June 2023
Intermediate to advanced
460 pages
6h 20m
Japanese
Content preview from Pythonではじめるバイオインフォマティクス ―可読性・拡張性・再現性のあるコードを書くために
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18章
FASTXサンプラー：配列ファイルからランダムにサンプリング
ゲノミクスやメタゲノミクスでの配列データはとても大きいため、解析するには膨大な時間と計算リソースを必要とします。多くのシーケンサはサンプルごとに数千万のリードを生成し、実験のサンプル数は10から100になります。それぞれのレプリケーションが存在するため、結果的にギガバイトやテラバイトの容量になります。配列をランダムにサブサンプリングして入力ファイルの容量を小さくすれば、データをより速く探索できます。この章では、Pythonのrandomモジュールを用いてFASTA/FASTQ配列ファイルからリードの一部分を選択する方法を紹介します。
この章では以下のことを学びます。
- 非決定論的サンプリング
18.1 はじめましょう
この演習のコードと実行結果は、18_fastx_samplerディレクトリにあります。まずsampler.pyという解法プログラムのコピーから始めます。
$ cd 18_fastx_sampler/$ cp solution.py sampler.py
このプログラムのテストに使うFASTA入力ファイルは第17章で作成したプログラムsynth.pyにより生成されます。このプログラムの作成が終わっていなければ、make fastaを実行する前に必ずプログラムをコピーし、1,000、10,000、100,000個のリードを含む3つのFASTAファイルを作成します。個々の配列長さはおよそ75bpから200bpの間で、ファイル名はそれぞれn1k.fa、n10k.fa、n100k.fa になります。
$ ../15_seqmagique/seqmagique.py tests/inputs/n1* ...
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I wanted to learn C and C++, but it didn't click for me until I picked up an O'Reilly book. When I went on the O’Reilly platform, I was astonished to find all the books there, plus live events and sandboxes so you could play around with the technology.Addison B.
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I'm always learning. So when I got on to O'Reilly, I was like a kid in a candy store. There are playlists. There are answers. There's on-demand training. It's worth its weight in gold, in terms of what it allows me to do.