GfaPy: a flexible and extensible software library for handling sequence graphs in Python']Python

被引：5
|
作者：
Gonnella, Giorgio [1 ]
Kurtz, Stefan [1 ]
机构：
[1] Univ Hamburg, MIN Fak, ZBH Ctr Bioinformat, D-20146 Hamburg, Germany
来源：
BIOINFORMATICS | 2017年 / 33卷 / 19期
关键词：
D O I：
10.1093/bioinformatics/btx398
中图分类号：
Q5 [生物化学];
学科分类号：
071010 ; 081704 ;
摘要：
GFA 1 and GFA 2 are recently defined formats for representing sequence graphs, such as assembly, variation or splicing graphs. The formats are adopted by several software tools. Here, we present GfaPy, a software package for creating, parsing and editing GFA graphs using the programming language Python. GfaPy supports GFA 1 and GFA 2, using the same interface and allows for interconversion between both formats. The software package provides a simple interface for custom record types, which is an important new feature of GFA 2 (compared to GFA 1). This enables new applications of the format.
引用
收藏
页码：3094 / 3095
页数：2
相关论文
共 23 条
  • [1] tegdet: An extensible Python']Python library for anomaly detection using time evolving graphs
    Bernardi, Simona
    Javierre, Rail
    Merseguer, Jose
    [J]. SOFTWAREX, 2023, 22
  • [2] Case Recommender: A Flexible and Extensible Python']Python Framework for Recommender Systems
    da Costa, Arthur
    Fressato, Eduardo
    Neto, Fernando
    Manzato, Marcelo
    Campello, Ricardo
    [J]. 12TH ACM CONFERENCE ON RECOMMENDER SYSTEMS (RECSYS), 2018, : 494 - 495
  • [3] A Python']Python Software Library for Computing with Words and Perceptions
    Sharma, Deepak
    Gupta, Prashant K.
    Andreu-Perez, Javier
    Mendel, Jerry M.
    Martinez Lopez, Luis
    [J]. IEEE CIS INTERNATIONAL CONFERENCE ON FUZZY SYSTEMS 2021 (FUZZ-IEEE), 2021,
  • [4] Software review: DEAP (Distributed Evolutionary Algorithm in Python']Python) library
    Kim, Jinhan
    Yoo, Shin
    [J]. GENETIC PROGRAMMING AND EVOLVABLE MACHINES, 2019, 20 (01) : 139 - 142
  • [5] Pybedtools: a flexible Python']Python library for manipulating genomic datasets and annotations
    Dale, Ryan K.
    Pedersen, Brent S.
    Quinlan, Aaron R.
    [J]. BIOINFORMATICS, 2011, 27 (24) : 3423 - 3424
  • [6] PyHMMER: a Python']Python library binding to HMMER for efficient sequence analysis
    Larralde, Martin
    Zeller, Georg
    [J]. BIOINFORMATICS, 2023, 39 (05)
  • [7] PyFLEXTRKR: a flexible feature tracking Python']Python software for convective cloudanalysis
    Feng, Zhe
    Hardin, Joseph
    Barnes, Hannah C.
    Li, Jianfeng
    Leung, L. Ruby
    Varble, Adam
    Zhang, Zhixiao
    [J]. GEOSCIENTIFIC MODEL DEVELOPMENT, 2023, 16 (10) : 2753 - 2776
  • [8] Python']Python BMDS: A Python']Python interface library and web application for the canonical EPA dose-response modeling software
    Pham, Ly Ly
    Watford, Sean
    Friedman, Katie Paul
    Wignall, Jessica
    Shapiro, Andrew J.
    [J]. REPRODUCTIVE TOXICOLOGY, 2019, 90 : 102 - 108
  • [9] DNA Features Viewer: a sequence annotation formatting and plotting library for Python']Python
    Zulkower, Valentin
    Rosser, Susan
    [J]. BIOINFORMATICS, 2020, 36 (15) : 4350 - 4352
  • [10] EEGraph: An open-source Python']Python library for modeling electroencephalograms using graphs
    Maitin, Ana M.
    Nogales, Alberto
    Chazarra, Pedro
    Jose Garcia-Tejedor, Alvaro
    [J]. NEUROCOMPUTING, 2023, 519 : 127 - 134
123