Sequence lengths

table · content hash f218bee2620f5a308facbbc0e2ba99f22515e2395937fbb156723b0d093115e3 · pid local:f218bee2620f5a30

header	length
pdi2001denovo	1,124
pdi2002denovo	610
pdi2003denovo	912
pdi2004denovo	1,570
pdi2005denovo	836
pdi2006denovo	750
pdi2007denovo	1,198
pdi2008denovo	1,090
pdi2009denovo	615
pdi2010denovo	913

Sequence lengths Length of every sequence in the input.

Methods

Data were processed with the IoSCore components FileSource 0.2.0 (filePath = data/experimental/fasta/00010.fasta, chunkSize = 65536; 1 out), then FASTAReader 0.2.0 (strict = true; 1 in, 10 out), then SequenceLengths 0.1.0 (default parameters; 10 in, 10 out), then TableArtefact 0.1.0 (title = Sequence lengths, caption = Length of every sequence in the input.; 10 in), then FigureArtefact 0.1.0 (title = Length distribution, type = histogram, x = length, bins = 10, width = 640, height = 400; 10 in), using IoSCore 0.3.0 on Node v20.19.1 (darwin arm64), run on 2026-10-25T11:28:10.059Z. Input: data/experimental/fasta/00010.fasta. Element types were validated at every component boundary (sample, 4 elements).

Inputs

experimental/fasta/00010.fasta — FASTA · md5 1d40751347614fcc54bd96ff15b5f485 · licence: unknown — to be confirmed by the contributor · unknown until 2027-01-31
Small transcript set and its annotation / renaming map (pre-restructure data/README.md). Ten de novo-assembled transcripts (pdi2001denovo … pdi2010denovo, 610–1570 nt) sampled from a plant (Liliopsida) de novo transcriptome assembly; the same assembly (Transcript_2002 = pdi2002denovo, see map_00010.tab) is the reference of experimental/sam/SAMsample.sam. Query file of the blastx run recorded in 00010.complete.tab.

Credits

Data curation: Jens Allmer
Software: Jens Allmer

Reproduce

Workflow Sequence lengths of a FASTA file: table and histogram · document hash 904dcb45448d… · endpoint table · open workflow

Workflow document

{
  "description": "Reads a FASTA file, turns every record into a row { header, length } and ends in two endpoints (ADR 0013): a table of the lengths and a histogram of their distribution. Run with: node bin/ios.js run-workflow src/workflows/examples/fasta-lengths-report.workflow.json --set in.filePath=data/experimental/fasta/00010.fasta --artefacts <dir>",
  "edges": [
    {
      "from": "in",
      "to": "parse"
    },
    {
      "from": "parse",
      "to": "lengths"
    },
    {
      "from": "lengths",
      "to": "table"
    },
    {
      "from": "lengths",
      "to": "figure"
    }
  ],
  "name": "Sequence lengths of a FASTA file: table and histogram",
  "nodes": [
    {
      "id": "in",
      "params": {
        "filePath": "data/experimental/fasta/00010.fasta"
      },
      "type": "FileSource"
    },
    {
      "id": "parse",
      "type": "FASTAReader"
    },
    {
      "id": "lengths",
      "type": "SequenceLengths"
    },
    {
      "id": "table",
      "params": {
        "caption": "Length of every sequence in the input.",
        "title": "Sequence lengths"
      },
      "type": "TableArtefact"
    },
    {
      "id": "figure",
      "params": {
        "bins": 10,
        "title": "Length distribution",
        "type": "histogram",
        "x": "length"
      },
      "type": "FigureArtefact"
    }
  ],
  "schema": "ioscore/workflow/1"
}

Execution record (JSON)

{
  "schema": "ioscore/execution-record/1",
  "name": "Sequence lengths of a FASTA file: table and histogram",
  "ioscore": "0.3.0",
  "node": "v20.19.1",
  "platform": "darwin arm64",
  "startedAt": "2026-10-25T11:28:10.059Z",
  "finishedAt": "2026-10-25T11:28:10.066Z",
  "inputs": [
    "data/experimental/fasta/00010.fasta"
  ],
  "steps": [
    {
      "type": "FileSource",
      "version": "0.2.0",
      "params": {
        "filePath": "data/experimental/fasta/00010.fasta",
        "chunkSize": 65536
      },
      "stats": {
        "out": 1
      },
      "origin": "core"
    },
    {
      "type": "FASTAReader",
      "version": "0.2.0",
      "params": {
        "strict": true
      },
      "stats": {
        "in": 1,
        "out": 10,
        "dropped": 0
      },
      "origin": "core"
    },
    {
      "type": "SequenceLengths",
      "version": "0.1.0",
      "params": {},
      "stats": {
        "in": 10,
        "out": 10,
        "dropped": 0
      },
      "origin": "core"
    },
    {
      "type": "TableArtefact",
      "version": "0.1.0",
      "params": {
        "title": "Sequence lengths",
        "caption": "Length of every sequence in the input.",
        "columns": []
      },
      "stats": {
        "in": 10
      },
      "origin": "core"
    },
    {
      "type": "FigureArtefact",
      "version": "0.1.0",
      "params": {
        "title": "Length distribution",
        "caption": "",
        "type": "histogram",
        "x": "length",
        "y": "",
        "bins": 10,
        "width": 640,
        "height": 400
      },
      "stats": {
        "in": 10
      },
      "origin": "core"
    }
  ],
  "qc": {
    "level": "sample",
    "sample": 100,
    "checked": 4,
    "violations": [],
    "edges": 4
  }
}