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# 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
```

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