Covidor

Python version

Python 3.7, 3.8, 3.9

Source

See http://github.com/sequana/covidor.

Issues

Please fill a report on github

Platform

This is currently only available for Linux distribution with bash shell (contributions are welcome to port the tool on MacOSX and other platforms)

Overview

pip install covidor

third-party tools

kraken2 and art_illumina are required for the simulation and analysis.

pip install damona
# for kraken2 only:
damona install kraken:2.0.9
# to install kraken2 and art_illumina altogether, there are both provided in the sequana_tools package:
damona install sequana_tools

Installation

For Users:

pip install covidor

For developers:

git clone git@github.com:sequana/covidor.git
cd covidor
pip install .

Testing

pytest -v ./tests

User guide and reference

User Guide

Table of Contents

• User Guide

  • Getting help

Getting help

Coming soon

References

covidor.kmers
covidor.distance
covidor.main

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

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")

Covidor standalone (script module)

covidor

This is the main entry point

covidor [OPTIONS] COMMAND [ARGS]...

Options

--version

Show the version and exit.

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>

stats

covidor stats [OPTIONS]

Options

--tag <tag>

--rl <rl>

--paired

--factor <factor>