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.

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