November 2024
Intermediate to advanced
456 pages
11h 58m
French
Content preview from Maîtriser Python pour la bioinformatique
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Chapitre 15. Seqmagique : Créer et formater des rapports
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Dans les projets de bio-informatique, tu te retrouves souvent face à un répertoire rempli de fichiers de séquences, probablement au format FASTA ou FASTQ. Tu voudras probablement commencer par te faire une idée de la distribution des séquences dans les fichiers, par exemple le nombre de séquences dans chaque fichier et les longueurs moyenne, minimale et maximale des séquences. Tu dois savoir si des fichiers sont corrompus - peut-être n'ont-ils pas été transférés complètement depuis ton centre de séquençage - ou si des échantillons ont beaucoup moins de lectures, ce qui indique peut-être un mauvais séquençage qui doit être refait. Dans ce chapitre, je présenterai quelques techniques pour vérifier tes fichiers de séquence à l'aide de hachages et de l'outil Seqmagick. Ensuite, j'écrirai un petit utilitaire pour imiter une partie de Seqmagick afin d'illustrer comment créer des tableaux de texte formatés. Ce programme sert de modèle à tout programme qui doit traiter tous les enregistrements d'un ensemble donné de fichiers et produire un tableau de statistiques récapitulatives.
Tu apprendras :
-
Comment installer l'outil
seqmagick -
Comment utiliser les hachages MD5
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Comment utiliser
choicesdansargparsepour contraindre les arguments -
Comment utiliser le module
numpy -
Comment se moquer d'un ...
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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.