Metadata-Version: 2.1
Name: hictools
Version: 0.1.3
Summary: Tools for handling hic data
Home-page: https://github.com/zhqu1148980644/hictools
Author: BAKEZQ
Author-email: zhongquan789@gmail.com
License: MIT
Description: 
        # hictools
        
        hictools is a collection of handful tools for processing hic data based on:
        
        - `nextflow` [<sup>1</sup>](#1) `pairtools` [<sup>2</sup>](#2) `cooler` [<sup>3</sup>](#3) `higlass` [<sup>4</sup>](#4) `......`
        
        Currently, hictools is mainly composed of 3 parts:
        
        - A `nextflow` based hic-data processing `pipeline`.
        - Python `api` for handling outputs of the pipeline(`.cool`).
        - A simple yet user friendly `higlass server`.
        
        
        # Install
        
        ```
        git clone https://github.com/zhqu1148980644/hictools.git
        cd hictools && pip install ./
        ```
        
        # Usage
        
        ## Pipeline
        
        
        - ##### **Install** [nextflow](https://www.nextflow.io/)
        - #####  Fill in the config file and run.
        
         Fill in a config file in order to  specify the desired sample files(.fastq) to process.
        You can find a template config file in the current folder named `config_template.yml` after you executed this command:
        
        ```bash
        nextflow run zhqu1148980644/hictools
        ```
        
        - ##### Run the pipeline with this config file.
        
        ```bash
        nextflow run -params-file config_template.yml hictools -resume \
        -profile standard
        # Choose the cluster profile if you wish to run in a another executor(platform) by using:
        # -profile cluster
        ```
         
        - ##### Outputs
        
        You can find output folders after the execution of pipeline finished in the same directory as the current config file.
        
        ```bash
        work/         # Working directory generated by nextflow.
        log/          # Logging file generated by nextflow.
        results/      # Main folder containing results of this pipeline.
            fastqc/ bams/ pairs/ cools/ features/ other/
        ```
        
        ***
        
        ## Visualize
        
        - ##### Start a api server to provide tilesets
        
        Files added into this folder will be automatically recorded and converted using `clodius`.
        
        e.g. `.mcool` `.bam` `.bigwig` `.bed` ....
        
        ```bash
        hictools hgserver serve --paths ./ --port 7777 --workers 10
        >>
        Monitering folders:
                /store/home/user/path_you_run_pipeline/work
        Openning api server: http://ip_address:7777/api/v1
        ```
        
        - ##### Start higlass web app and visit in browser
        
        ```bash
        hictools hgserver view --api_port 7777 --port 8888
        >>
        Go visit http://ip_address:8888 in browser.
        ```
        
        ***
        
        ## CLI
        
        ```bash
        hictools
        >>
          compartments  Tools for topological associated domain analysis.
          expected      Compute expected values from a .cool file.
          hgserver      View results with higlass.
          peaks         Call peaks(loops) by using hiccups or cloops methods.
          tads          Tools for topological associated domain analysis.
        ```
        
        ***
        
        ## API
        
        Check source code `api.py` for details.
        
        ---
        
        ## Notes
        
        > `nextflow` is a pipeline framework based on the dataflow programing model, which can be spectacularly expressive when writing complex distributed pipelines.
        
        > Pipeline built by `Nextflow` can be executed in multi platforms including SGE, LSF, SLURM, PBS, HTCondor batch schedulers , Kubernetes and Amazon AWS cloud platform by changing the executor specified in `~/.nextflow/assets/zhqu1148980644/hictools/nextflow.config`. The default executor is `SGE`(Sun Grid Engine). You may need to change it depending on the platform you use.
        
        > The pipeline procesures in hictools are similar to that of the `Hi-C Processing Pipeline` used by `4DN`.
        
         ## Reference
        
        - [nextflow](https://github.com/nextflow-io/nextflow "nextflow") A DSL for data-driven computational pipelines. <a class="anchor" id="1"></a>
        
        - [pairtools](https://github.com/mirnylab/cooler "pairtools") A cool place to store your Hi-C. <a class="anchor" id="2"></a>
        
        - [cooler](https://github.com/mirnylab/pairtools "cooler") CLI tools to process mapped Hi-C data. <a class="anchor" id="3"></a>
        
        - [higlass](https://github.com/higlass/higlass "higlass") Fast large scale matrix visualization for the web. <a class="anchor" id="4"></a>
        
Platform: UNKNOWN
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: Implementation :: CPython
Classifier: Programming Language :: Python :: Implementation :: PyPy
Requires-Python: >=3.6.0
Description-Content-Type: text/markdown
Provides-Extra: test
