Ali2D

The following packages are currently included:

prepare

Build with:

cd prepare
go build

which will build the prepare executable. It reflects the functionality of the former prepareAli2D.jar.

Example call

The call ./prepare tcoffee_alignment_7956270.fasta 50 output.json has produced the following JSON:

[
  {
    "sequenceFile": "/home/lukas/repos/ali2d/prepare/tcoffee_alignment_7956270.fasta.0.fas",
    "coveredBy": "/home/lukas/repos/ali2d/prepare/tcoffee_alignment_7956270.fasta.4.fas",
    "sequenceIdentity": 78.1021897810219
  },
  {
    "sequenceFile": "/home/lukas/repos/ali2d/prepare/tcoffee_alignment_7956270.fasta.1.fas",
    "coveredBy": "/home/lukas/repos/ali2d/prepare/tcoffee_alignment_7956270.fasta.4.fas",
    "sequenceIdentity": 80.2919708029197
  },
  {
    "sequenceFile": "/home/lukas/repos/ali2d/prepare/tcoffee_alignment_7956270.fasta.2.fas",
    "coveredBy": "/home/lukas/repos/ali2d/prepare/tcoffee_alignment_7956270.fasta.4.fas",
    "sequenceIdentity": 80.88235294117648
  },
  {
    "sequenceFile": "/home/lukas/repos/ali2d/prepare/tcoffee_alignment_7956270.fasta.3.fas",
    "coveredBy": "/home/lukas/repos/ali2d/prepare/tcoffee_alignment_7956270.fasta.4.fas",
    "sequenceIdentity": 70.8029197080292
  },
  {
    "sequenceFile": "/home/lukas/repos/ali2d/prepare/tcoffee_alignment_7956270.fasta.4.fas",
    "coveredBy": null,
    "sequenceIdentity": null
  },
  {
    "sequenceFile": "/home/lukas/repos/ali2d/prepare/tcoffee_alignment_7956270.fasta.5.fas",
    "coveredBy": "/home/lukas/repos/ali2d/prepare/tcoffee_alignment_7956270.fasta.4.fas",
    "sequenceIdentity": 67.62589928057554
  },
  {
    "sequenceFile": "/home/lukas/repos/ali2d/prepare/tcoffee_alignment_7956270.fasta.6.fas",
    "coveredBy": null,
    "sequenceIdentity": null
  }
]