Metadata-Version: 1.0
Name: covfuzze
Version: 0.1.2
Summary: UNKNOWN
Home-page: https://github.com/al-mcintyre/CovFuzze
Author: al-mcintyre
Author-email: abm237@cornell.edu
License: LICENSE
Description: # CovFuzze Plot
        A python script to plot gene coverage and IP peaks with standard deviations calculated from multiple replicates. 
        
        usage: gene_peak_plot.py [-h] [-g GENE] [-o OUT] --bams BAMS [BAMS ...] --bed 
                                 BED [--gtf GTF] [-p PEAKS] -l LABELS [LABELS ...]
                                 [-n NSUBPLOTS] [--normalize]
        
        ## dependencies:
        - numpy, tested with 1.11.1
        - pysam, tested with 0.9.1
        - pandas, tested with 0.18.1
        - seaborn, tested with 0.7.1 
        - matplotlib, tested with 2.0.2
        - pybedtools, tested with 0.7.10 - requires bedtools available in path
        
        ## required arguments:
        ```
          -o OUT, --out OUT     output prefix (incl. dir) 
          --bams BAMS [BAMS ...] 
                                bam files (separated by spaces) 
          --bed BED             bed file for region(s) of interest  
          -l LABELS [LABELS ...], --labels LABELS [LABELS ...] 
                                labels associated with bams - if replicates, use same 
                                labels
        ```
        ## optional arguments:
        ```
          -h, --help            show this help message and exit 
          -g GENE, --gene GENE  gene name (default = GeneDoe) 
          --gtf GTF             gtf file for gene to plot exons as shaded regions 
          -p PEAKS, --peaks PEAKS 
                                bed file with peaks
          -n NSUBPLOTS, --nsubplots NSUBPLOTS 
                                number of subplots- bams will be split evenly based on 
                                the order given (default = 1) 
          --normalize           normalize by gene length/summed coverage (default = 
                                False)
        ```
        
        ## Example:
        ```
        covfuzze.py -o $outdir/$prefix --bams 
            alignments/sample_1_Input.sample.star.bam alignments/sample_1_IP.sample.star.bam 
            alignments/sample_2_Input.sample.star.bam alignments/sample_2_IP.sample.star.bam 
            alignments/sample_3_Input.sample.star.bam alignments/sample_3_IP.sample.star.bam 
            --bed ${gene}_exons.bed 
            -l sample_Input sample_IP sample_Input sample_IP sample_Input sample_IP 
            --gene ${gene} -n 1 --normalize
        ```
        
Platform: UNKNOWN
