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Jul 20, 2023
Handler for FeatureIO
BioFeatureIO is an iterator subsystem for genomic sequence features.
BioFeatureIO is a handler module for the formats in the FeatureIO set eg, BioFeatureIOGFF. It is the officially sanctioned way of getting at the format objects, which most people should use.
The BioFeatureIO system can be thought of like biological file handles. They are attached to filehandles with smart formatting rules eg, GFF format, or BED format and can either read or write feature objects BioSeqFeature objects, or more correctly, BioFeatureHolderI implementing objects, of which BioSeqFeature is one such object. If you want to know what to do with a BioSeqFeatureI object, read BioSeqFeatureI.
The idea is that you request a stream object for a particular format. All the stream objects have a notion of an internal file that is read from or written to. A particular FeatureIO object instance is configured for either input or output. A specific example of a stream object is the BioFeatureIOgff object.
Checkout these related ports:
- Wise - Intelligent algorithms for DNA searches
- Wfa2-lib - Exact gap-affine algorithm using homology to accelerate alignment
- Vt - Discovers short variants from Next Generation Sequencing data
- Vsearch - Versatile open-source tool for metagenomics
- Viennarna - Alignment tools for the structural analysis of RNA
- Velvet - Sequence assembler for very short reads
- Vcftools - Tools for working with VCF genomics files
- Vcflib - C++ library and CLI tools for parsing and manipulating VCF files
- Vcf2hap - Generate .hap file from VCF for haplohseq
- Vcf-split - Split a multi-sample VCF into single-sample VCFs
- Unikmer - Toolkit for nucleic acid k-mer analysis, set operations on k-mers
- Unanimity - Pacific Biosciences consensus library and applications
- Ugene - Integrated bioinformatics toolkit
- Ucsc-userapps - Command line tools from the UCSC Genome Browser project
- Trimmomatic - Flexible read trimming tool for Illumina NGS data