2. References

covidor.kmers
covidor.distance
covidor.main

2.1. kmer module

class KmerOverlap(kmer_len=35)

from covidor import KmerOverlap ko = KmerOverlap() for fasta in fastas:

ko.enumerate_unique_kmers(fasta)

names = self.kmer_dict.keys() ko.get_list_specific_kmers(name)

enumerate_unique_kmers(fasta_files)

populate kmers for each fasta

get_list_specific_kmers(name)

Returns kmer specific (unique) to a fasta

get_proportion_kmer_specific(name)

Gives same results as get_specific_kmers but normalised and for a given name

get_proportion_reads_specific(name, N=100, read_length=75, paired=False)

import glob fastas = glob.glob("databases/genomes/*fasta") kmer_dict = get_all_kmers() expected_percentage = get_proportion_reads_specific(kmer_dict, "NAME_ONE_FASTA")

get_specific_kmers()

Return dataframe with number of unique kmers in each fasta

2.2. distance module

class Distance

compute_pdistance(alignment, mode='spike')

Compute distance between genomes on the spike gene

This takes as input the ouput of mafft tool on a set of input fasta file:

cat *fasta > in.fasta
mafft --auto in.fasta > alignment.fasta

Then:

from covidor.distance import Distance
d = Distance()
d.compute_pdistance("alignment.out")

distance is computed as the number of bases that are different along 2 sequences, normalised by the length (and multiplied by 100). Each sequence is identified by the starting and ending 20-bases long sequences.

plot(alignment, mode='spike')

d = Distance()
d.plot("alignment.out")

2.3. Covidor standalone (script module)

2.3.1. covidor

This is the main entry point

covidor [OPTIONS] COMMAND [ARGS]...

Options

--version

Show the version and exit.

2.3.1.1. analyse

Example of mix of wuhan and beta (PE):

covidor --file1 4520_S4_L001_R1_001.fastq.gz --file2 4520_S4_L001_R2_001.fastq.gz

Example of omicron (SE):

fastq-dump SRR17673561 covidor analyse --file1 SRR17673561.fastq --db databases/default/

covidor analyse [OPTIONS]

Options

--file1 <file1>

Required

--file2 <file2>

--tag <tag>

--db <db>

--factor <factor>

2.3.1.2. stats

covidor stats [OPTIONS]

Options

--tag <tag>

--rl <rl>

--paired

--factor <factor>