biopython v1.71.0 Bio.Blast.Applications.NcbiblastformatterCommandline

Wrapper for the NCBI BLAST+ program blast_formatter.

With the release of BLAST 2.2.24+ (i.e. the BLAST suite rewritten in C++ instead of C), the NCBI added the ASN.1 output format option to all the search tools, and extended the blast_formatter to support this as input.

The blast_formatter command allows you to convert the ASN.1 output into the other output formats (XML, tabular, plain text, HTML).

 >>> from Bio.Blast.Applications import NcbiblastformatterCommandline
 >>> cline = NcbiblastformatterCommandline(archive="example.asn", outfmt=5, out="example.xml")
 >>> cline
 NcbiblastformatterCommandline(cmd='blast_formatter', out='example.xml', outfmt=5, archive='example.asn')
 >>> print(cline)
 blast_formatter -out example.xml -outfmt 5 -archive example.asn

You would typically run the command line with cline() or via the Python subprocess module, as described in the Biopython tutorial.

Note that this wrapper is for the version of blast_formatter from BLAST 2.2.24+ (or later) which is when the NCBI first announced the inclusion this tool. There was actually an early version in BLAST 2.2.23+ (and possibly in older releases) but this did not have the -archive option (instead -rid is a mandatory argument), and is not supported by this wrapper.

Link to this section Summary


Initialize the class

Link to this section Functions

Initialize the class.