This code can be used to probe user-defined target sequences in GISAID sequences of SARS-CoV-2 viruses from COVID-19 patients from around the world.
The main input of this code is as follows --
-
fasta: standard fasta file containing the genomes in which the target sequences need to be probed -
targets: CSV file with each row being a target sequence and the following columns (fields)- 'id': id of the target sequence
- 'sequence': target sequence in capital letter 'ATCG'
- 'lineage': the lineage that is being detected using the target sequence
An example of this CSV file is given in
data/target_sequences.csv. -
meta: Metadata file containing additional information of each genome in the fasta file. We specifically use the date of collection and the Pango lineage.
This code has three modes -- probe, analyze and plot.
The output for the probe mode of the code is a CSV file that contains information about the presence of the target sequences in each sequence in the input fasta file.
The output for the analyze mode of the code is a CSV file that contains statistics like sensitivity and specificity for different combination of tests using the target sequences for each lineage mentioned in the input target sequences file.
usage: primer_analysis.py [-h] [--probe] [--meta META] [--fasta FASTA]
[--targets TARGETS] [--outprobe OUTPROBE]
[--condmeta CONDMETA] [--analyze]
[--inprobe INPROBE] [--outanalysis OUTANALYSIS]
[--outprobemeta OUTPROBEMETA] [--outhtml OUTHTML]
[--country COUNTRY] [--startdate STARTDATE]
[--enddate ENDDATE] [--plot]
[--inanalysis INANALYSIS]
[--inprobemeta INPROBEMETA] [--prefix PREFIX]
optional arguments:
-h, --help show this help message and exit
--probe probe target sequences
--meta META metadata of the SARS-CoV-2 genomes
--fasta FASTA fasta file with SARS-CoV-2 genomes
--targets TARGETS csv file with target sequences and their probe
lineages
--outprobe OUTPROBE output file name for updated metadata file
--condmeta CONDMETA output file name for condensed form of metadata file
--analyze analyze target sequences
--inprobe INPROBE input metadata file of probed target sequences
--outanalysis OUTANALYSIS
output csv file with analysis results
--outprobemeta OUTPROBEMETA
output csv file with probing results along with
metadata
--outhtml OUTHTML output html file with anlaysis results
--country COUNTRY focus on a specific country for analysis
--startdate STARTDATE
date (YYYY-MM-DD) after which the analysis should be
performed [2020-12-01]
--enddate ENDDATE date (YYYY-MM-DD) until which the analysis should be
performed [last entry in the metadata file]
--plot plot the analysis results
--inanalysis INANALYSIS
csv file with analysis results
--inprobemeta INPROBEMETA
csv file with probing results along with metadata
(output of analyze mode)
--prefix PREFIX prefix for output files of plotting
If sequences.fasta is the fasta file with GISAID sequences and metadata.tsv is the metadata file, then the following is an example of probing target sequences, analyzing the results and finally plotting some venn diagrams.
$ python primer_analysis.py --probe --analyze --plot --fasta ../data/sequences.fasta --targets ../data/target_sequences.csv --meta ../data/metadata.tsv --outprobemeta ../data/output_probe_metadata.csv --outanalysis ../data/output_analysis.csv --prefix ../data/
This is an example of venn figure generated with the above command using GISAID sequences until 15th May 2021.
It shows the overlap of sequences classified as belonging to lineage B.1.1.7 with three target sequences from the Yale protocol.
This plot shows the number of true positive, false positive and false negative samples for the first target sequence in the Yale protocol. The start date for this plot is 1st December 2020.