Package: wnpp Severity: wishlist Owner: Étienne Mollier <emollier@emlwks999.eu> X-Debbugs-Cc: debian-devel@lists.debian.org X-Debbugs-Cc: debian-med@lists.debian.org * Package name : pyfastx Version : 0.8.4 Upstream Author : Lianming Du * URL : https://github.com/lmdu/pyfastx/ * License : Expat Programming Lang: C, Python3 Description : fast random access to sequences from FASTA/Q file 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 is required for upgrading to augur 18.2.0. It will be maintained in the Debian Med team. The packaging occurs in the Debian Med group on Salsa[1]. [1]: https://salsa.debian.org/med-team/pyfastx Have a nice day, :) -- Étienne Mollier <emollier@emlwks999.eu> Fingerprint: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da Sent from /dev/pts/4, please excuse my verbosity.
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