Metadata-Version: 2.1
Name: g3dtools
Version: 0.2.0
Summary: Generating and querying .g3d file
Home-page: https://github.com/lidaof/g3d
Author: Daofeng Li
Author-email: lidaof@gmail.com
License: UNKNOWN
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):
        
        ```bash
        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` for `maternal`, `p` for `paternal`, `s` for `shared`, if omitted, `s` will be used, or user `cell-1`, `cell-2` etc. for cell identifier...
        
        This file input looks simiar to [3dg format](https://github.com/tanlongzhi/dip-c#3dg) except we put haplotype or category info on last column.
        
        ## Generate a new .g3d file using the format listed above
        
        ```console
        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:
        
        ```console
        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](http://projets.cbio.mines-paristech.fr/~nvaroquaux/pastis/) output.
        
        ```console
        g3dtools pastis -g Pfal3D7 -n Rings -o ../testOut/rings ../test/RINGS.3D_coord.txt
        ```
        
        ```console
        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](https://github.com/nucleome/nucle3d) format.
        
        ```console
        g3dtools nucle3d -n k562 -g hg38 -o ../testOut/k562 ../test/K562.nucle3d
        ```
        
        ## Query
        
        By region:
        
        ```console
        g3dtools query testOut/test.g3d -c chr7 -s 27053397 -e 27373765
        ```
        
        change resolution:
        
        ```console
        g3dtools query testOut/test.g3d -c chr7 -s 27053397 -e 27373765 -r 100000
        ```
        
        when resolution not exists:
        
        ```console
        $ 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]
        ```
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Description-Content-Type: text/markdown
