simple-blast 0.0.5

A simple library for executing BLAST searches with ncbi-blast+

simple_blast

This is a library that provides a very basic wrapper around ncbi-blast+. Currently, the library supports searches with blastn only, but I may expand the library to include wrappers for other BLAST executables if I need them.

Requirements

This library depends on Pandas for parsing BLAST output. The library has been tested with Pandas 1.5.3, but it likely works with other versions.

Of course, this library assumes that ncbi-blast+ is installed. The library has been tested with ncbi-blast 2.12.0+, and it likely works with newer versions of the software as well.

Basic usage

You can define a blastn search to be carried out using the BlastnSearch class. BlastnSearchobjects are constructed with two required arguments—the subject sequence and the query sequence files, in that order. For example, to set up a balstn search for sequences in seqs1.fasta against those in seqs2.fasta, you could construct a BlastnSearch object like this:

from simple_blast import BlastnSearch

search = BlastnSearch("seqs2.fasta", "seqs1.fasta")

The BLAST search is not carried out until you ask for the results by accessing the hits property of the search. This property returns a Pandas dataframe containing the HSPs identified in the BLAST search.

results = search.hits

The columns in the output may be configured by passing either the out_columns or additional_columns arguments when constructing the BlastnSearch. The former argument overrides the set of output columns; the latter argument is added to the list of default output columns.

You can also specify an e-value cutoff through the evalue argument.

DB caches

When the same sequence file is used as a subject in multiple searches, it can be efficient to build a BLAST database up front. The BlastDBCache class can be used to handle this mostly automatically. To make a BlastDBCache, you need to specify the location of the on the file system.

from simple_blast import BlastDBCache

cache = BlastDBCache("cache_dir")

To add a file to the cache, use the makedb method.

cache.makedb("seqs2.fasta")

When constructing a BlastnSearch object, give it the BlastDBCache as the db_cache parameter to make the BlastnSearch object use the cache for searches.

search = BlastnSearch("seqs2.fasta", "seqs1.fasta", db_cache=cache)

Now search will use the database we created for seqs2.fasta.