Pybedtools
|
Application data |
|
| Created by | Dale RK, Pedersen BS, Quinlan AR |
|---|---|
| Biological application domain(s) | Genomics |
| Principal bioinformatics method(s) | Read mapping |
| Created at | National Institutes of Health |
| Maintained? | Yes |
| Input format(s) | BED, GTF, GFF, GFF3, VCF, BAM, SAM |
| Output format(s) | BED, GTF, GFF, GFF3, VCF, BAM, SAM |
| Software features | See full description |
| Programming language(s) | Python |
| Licence | GPLv2 |
| Operating system(s) | Windows (Cygwin), Linux, Linux 64, Mac OS X |
Summary: Python extension to BEDTools that allows use of all BEDTools programs directly from Python, as well as feature-by-feature manipulation, automatic handling of temporary files, and more.
"Error: no local variable "counter" was set." is not a number.
Description
Pybedtools is a Python package that provides a convenient and flexible interface to both the BEDTools command-line tools and efficient functions in the BEDTools C++ libraries. Pybedtools simplifies complicated analyses by extending the functionality in BEDTools and by providing (to the authors' knowledge) the first Python library offering a common interface for manipulating datasets in diverse formats.
Other new functionality includes:
- set operations on multiple datasets using a simple, intuitive syntax
- the ability to filter features and
- select specific columns of a BED/GTF/GFF/VCF/SAM/BAM line using numerical indexing or by attributes
- a unified interface to common attributes (e.g., chromosome, start, end, name, and strand) from many file formats
- a documented command history.
A brief example showing how to identify the closest genes within 5kb away from intergenic SNPs, given a GFF file of genes and a BED file of SNPs:
from pybedtools import BedTool
genes = BedTool(’hg19.gff’)
snps = BedTool(’snps.bed’)
intergenic_snps = (snps - genes)
nearby = genes.closest(intergenic_snps, d=True,
stream=True)
for gene in nearby:
if int(gene[-1]) < 5000:
print gene.name
Pybedtools provides researchers with a simple and efficient interface for exploring complex genomics datasets in widely used formats.
Links
References
To add a reference for Pybedtools, enter the PubMed ID in the field below and click 'Add'.
Search for "Pybedtools" in the SEQanswers forum / BioStar or:
| Web Search | Wiki Sites | Scientific |
|---|---|---|
