Metadata-Version: 2.1
Name: chromosight
Version: 0.0.6
Summary: Detect loops (and other patterns) in Hi-C contact maps.
Home-page: https://github.com/koszullab/chromosight
Author: axel.cournac@pasteur.fr
License: GPLv3
Description: # Chromosight
        <img src="docs/chromosight.gif" alt="animated logo" width="200"/>
        
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        [![License: GPLv3](https://img.shields.io/badge/License-GPL%203-0298c3.svg)](https://opensource.org/licenses/GPL-3.0)
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        Detect chromatin loops (and other patterns) in Hi-C contact maps.
        
        ## Installation
        
        ```sh
        pip3 install -U chromosight
        ```
        
        or, if you want to get the very latest version:
        
        ```
        sudo pip3 install -e git+https://github.com/koszullab/chromosight.git@master#egg=chromosight
        ```
        
        ## Usage
        
        ```
        chromosight detect <contact_maps> [<output>] [--kernels=None] [--loops]
                               [--borders] [--precision=4] [--iterations=auto]
                               [--output]
        ```
        
        ## Input
        
        Input Hi-C contact maps can be either in bedgraph2d or cool format. Bedgraph2d is defined as a tab-separated text file with 7 columns: chr1 start1 end1 chr2 start2 end2 contacts. The cool format is an efficient and compact format for Hi-C data based on HDF5. It is maintained by the Mirny lab and documented here: https://mirnylab.github.io/cooler/
        
        ## Output
        Two files are generated in the output directory (replace pattern by the pattern used, e.g. loops or borders):
          * pattern.txt: List of genomic coordinates, bin ids and correlation scores for the pattern identified
          * pattern.json: JSON file containing the windows (of the same size as the kernel used) around the patterns from pattern.txt
        
        ## Options
        
        ```
        Pattern exploration and detection
        
        Explore and detect patterns (loops, borders, centromeres, etc.) in Hi-C contact
        maps with pattern matching.
        
        Usage:
            chromosight detect <contact_map> [<output>] [--kernel-config FILE]
                                [--pattern=loops] [--precision=auto] [--iterations=auto]
                                [--win-fmt={json,npy}] [--subsample=no]
                                [--inter] [--max-dist=auto] [--no-plotting] [--threads 1]
            chromosight generate-config <prefix> [--preset loops]
        
            detect: 
                performs pattern detection on a Hi-C contact map using kernel convolution
            generate-config:
                Generate pre-filled config files to use for `chromosight detect`. 
                A config consists of a JSON file describing analysis parameters for the
                detection and path pointing to kernel matrices files. Those matrices
                files are tsv files with numeric values ordered in a square dense matrix
                to use for convolution.
        
        Arguments for detect:
            -h, --help                  Display this help message.
            --version                   Display the program's current version.
            contact_map                 The Hi-C contact map to detect patterns on, in
                                        bedgraph2d or cool format. 
            output                      name of the output directory
            -I, --inter                 Enable to consider interchromosomal contacts.
            -i, --iterations auto       How many iterations to perform after the first
                                        template-based pass. Auto sets an appropriate
                                        value loaded from the kernel configuration
                                        file. [default: auto]
            -k, --kernel-config FILE    Optionally give a path to a custom JSON kernel
                                        config path. Use this to override pattern if 
                                        you do not want to use one of the preset 
                                        patterns.
            -m, --max-dist auto         Maximum distance from the diagonal (in base pairs)
                                        at which pattern detection should operate. Auto
                                        sets a value based on the kernel configuration
                                        file and the signal to noise ratio. [default: auto]
            -n, --no-plotting           Disable generation of pileup plots.
            -P, --pattern loops         Which pattern to detect. This will use preset
                                        configurations for the given pattern. Possible
                                        values are: loops, borders, hairpin. [default: loops]
            -p, --precision auto        Precision threshold when assessing pattern
                                        probability in the contact map. A lesser value
                                        leads to potentially more detections, but more
                                        false positives. [default: auto]
            -s, --subsample=INT         Subsample contacts from the matrix to INT contacts.
                                        This is useful when comparing matrices with different
                                        coverages. [default: no]
            -t, --threads 1             Number of CPUs to use in parallel. [default: 1]
            -w, --win-fmt={json,npy}    File format used to store individual windows
                                        around each pattern. Window order match
                                        patterns inside the associated text file.
                                        Possible formats are json and npy. [default: json]
        
        Arguments for generate-config:
            prefix                      Path prefix for config files. If prefix is a/b,
                                        files a/b.json and a/b.1.txt will be generated.
                                        If a given pattern has N kernel matrices, N txt
                                        files are created they will be named a/b.[1-N].txt.
            -p, --preset loops          Generate a preset config for the given pattern.
                                        Preset configs available are "loops" and 
                                        "borders". [default: loops]
                                        
        ```
        
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: Artistic License
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Visualization
Classifier: Operating System :: OS Independent
Requires-Python: >=3.6
Description-Content-Type: text/markdown
