ProjetM1S1Bioinfo

Master Bioinformatique : Développement de logiciels et Analyse de données - Projet dans le cadre de l'UE : Introduction à l'informatique et à la programmation

GUIless Demo

• Let's import our two classes :

from blast_hitter import BlastHitter
from clusterizer import Clusterizer

• Proteomes can be downloaded with RefSeqScraper script, or manually saved to data/genomes repository. A list of all paths should be initalised, so that we can use BlastHitter's factory method to create a bunch of blasthitter objects of all possible permutations.

proteomes = ["../data/genomes/Rickettsia_rickettsii_str._Arizona_strain=Arizona_protein.faa",            
"../data/genomes/Streptococcus_pneumoniae_R6_strain=R6_protein.faa",
"../data/genomes/Streptococcus_pyogenes_strain=NCTC8232_protein.faa",
"../data/genomes/Streptococcus_thermophilus_LMD-9_strain=LMD-9_protein.faa",
"../data/genomes/Piscirickettsia_salmonis_strain=Psal-158_protein.faa"]

bhitters = BlastHitter.from_list(proteomes)

• We can blast them and accumulate the reciprocal best hits with a for loop :

for bh in bhitters  : 
    bh.blast_them()
    bh.rbh_them()

• Now let's create a Clusterizer object after populating our blasthitters with RBH files :

clust = Clusterizer(bhitters, proteomes)

• The next and final step would be to create clusters, aligning each one and concatenating all of them and last but not least would be to launch the phylogenetic algorithm and to draw the newick tree:

clust.cluster_them()
clust.one_align_to_rule_them_all()
clust.draw_tree()

Ressources (05/10/2020) :

BLAST® Command Line Applications User Manual
Téléchargement Blast+