Metadata-Version: 2.1
Name: bamsnap
Version: 0.2.0
Summary: A converter from .bam to .png for specific genomic region.
Home-page: https://github.com/danielmsk/bamsnap
Author: Daniel Minseok Kwon
Author-email: daniel.minseok.kwon@gmail.com
License: MIT
Download-URL: https://github.com/danielmsk/bamsnap/archive/0.1.tar.gz
Description: # <img src="https://bampdx.com/wp-content/uploads/2015/12/BAMPDX-logo.png" height=28px width=45px>&nbsp;BAMsnap
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        ## Installation
        
        ### Prerequisites
        * python 3.0+
        * [Pillow (Python Imaging Library)][pil] (5.0.0+)
        * [pysam][ps] (1.8.1+)
        * pyfasta
        	* numpy
        
        ```bash
        pip install bamsnap
        ```
        
        ## Usage
        
        ### Simple usage
        ```bash
        $ bamsnap -bam test.bam -pos 1:7364529 -out outpath
        ```
        
        ### Options
        ```
        optional arguments:
          -h, --help            show this help message and exit
          -v, --version         show program's version number and exit
          -bam [BAM [BAM ...]]  bam file
          -bamlist BAMLIST      list file with bam file paths
          -pos [POS [POS ...]]  genomic position (ex. 1:816687-818057, 12:7462545)
          -vcf VCF              list file with genomic positions with VCF format
          -bed BED              list file with genomic positions with BED format
          -out OUT              title of output file
          -out_type {png,jpg,html,image}
                                output file type
          -conf CONF            configuration file
          -ref REF              Reference sequence fasta file (ex. hg19.fa)
          -width WIDTH          image size : width (unit:px)
          -height HEIGHT        image size : height (unit:px)
          -read_thickness READ_THICKNESS
                                read width (unit:px)
          -read_gap_h READ_GAP_H
                                read gap height (unit:px)
          -read_gap_w READ_GAP_W
                                read gap width (unit:px)
          -draw DRAW            plot (default: -draw coverage,heatmap,read )
          -margin MARGIN        genomic margin size
          -center_line CENTER_LINE
                                draw center line
          -no_target_line NO_TARGET_LINE
                                do not draw target line
          -coverage_height COVERAGE_HEIGHT
                                coverage plot height
          -coverage_vaf COVERAGE_VAF
                                coverage variant allele fraction threshold (unit:%)
          -heatmap_height HEATMAP_HEIGHT
                                coverage heatmap height
          -draw_gene DRAW_GENE  draw gene structure
          -merged_image MERGED_IMAGE
                                draw a merged plot
          -colormap COLORMAP    colormap file
          -silence              don't print any log.
          -debug                turn on the debugging mode
        ```
        
        
        ### Examples
        
        ```
        bamsnap -bam data/test11.bam -pos 1:715348 -out data/ex1
        bamsnap -bam data/test11.bam -bed data/region.bed -out data/ex2
        bamsnap -bamlist data/bamlist.txt -pos 1:817187 1:817848 -out data/ex3
        bamsnap -bamlist data/bamlist.txt -bed data/region2.bed -out data/ex4
        bamsnap -bam data/test11.bam -pos 1:715348 -out data/ex1 -draw_gene 
        ```
        
        
        
        
        
        
        
        
        
        
Keywords: genomics,bioinformatics
Platform: UNKNOWN
Classifier: Operating System :: OS Independent
Classifier: Topic :: Software Development :: Libraries
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Description-Content-Type: text/markdown
