October 2024
Intermediate to advanced
456 pages
11h 48m
German
Content preview from Python für die Bioinformatik beherrschen
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Kapitel 16. FASTX grep: Ein Hilfsprogramm zur Auswahl von Sequenzen erstellen
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Ein Kollege bat mich einmal, alle RNA-Sequenzen in einer FASTQ-Datei zu finden, deren Beschreibung oder Name die Zeichenfolge LSU (für Long Subunit RNA) enthält. Obwohl es möglich ist, dieses Problem für FASTQ-Dateien zu lösen, indem man das Programm grep 1 verwenden, um alle Zeilen einer Datei zu finden, die einem bestimmten Muster entsprechen. Wenn du aber eine Lösung in Python schreibst, kannst du ein Programm erstellen, das auch andere Formate wie FASTA verarbeiten und Datensätze nach anderen Kriterien wie Länge oder GC-Gehalt auswählen kann. Außerdem kannst du Optionen hinzufügen, um das Format der Ausgabesequenz zu ändern, und dem Benutzer Annehmlichkeiten wie das Erraten des Formats der Eingabedatei anhand der Dateierweiterung bieten.
In diesem Kapitel lernst du:
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Über die Struktur einer FASTQ-Datei
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Wie man einen regulären Ausdruck ohne Berücksichtigung der Groß- und Kleinschreibung findet
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Über DWIM (Do What I Mean) und DRY (Don't Repeat Yourself) Ideen im Code
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Wie man
andundorOperationen verwendet, um boolesche Werte und Bits zu reduzieren
Mit grep Zeilen in einer Datei finden
Das Programm grep kann alle Zeilen in einer Datei finden, die einem bestimmten Muster entsprechen. Wenn ich in einer der FASTQ-Dateien nach LSU suche, findet es zwei Kopfzeilen, ...
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