A converter from .bam to .png for specific genomic region.
Project description
BAMsnap
BAMSNAP is high-performed command-based visualization tool for the aligned BAM file.
Installation
Prerequisites
- python 3.4+
- [Pillow (Python Imaging Library)][pil] (5.0.0+)
- [pysam][ps] (1.8.1+)
- pyfaidx
- pytabix
Install with pip
pip install bamsnap
Install with github
git clone https://github.com/parklab/bamsnap
cd bamsnap
python setup.py install
Usage
Simple usage
$ 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
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
bamsnap-0.2.5.tar.gz
(20.7 MB
view hashes)
Built Distribution
bamsnap-0.2.5-py3-none-any.whl
(20.7 MB
view hashes)