isolate_parsers
Usage
python isolateset_parser.py [-h] [-i FOLDER] [--no-fasta] [-w WHITELIST]
[-b BLACKLIST] [-m SAMPLE_MAP] [--filter-1000bp]
optional arguments:
-h, --help show this help message and exit
-i FOLDER, --input FOLDER
The breseq folder to parse.
--no-fasta Whether to generate an aligned fasta file of all snps
in the breseq VCF file.
-w WHITELIST, --whitelist WHITELIST
Samples not in the whitelist are ignored. Either a
comma-separated list of sample ids for a file with
each sample id occupying a single line.
-b BLACKLIST, --blacklist BLACKLIST
Samples to ignore. See `--whitelist` for possible
input formats.
-m SAMPLE_MAP, --sample-map SAMPLE_MAP
A file mapping sample ids to sample names. Use if the
subfolders in the breseqset folder are named
differently from the sample names. The file should
have two columns: `sampleId` and `sampleName`,
separated by a tab character.
--filter-1000bp Whether to filter out variants that occur within
1000bp of each other. Usually indicates a mapping
error.
Input
The scripts expect a folder of individual breseq runs, with each folder named after the isolate/sample.
The scipts only require the output.vcf, annotated.gd, and index.html files located in each folder.
Example folder:
.breseq_folder
|-- sample1
| |-- data
| | |-- output.vcf
| |-- output
| | |-- index.html
| | |-- evidence
| | | |-- annotated.gd
|-- sample2
| |-- data
| | |-- output.vcf
| |-- output
| | |-- index.html
| | |-- evidence
| | | |-- annotated.gd
|-- sample3
| |-- data
| | |-- output.vcf
| |-- output
| | |-- index.html
| | |-- evidence
| | | |-- annotated.gd
Output
The scripts generate an excel file in the breseq run folder with 4 sheets: comparison, variant, coverage, and junction.
The variant, coverage, and junction tables are just the concatenated tables of all samples in the breseq run.
Comparision table
A table in which every row represents a single mutation seen in the sample callset and samples are represented by columns with the alternate sequence for each sample.
| Sample1 | Sample2 | Sample3 | annotation | description | gene | locusTag | mutationCategory | position | presentIn | presentInAllSamples | ref | seq id |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| GG | GG | GG | intergenic (+65/+20) | putative lipoprotein/putative hydrolase | PFLU0045 - / - PFLU0046 | PFLU0045/PFLU0046 | small_indel | 45881 | 3 | 1 | G | NC_012660 |
| CC | CC | CC | intergenic (+17/-136) | microcin-processing peptidase 1. Unknown type peptidase. MEROPS family U62/hypothetical protein | PFLU0872 - / - PFLU0873 | PFLU0872/PFLU0873 | small_indel | 985333 | 3 | 1 | C | NC_012660 |
| intergenic (+57/+21) | hypothetical protein/putative helicase | PFLU3154 - / - PFLU3155 | PFLU3154/PFLU3155 | small_indel | 3447986 | 3 | 1 | NC_012660 | ||||
| A | A | G | M350I (ATG-ATA) | putative GGDEF domain signaling protein | PFLU3571 - | PFLU3571 | snp_nonsynonymous | 3959631 | 2 | 0 | G | NC_012660 |
| A | A | C | T238P (ACC-CCC) | hybrid sensory histidine kinase in two-component regulatory system with UvrY | PFLU3777 - | PFLU3777 | snp_nonsynonymous | 4173231 | 1 | 0 | A | NC_012660 |
| G | G | GG | coding (322/1476 nt) | putative two-component system response regulator nitrogen regulation protein NR(I) | PFLU4443 - | PFLU4443 | small_indel | 4908233 | 1 | 0 | G | NC_012660 |
Aligned fasta files
The scripts also generates 3 fasta files (breseq.snp.fasta, breseq.amino.fasta, breseq.codon.fasta)
with all nonsynonymous snps from each sample represented by the replacement bases, amino acids, and codons.
Example:
>reference
GA
>Sample1
AA
>Sample2
AA
>Sample3
GC
