Paket: python3-pyfastx (2.1.0-2)

[ Källkod: pyfastx  ]

fast random access to sequences from FASTA/Q file - python3 module

The pyfastx is a lightweight Python C extension that enables users to randomly access to sequences from plain and gzipped FASTA/Q files. This module aims to provide simple APIs for users to extract sequence from FASTA and reads from FASTQ by identifier and index number. The pyfastx will build indexes stored in a sqlite3 database file for random access to avoid consuming excessive amount of memory. In addition, the pyfastx can parse standard (sequence is spread into multiple lines with same length) and nonstandard (sequence is spread into one or more lines with different length) FASTA format.

It features:

 * a single file for the Python extension;
 * lightweight, memory efficient FASTA/Q file parsing;
 * fast random access to sequences from gzipped FASTA/Q file;
 * sequences reading from FASTA file line by line;
 * N50 and L50 calculation of sequences in FASTA file;
 * GC content and nucleotides composition calculation;
 * reverse, complement and antisense sequences extraction;
 * excellent compatibility: support for parsing nonstandard FASTA file;
 * support for FASTQ quality score conversion;
 * a command line interface for splitting FASTA/Q file.

This package provides the python3 module.

Andra paket besläktade med python3-pyfastx

• dep: libc6 (>= 2.28)

  GNU C-bibliotek: Delade bibliotek
  också ett virtuellt paket som tillhandahålls av libc6-udeb

• dep: libsqlite3-0 (>= 3.5.9)

  SQLite 3 shared library

• dep: python3

  interactive high-level object-oriented language (default python3 version)

• dep: python3-pyfaidx

  efficient random access to fasta subsequences for Python 3

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Arkitektur	Paketstorlek	Installerad storlek	Filer
i386	60,8 kbyte	185,0 kbyte	[filförteckning]