtools.py query testOut/GSM3271347_gm12878_01.impute3.round4.clean.g3d -c chr7 -s 27053397 -e 27373765 -r 130000 [Query] Error, resolution 130000 not exists for this file, available resolutions: [20000, 40000, 60000, 80000, 100000, 120000, 140000, 160000, 180000, 200000]
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