Metadata-Version: 2.1
Name: bamsnap
Version: 0.2.5
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
        <!--[![Build Status](https://travis-ci.org/bamsnap/bamsnap.svg?branch=develop)](https://travis-ci.org/bamsnap/bamsnap) 
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        BAMSNAP is high-performed command-based visualization tool for the aligned BAM file.
        
        <!--<img src="https://raw.githubusercontent.com/parklab/bamsnap/master/data/ex1/snapfiles/snap_test11.bam_1_715347-715348.png" height=128px width=405px>-->
        
        
        ## Installation
        
        ### Prerequisites
        * python 3.4+
        * [Pillow (Python Imaging Library)][pil] (5.0.0+)
        * [pysam][ps] (1.8.1+)
        * pyfaidx
        * pytabix
        
        ### Install with pip
        
        ```bash
        pip install bamsnap
        ```
        ### Install with github
        
        ```
        git clone https://github.com/parklab/bamsnap
        cd bamsnap
        python setup.py install
        ```
        
        ## Usage
        
        ### Simple usage
        ```bash
        $ bamsnap -bam test.bam -pos 1:7364529 -out test.png
        ```
        
        ### 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(s)
          -bamlist BAMLIST      list file with bam file paths
          -title [TITLE [TITLE ...]]
                                title (name) of bam file(s)
          -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              output file or title of output file
          -imagetype IMAGETYPE  output file type
          -conf CONF            configuration file
          -ref REF              Reference sequence fasta file (ex. hg19.fa)
          -save_image_only      save image only
          -image_dir_name IMAGE_DIR_NAME
                                image directory name
          -draw [DRAW [DRAW ...]]
                                plot (default: -draw coordinates bamplot base gene)
          -bamplot [BAMPLOT [BAMPLOT ...]]
                                plot (default: -bamplot coverage base read)
          -width WIDTH          image file size : width (unit:px)
          -height HEIGHT        image file size : height (unit:px)
          -bgcolor BGCOLOR      background color
          -plot_margin_top PLOT_MARGIN_TOP
                                top margin size of plot
          -plot_margin_bottom PLOT_MARGIN_BOTTOM
                                bottom margin size of plot
          -plot_margin_left PLOT_MARGIN_LEFT
                                left margin size of plot
          -plot_margin_right PLOT_MARGIN_RIGHT
                                right margin size of plot
          -border               draw border in plot
          -read_thickness READ_THICKNESS
                                read thickness (unit:px)
          -read_gap_height READ_GAP_HEIGHT
                                read gap height (unit:px)
          -read_gap_width READ_GAP_WIDTH
                                read gap width (unit:px)
          -read_bgcolor READ_BGCOLOR
                                read background color
          -read_color READ_COLOR
                                read color
          -read_pos_color READ_POS_COLOR
                                positive strand read color
          -read_neg_color READ_NEG_COLOR
                                negative strand read color
          -read_group READ_GROUP
                                read group
          -margin MARGIN        genomic margin size
          -center_line          draw center line
          -no_target_line       do not draw target line
          -base_fontsize BASE_FONTSIZE
                                font size of base plot
          -base_height BASE_HEIGHT
                                base plot height
          -base_margin_top BASE_MARGIN_TOP
                                top margin size of base plot
          -base_margin_bottom BASE_MARGIN_BOTTOM
                                bottom margin size of base plot
          -coverage_height COVERAGE_HEIGHT
                                coverage plot height
          -coverage_fontsize COVERAGE_FONTSIZE
                                coverage font size
          -coverage_vaf COVERAGE_VAF
                                coverage variant allele fraction threshold (default:
                                0.2)
          -coverage_color COVERAGE_COLOR
                                coverage color
          -coverage_bgcolor COVERAGE_BGCOLOR
                                coverage plot background color
          -heatmap_height HEATMAP_HEIGHT
                                coverage heatmap height
          -heatmap_bgcolor HEATMAP_BGCOLOR
                                coverage heatmap plot background color
          -no_title             do not draw label.
          -gene_height GENE_HEIGHT
                                gene plot height
          -gene_fontsize GENE_FONTSIZE
                                font size of gene plot
          -gene_pos_color GENE_POS_COLOR
                                positive strand color
          -gene_neg_color GENE_NEG_COLOR
                                negative strand color
          -coordinates_height COORDINATES_HEIGHT
                                coordinate height
          -coordinates_fontsize COORDINATES_FONTSIZE
                                coordinate font size
          -coordinates_axisloc COORDINATES_AXISLOC
                                coordinate axis location
          -coordinates_bgcolor COORDINATES_BGCOLOR
                                coordinate background color
          -coordinates_labelcolor COORDINATES_LABELCOLOR
                                coordinate label color
          -separated_bam        draw a plot for each bam
          -title_fontsize TITLE_FONTSIZE
                                font size of title
          -debug                turn on the debugging mode
          -silence              don't print any log.
        ```
        
        
        ### 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 :: 3.4
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Description-Content-Type: text/markdown
