seqspec 0.0.0

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seqspec

seqspec is a machine-readable YAML file format for genomic library sequence and structure. It was inspired by and builds off of the Teichmann Lab Single Cell Genomics Library Structure by Xi Chen.

A list of seqspec examples for multiple assays can be found in the assays/ folder. Each spec.yaml describes the 5'->3' "Final library structure" for the assay. Sequence specification files can be formatted with the seqspec command line tool.

pip install git+https://github.com/sbooeshaghi/seqspec.git
seqspec format --help

Specification

Each assay is described by two objects: the Assay object and the Region object. A library is described by one Assay object and multiple (possibly nested) Region objects. The Region objects are grouped with a join operation and an order on the subRegions specified. A simple (but not fully specified example) looks like the following:

modalities:
    - Modality1
    - Modality2
assay_spec:
    - region_id: Modality1
      join:
          how: Union
          order: [Region2, Region1]
          regions:
              - region_id: Region1
                  ...
              - region_id: Region2
                  ...
    - region_id: Modality2
        ...

In order to catalogue relevant information for each library structure, multiple properties are specified for each Assay and each Region.

Assay object

Assays have the following structure:

---
"$schema": https://json-schema.org/draft/2020-12/schema
"$id": Assay.schema.yaml
title: Assay
description: A Assay of DNA
type: object
properties:
  name:
    description: The name of the assay
    type: string
  doi:
    description: the doi of the paper that describes the assay
    type: string
  description:
    description: A short description of the assay
    type: string
  modalities:
    description: The modalities the assay targets
    type: array
    items:
      type: string
  lib_struct:
    description: The link to Teichmann's libstructs page derived for this sequence
    type: string
  assay_spec:
    description: The spec for the assay
    type: array
    items:
      "$ref": "Region.schema.yaml"
required:
- name
- doi
- description
- modalities
- lib_struct

Region object

Regions have the following structure:

---
"$schema": https://json-schema.org/draft/2020-12/schema
"$id": Region.schema.yaml
title: Region
description: A region of DNA
type: object
properties:
  region_id:
    description: identifier for the region
    type: string
  sequence_type:
    description: The type of the sequence
    type: string
  sequence:
    description: The sequence
    type: string
  min_len:
    description: The minimum length of the sequence
    type: integer
    minimum: 0
    maximum: 2048
  max_len:
    description: The maximum length of the sequence
    type: integer
    minimum: 0
    maximum: 2048
  onlist:
    description: The file containing the sequence if seq_type = onlist
    type:
    - object
    - 'null'
    properties:
      filename:
        description: filename for the onlist
        type: string
      md5:
        description: md5sum for the file pointed to by filename
        type: string
  join:
    description: Join operator on regions
    type:
    - object
    - 'null'
    properties:
      how:
        description: How the regions will be joined
        type: string
      order:
        description: The order of the regions being joined
        type: array
        items:
          type: string
      regions:
        description: The regions being joined
        type: array
        items:
          "$ref": "#/$defs/region"
    required:
    - how
    - order
    - regions
required:
- region_id
- sequence_type
- sequence
- min_len
- max_len

Contributing

Thank you for wanting to improve seqspec. If you have a bug that is related to seqspec please create an issue. The issue should contain

• the seqspec command ran,
• the error message, and
• the seqspec and python version.

If you'd like to add assays sequence specifications or make modifications to the seqspec tool please do the following:

1. Fork the project.

# Press "Fork" at the top right of the GitHub page

2. Clone the fork and create a branch for your feature

git clone https://github.com/<USERNAME>/seqspec.git
cd seqspec
git checkout -b cool-new-feature

3. Make changes, add files, and commit

# make changes, add files, and commit them
git add path/to/file1.yaml path/to/file2.yaml
git commit -m "I made these changes"

4. Push changes to GitHub

git push origin cool-new-feature

5. Submit a pull request

If you are unfamilar with pull requests, you can find more information on the GitHub help page.