lib-jvm-blast

Warning

This repository has been migrated into the MultiBlast Monorepo Maven packages will continue to be published to this repository as per GitHub’s rules, however all future code updates will be published to the MultiBlast Monorepo.

Table of Contents

• Usage
• Default Values
• Validation
  • Field Level Validation
  • Config Level Validation

Library for parsing, serializing, and validating JSON BLAST+ cli configs.

Configs may be constructed or parsed from JSON and written out to several formats including a CLI call string.

Supports ncbi/blast 2.11.0, 2.12.0, and 2.13.0

Requires Java 16+.

Usage

Building a CLI Command

val config = Blast.blastn()

config.task      = BlastNTaskType.DiscontiguousMegablast
config.queryFile = "my-query.txt"
config.dbFile    = "my-blast-db"

config.toCliString() == "blastn -task 'dc-megablast' -query 'my-query.txt' -db 'my-blast-db'"

Serializing to JSON

val config = Blast.blastp()

config.task      = BlastPTaskType.BlastPFast
config.queryFile = "my-query.txt"
config.dbFile    = "my-blast-db"

config.toJson() == """
{
  "tool"   : "blastp",
  "-task"  : "blastp-fast",
  "-query" : "my-query.txt"
  "-db"    : "my-blast-db"
}
"""

Deserializing from JSON

val inputJson = """
{
  "tool"   : "blastx",
  "-task"  : "blastx-fast"
  "-query" : "my-query.txt"
  "-db"    : "my-blast-db"
}
"""

val config = Blast.blastx(inputJson) // or Blast.of(inputJson) if the tool is unknown.

assert(config.task == BlastXTaskType.BlastXFast)
assert(config.queryFile == "my-query.txt")
assert(config.dbFile == "my-blast-db")

Default Values

This library knows all the documented default values for all flags for each BLAST+ tool, and will omit those values from serialized forms. This is done to keep the serialized form of each config down to the bare minimum as the BLAST+ tools have a large number of flags and options.

Setting Default Values

val config = Blast.deltablast()

config.seg            = SegDelta.no()
config.gapTrigger     = 22.0
config.compBasedStats = CompBasedStatsDeltaValue.CompBasedStats

config.toCliString() == "deltablast"

config.toJson() == """
{
  "tool" : "deltablast"
}
"""

Validation

Field Level Validation

Each field that has a documented set or range of valid values validates the set value on construction, preventing an invalid flag being used when building a BLAST+ tool configuration.

If an invalid value is used when constructing a field, an IllegalArgumentException will be thrown.

val field = LineLength(-1) // Throws an exception

Config Level Validation

In addition to the field level validation, whole configs come with a validate method that builds a list of errors for flags that are incompatible with one another or require an additional flag that is missing.

This validation method returns a Map of all the errors encountered keyed on the name of the relevant flag.

val config = Blast.blastFormatter()

config.archive = "some-archive"
config.rid     = "some-request-id"

val errors = config.validate()

errors.toJson() == """
{
  "-archive" : [ "Incompatible with -rid" ],
  "-rid"     : [ "Incompatible with -archive" ]
}
"""