workflow.py 0.1.0

A set of scripts to convert multiple breseq analyses together and highlight variabls of interest.

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