View on GitHub

Find overlap reads

Parse a BAM file and extract reads ovelapping given genomic coordinates

Download this project as a .zip file Download this project as a tar.gz file

Find_overlap_reads

Motivation

Find_overlap_reads is a python3 object oriented script, developed to parse a genomic alignment files(BAM/SAM). The program is intended to count and extract reads or read pairs overlapping genomic intervals provided in a tab-separated text file.

Principle

The interval file is parsed and Interval objects are created for each valid line within it.
Sam/Bam (CRAM?) files are parsed iteratively with pysam.
For each read the program verify if the read itself or the template covered by the read and its pair overlap one of the genomic interval.
A report containing the total number of reads, the number of read mapped and the reads overlapping each interval is created in the current dir.
A subset of bam containing only read overlapping intervals is generated, sorted and indexed.

Dependencies

pysam 0.8.1+ (based on htslib and samtools versions 1.1)

If you have pip already installed, enter the following line to install pysam:

sudo pip install pysam

Get Find_overlap_reads

Clone the repository with --recursive option to also pull the submodule

$ git clone --recursive https://github.com/a-slide/Find_overlap_reads/ my_folder/

Enter the root of the program folder and make the main script executable

$ sudo chmod u+x Find_overlap_reads.py

Add Find_overlap_reads.py in your PATH

Usage

Usage: find_overlap_read -f genomic_interval.csv [-b/-r] f1.bam(sam),[f2.bam(sam)...fn.bam(sam)
Parse a BAM/SAM file(s) and extract reads overlapping given genomic coordinates

Options:
    --version         show program's version number and exit
    -h, --help        show this help message and exit
    -f INTERVAL_FILE  Path of the tab separated file contaning genomic interval (mandatory)
    -t TEMPLATE_LEN   Maximum length of the template between 2 paired reads to be considered as a concordant pair (default = 1000)
    -b, --no_bam      Don't output bam file(s) (default = True)
    -r, --no_report   Don't output report file(s) (default = True)

Genomic interval file

The file containing genomic intervals have to be formated as a tab-separated values text format as follow:

Name_of_the_the_reference start_coordinate(INT) end_coordinate(INT) Name_of_the_interval (facultative)

Lines with invalid integer values or less than 3 fields will be skipped. An error will be raised if no valid interval was found. Examples of valid and invalid files are provided in the demo/ folder. A standard Bed file would be considered as a

Aligment files (sam/bam)

A list of bam, sam and or cram files containing

Development notebook

2 possibilities:

Use ipython notebook with Dev_notebook.ipynb
Consult directly online through nbviewer : Notebook

Authors and Contact

Adrien Leger - 2014