Package: workflow.py
isolate_parsersUsagepython 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.InputThe scripts expect a folder of individual breseq runs, with each folder named after the isolate/sample.
The scipts only require theoutput.vcf,annotated.gd, andindex.htmlfiles 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.gdOutputThe scripts generate an excel file in the breseq run folder with 4 sheets:comparison,variant,coverage, andjunction.
Thevariant,coverage, andjunctiontables are just the concatenated tables of all samples in the breseq run.Comparision tableA 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.Sample1Sample2Sample3annotationdescriptiongenelocusTagmutationCategorypositionpresentInpresentInAllSamplesrefseq idGGGGGGintergenic (+65/+20)putative lipoprotein/putative hydrolasePFLU0045 - / - PFLU0046PFLU0045/PFLU0046small_indel4588131GNC_012660CCCCCCintergenic (+17/-136)microcin-processing peptidase 1. Unknown type peptidase. MEROPS family U62/hypothetical proteinPFLU0872 - / - PFLU0873PFLU0872/PFLU0873small_indel98533331CNC_012660intergenic (+57/+21)hypothetical protein/putative helicasePFLU3154 - / - PFLU3155PFLU3154/PFLU3155small_indel344798631NC_012660AAGM350I (ATG-ATA)putative GGDEF domain signaling proteinPFLU3571 -PFLU3571snp_nonsynonymous395963120GNC_012660AACT238P (ACC-CCC)hybrid sensory histidine kinase in two-component regulatory system with UvrYPFLU3777 -PFLU3777snp_nonsynonymous417323110ANC_012660GGGGcoding (322/1476 nt)putative two-component system response regulator nitrogen regulation protein NR(I)PFLU4443 -PFLU4443small_indel490823310GNC_012660Aligned fasta filesThe 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