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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16章
FASTX grep：配列を選択するユーティリティプログラムの作成
以前同僚から、LSU（大サブユニットRNAの略）文字列に関する記述や名称を含むFASTQファイルから、その中にあるすべてのRNA配列を見つけてほしいと頼まれたことがあります。FASTQファイルに関するこの問題だけなら、grepプログラム＊1を使って、あるパターンにマッチするファイル中のすべての行を見つければ済みます。一方Pythonでコードを書けば、FASTAのような他のフォーマットを扱うだけでなく、配列長やGC含量などの他の基準に基づいたレコードを選択するように機能を拡張したプログラムを作成することができます。
＊1 grepは、「global regular expression print」の略だという説もある。
この章では以下のことを学びます。
- FASTQファイルの構造について
- 大小文字を区別しない正規表現マッチはどうやって行うか
- コード中のDWIM（Do What I Mean）とDRY（Don’t Repeat Yourself）の考え方
- 論理値やビットを削減するための
andおよびor演算子の使い方
16.1 grepを用いたファイル中の行の検索
grepプログラムは、与えられたパターンにマッチするファイル内のすべての行を見つけることができます。FASTQファイルの1つでLSUを検索すると、このパターンを含む2つのヘッダ行が見つかります。
$ grep LSU tests/inputs/lsu.fq@ITSLSUmock2p.ITS_M01380:138:000000000-C9GKM:1:1101:14440:2042 2:N:0@ITSLSUmock2p.ITS_M01384:138:000000000-C9GKM:1:1101:14440:2043 ...
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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.
I’ve been on the O’Reilly platform for more than eight years. I use a couple of learning platforms, but I'm on O'Reilly more than anybody else. When you're there, you start learning. I'm never disappointed.Amir M.
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.