Metadata-Version: 2.1
Name: gtracks
Version: 1.3.1
Summary: Plot genome track data
Home-page: https://github.com/anthony-aylward/gtracks.git
Author: Anthony Aylward
Author-email: aaylward@eng.ucsd.edu
License: UNKNOWN
Description: # gtracks
        
        Plot genome track data from bigWig files. Powered by [pyGenomeTracks](https://github.com/deeptools/pyGenomeTracks).
        
        ## Installation
        
        ```sh
        pip3 install gtracks
        ```
        or
        ```sh
        pip3 install --user gtracks
        ```
        
        ## Examples
        
        An example bigwig file with ATAC-seq data from the insulin region is included.
        You can generate a test plot like this:
        ```sh
        gtracks INS-IGF2 test.png
        ```
        ![test plot](https://github.com/anthony-aylward/gtracks/raw/master/test.png)
        
        You can plot your own tracks over other genomic regions by providing more
        positional arguments: a region or gene name and paths to one or more bigWig
        files. The file type of the plot will be determined by the
        output file extension.
        ```sh
        gtracks chr11:2150341-2182439 track1.bw track2.bw output.pdf
        gtracks INS track1.bw track2.bw output.svg
        ```
        
        ### Modifying the gene annotations track
        
        GRCh37/hg19 gene annotations are used by default, but you can plot GRCh38/hg38
        genes by adding `--genes GRCh38` or `--genes hg38`. You can use your own gene
        annotations file (BED or BED12 format) by providing
        `--genes <path/to/genes.bed.gz>`.
        
        You may want to add more rows to the genes track. You can do this using
        the `--genes-height` and `--gene-rows` options.
        
        ```sh
        gtracks INS test-genes.png --genes-height 6 --gene-rows 6
        ```
        ![test plot with more gene rows](https://github.com/anthony-aylward/gtracks/raw/master/test-genes.png)
        
        ### Changing the color palette
        
        You can change the color palette for bigWig tracks using the `--color-palette` option.
        ```sh
        gtracks INS track1.bw track2.bw track3.bw output.pdf --color-palette "#color1" "#color2" "#color3"
        ```
        
        ### Setting y-axis height
        
        By default, tracks have different y-axis heights depending on signal height.
        You can set a uniform y-axis height for all tracks using the `--max` option.
        
        ```sh
        gtracks INS track1.bw track2.bw track3.bw output.pdf --max 400
        ```
        
        For more command-line options, see the usage page below.
        
        ## Environment variables
        
        If you want to use your own bigWig files but don't want to write out their
        paths every time you run `gtracks`, you can set your own default tracks using
        the environment variable `GTRACKS_TRACKS`.
        ```
        export GTRACKS_TRACKS=track1.bw,track2.bw,track3.bw
        gtracks output.pdf
        ```
        
        You can also change the default gene annotations file and color palette using
        environment variables `GTRACKS_GENES_PATH` and `GTRACKS_COLOR_PALETTE`.
        ```
        export GTRACKS_GENES_PATH=path/to/genes.bed.gz
        export GTRACKS_COLOR_PALETTE="#color1,#color2,#color3"
        gtracks output.pdf
        ```
        
        ## Usage
        
        ```
        usage: gtracks [-h] [--genes <{path/to/genes.bed.gz,GRCh37,GRCh38,hg19,hg38}>]
                       [--color-palette <#color> [<#color> ...]] [--max <float>]
                       [--tmp-dir <temp/file/dir>] [--width <int>]
                       [--genes-height <int>] [--gene-rows <int>]
                       <{chr:start-end,GENE}> [<track.bw> [<track.bw> ...]]
                       <path/to/output.{pdf,png,svg}>
        
        Plot bigWig signal tracks and gene annotations in a genomic region
        
        positional arguments:
          <{chr:start-end,GENE}>
                                coordinates or gene name to plot
          <track.bw>            bigWig files containing tracks
          <path/to/output.{pdf,png,svg}>
                                path to output file
        
        optional arguments:
          -h, --help            show this help message and exit
          --genes <{path/to/genes.bed.gz,GRCh37,GRCh38,hg19,hg38}>
                                compressed 6-column BED file or 12-column BED12 file
                                containing gene annotations. Alternatively, providing
                                a genome identifier will use one of the included gene
                                tracks. (default: GRCh37)
          --color-palette <#color> [<#color> ...]
                                color pallete for tracks
          --max <float>         max value of y-axis
          --tmp-dir <temp/file/dir>
                                directory for temporary files
          --width <int>         width of plot in cm (default: 40)
          --genes-height <int>  height of genes track (default: 2)
          --gene-rows <int>     number of gene rows (default: 1)
        ```
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Description-Content-Type: text/markdown
