Note: This repo is under active development. So it'll be changing a lot

any2tsv

Convert various bioinformatic outputs to TSV

Motivation

Well you see I have this pipeline called Bactopia for the analysis of bacterial genomes, and it produces a lot of output files. I started making parsers for these outputs, but I didn't want them to be hidden in Bactopia. Instead, I wanted create a simple tool (e.g. Torsten Seemann's any2fasta) the community could use.

Although, please keep in mind, unless there are outside contributions, the available parsers will be reflective of tools I use in Bactopia. I frankly don't have the bandwidth to expand further. But, please don't worry, if you would like to add a parser for a tool that you use, by all means lets get it added!

Installation

I'm too early in the game for this, but you can expect it to be available from pip and Bioconda in due time.

Usage

```{bash} any2tsv --help

Usage: any2tsv [OPTIONS]

╭─ Options ────────────────────────────────────────────────────────────────────────────────────────╮ │ --version Show the version and exit. │ │ --list_tools List tools with an available parser. │ │ --help -h Show this message and exit. │ ╰──────────────────────────────────────────────────────────────────────────────────────────────────╯

```

Example Usage

fastq-scan

Let's start with fastq-scan, which is a simple tool to output FASTQ summary statistics in JSON format. Because its already in JSON format, this is an easy conversion to TSV.

Example fastq-scan Output

```{bash} cat fastq-scan.json { "qcstats": { "totalbp":7500, "coverage":0.05, "readtotal":75, "readmin":100, "readmean":100, "readstd":0, "readmedian":100, "readmax":100, "read25th":100, "read75th":100, "qualmean":34.0267, "qualstd":0.711306, "qualmedian":34, "qual25th":34, "qual75th":34 }, "readlengths": {

    "100":75
},
"per_base_quality": {
    "1":30.7467,        "2":31.5467,        "3":31.5467,        "4":35.44,        "5":34.24,
    "6":34.12,        "7":34.7067,        "8":34.24,        "9":36.9333,        "10":37.0667,
    "11":35.88,        "12":36.0667,        "13":36.72,        "14":38.2667,        "15":37.48,
    "16":38.2133,        "17":36.7467,        "18":37.8267,        "19":36.3333,        "20":37.2933,
    "21":37.9867,        "22":37.1067,        "23":37.4133,        "24":38.2667,        "25":36.6133,
    "26":36.2,        "27":36.3067,        "28":35.8533,        "29":36.5067,        "30":37.72,
    "31":37.3333,        "32":36.0133,        "33":37.4933,        "34":36.1067,        "35":36.76,
    "36":34.8533,        "37":36.3733,        "38":35.1867,        "39":36.0133,        "40":35.3067,
    "41":35.6,        "42":36.7867,        "43":35.52,        "44":37.3333,        "45":36.6533,
    "46":36.8,        "47":35.9867,        "48":35.4533,        "49":35.2,        "50":37.2533,
    "51":35.04,        "52":36,        "53":35.28,        "54":36.16,        "55":35.2,
    "56":33.6133,        "57":36.0533,        "58":34.4533,        "59":35.88,        "60":35.3733,
    "61":35.6933,        "62":34.8267,        "63":35.1067,        "64":35.2933,        "65":32.2667,
    "66":34.4267,        "67":33.9333,        "68":33.6667,        "69":32.6133,        "70":33.4267,
    "71":32.8267,        "72":32.96,        "73":33.5467,        "74":33.1067,        "75":31.8667,
    "76":30.72,        "77":30.6133,        "78":30.2133,        "79":31.7467,        "80":33.8933,
    "81":32.72,        "82":33.1733,        "83":31.5867,        "84":32.6933,        "85":32.0667,
    "86":32.2933,        "87":30.7467,        "88":30.6933,        "89":32.48,        "90":31.08,
    "91":31.6133,        "92":31.72,        "93":30.3867,        "94":30.7067,        "95":29.9733,
    "96":31.96,        "97":32.44,        "98":30.2267,        "99":31.2533,        "100":30.2267
}

} ```

Converting fastq-scan to TSV

{bash} any2tsv fastq-scan fastq-scan.json filename total_bp coverage read_total read_min read_mean read_std read_median read_max read_25th read_75th qual_mean qual_std qual_median qual_25th qual_75th fastq-scan.json 7500 0.05 75 100 100 0 100 100 100 100 34.0267 0.711306 34 34 34

You might be wondering, Where'd the read lengths and per-base qualities go?. Well, honestly, I didn't think they were useful in TSV format, so out they went! But, if for some reason you think they would be useful, please let me know.

Naming

I think its pretty obvious, but the name any2tsv is inspired by Torsten Seemann's any2fasta. any2fasta converts many different formats to FASTA format. I wanted to do the same except TSV outputs. These TSV outputs can then be easily manipulated by the user.

Author

• Robert A. Petit III
• Web: https://www.robertpetit.com
• Twitter: @rpetit3