Generating and querying .g3d file
Project description
g3dtools
A tool for operating .g3d (genome 3D structure) format.
Require: Python (Recommend version 3 and above).
example input, 6 columns bed-like text file (6th column is optional):
chr7 16760000 -14.3866688728 -36.3919302029 19.8483965881 m
chr7 16760000 -24.9116268071 50.0521268287 9.91073185128 p
chr7 25160000 -10.1170055526 -34.8975763469 20.2401719179 m
chr7 25160000 -21.8210915649 27.1128556621 13.4856945965 p
chr7 33540000 -4.11059384846 -54.4940083464 4.21321135564 m
chr7 33540000 -12.0040359857 31.5960497183 26.6925954134 p
chr7 41940000 5.75342635105 -55.4976428728 8.65307697332 m
chr7 41940000 -23.7372022413 36.0614692267 31.919119243 p
chr7 50320000 -10.7099779927 -38.0214001171 25.8308473821 m
chr7 50320000 -28.5142098162 26.6468499001 28.8634805533 p
chr7 26200000 -11.5800097945 -37.9903257744 16.2461100893 m
chr7 26200000 -15.9552426623 27.016940724 17.5722080595 p
chr7 27260000 -14.1883124179 -44.7860807973 12.4104162757 m
chr7 27260000 -20.0857754297 30.9204143041 18.4774635708 p
chr7 28300000 -18.0160836669 -39.398544495 12.811858164 m
chr7 28300000 -14.9383020843 39.1464516779 17.3743509519 p
chr7 29360000 -11.8032470923 -47.3595095319 13.2828128833 m
chr7 29360000 -12.2445277916 41.2431968179 14.8844908717 p
chr7 30400000 -12.8674349856 -45.0752589744 9.15498568359 m
columns are:
- chromosome
- start position
- X (coordinates in 3D)
- Y
- Z
- category (optional), usually haplotype or cell/sample type, or time point information can be used, like for haplotype,
m
formaternal
,p
forpaternal
,s
forshared
, if omitted,s
will be used, or usercell-1
,cell-2
etc. for cell identifier...
This file input looks simiar to 3dg format except we put haplotype or category info on last column.
Generate a new .g3d file using the format listed above
g3dtools load ../test/test.g3d.bed.gz -o ../testOut/test -s 2,3,4,5,6,7,8,9,10 -n GM12878 -g hg19
Generate a new .g3d file from .3dg format
Input a file with high resolution, let the tool calculate lower resolutions:
g3dtools 3dg ../test/GSM3271347_gm12878_01.impute3.round4.clean.3dg.txt.gz -o ../testOut/GSM3271347_gm12878_01.impute3.round4.clean -n GM12878 -g hg19 -s 2,3,4,5,6,7,8,9,10
or prepare different resolution files in advance.
Generate a new .g3d file from PASTIS output
User can also generate .g3d file from pastis output.
g3dtools pastis -g Pfal3D7 -n Rings -o ../testOut/rings ../test/RINGS.3D_coord.txt
python g3dtools pastis-pdb -g Pfal3D7 -n Rings -o ../testOut/rings_pdb -s 2,3,4,5,6 ~/Downloads/RINGS.pdb
Generate a new .g3d from nucle3d format
User can also generate .g3d file from nucle3d format.
g3dtools nucle3d -n k562 -g hg38 -o ../testOut/k562 ../test/K562.nucle3d
Query
By region:
g3dtools query testOut/test.g3d -c chr7 -s 27053397 -e 27373765
change resolution:
g3dtools query testOut/test.g3d -c chr7 -s 27053397 -e 27373765 -r 100000
when resolution not exists:
$ g3dtools query testOut/test.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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