Tabix¶

tabix · 1 contributor · 2 versions

tabix – Generic indexer for TAB-delimited genome position files

Tabix indexes a TAB-delimited genome position file in.tab.bgz and creates an index file (in.tab.bgz.tbi or in.tab.bgz.csi) when region is absent from the command-line. The input data file must be position sorted and compressed by bgzip which has a gzip(1) like interface.

After indexing, tabix is able to quickly retrieve data lines overlapping regions specified in the format “chr:beginPos-endPos”. (Coordinates specified in this region format are 1-based and inclusive.)

Fast data retrieval also works over network if URI is given as a file name and in this case the index file will be downloaded if it is not present locally.

Quickstart¶

from janis_bioinformatics.tools.htslib.tabix.tabix_1_9 import Tabix_1_9

wf = WorkflowBuilder("myworkflow")

wf.step(
    "tabix_step",
    Tabix_1_9(
        inp=None,
    )
)
wf.output("out", source=tabix_step.out)

OR

Install Janis
Ensure Janis is configured to work with Docker or Singularity.
Ensure all reference files are available:

Note

More information about these inputs are available below.

Generate user input files for tabix:

# user inputs
janis inputs tabix > inputs.yaml

inputs.yaml

inp: inp.gz

Run tabix with:

janis run [...run options] \
    --inputs inputs.yaml \
    tabix

Information¶

ID:	`tabix`
URL:	http://www.htslib.org/doc/tabix.html
Versions:	1.9, 1.2.1
Container:	quay.io/biocontainers/htslib:1.9–ha228f0b_7
Authors:	Michael Franklin
Citations:	None
Created:	2018-12-24
Updated:	2019-01-24

Outputs¶

name	type	documentation
out	Gzipped<File>

Additional configuration (inputs)¶

name	type	prefix	position	documentation
inp	Gzipped<File>		8	File from which to create the index. The input data file must be position sorted and compressed by bgzip which has a gzip(1) like interface.
preset	Optional<String>	–preset	2	-p: Input format for indexing. Valid values are: gff, bed, sam, vcf. This option should not be applied together with any of -s, -b, -e, -c and -0; it is not used for data retrieval because this setting is stored in the index file. [gff]
zeroBased	Optional<Boolean>	–zero-based	1	-0: Specify that the position in the data file is 0-based (e.g. UCSC files) rather than 1-based.
begin	Optional<Integer>	–begin	4	-b: Column of start chromosomal position. [4]
comment	Optional<String>	–comment	7	-c: Skip lines started with character CHAR. [#]
csi	Optional<Boolean>	–csi	1	-C: Produce CSI format index instead of classical tabix or BAI style indices.
end	Optional<Integer>	–end	5	-e: Column of end chromosomal position. The end column can be the same as the start column. [5]
force	Optional<Boolean>	–force	1	-f: Force to overwrite the index file if it is present.
minShift	Optional<Integer>	–min-shift	1	-m: set minimal interval size for CSI indices to 2^INT [14]
sequence	Optional<Integer>	–sequence	3	-s: Column of sequence name. Option -s, -b, -e, -S, -c and -0 are all stored in the index file and thus not used in data retrieval. [1]
skipLines	Optional<Integer>	–skip-lines	6	-S: Skip first INT lines in the data file. [0]
printHeader	Optional<Boolean>	–print-header	1	-h: Print also the header/meta lines.
onlyHeader	Optional<Boolean>	–only-header	1	-H: Print only the header/meta lines.
listChroms	Optional<Boolean>	–list-chroms	1	-l: List the sequence names stored in the index file.
reheader	Optional<File>	–reheader	1	-r: Replace the header with the content of FILE
regions	Optional<File>	–regions	11	-R: Restrict to regions listed in the FILE. The FILE can be BED file (requires .bed, .bed.gz, .bed.bgz file name extension) or a TAB-delimited file with CHROM, POS, and, optionally, POS_TO columns, where positions are 1-based and inclusive. When this option is in use, the input file may not be sorted.
targets	Optional<File>	–targets	11	-T: Similar to -R but the entire input will be read sequentially and regions not listed in FILE will be skipped

Workflow Description Language¶

version development

task tabix {
  input {
    Int? runtime_cpu
    Int? runtime_memory
    Int? runtime_seconds
    Int? runtime_disks
    File inp
    String? preset
    Boolean? zeroBased
    Int? begin
    String? comment
    Boolean? csi
    Int? end
    Boolean? force
    Int? minShift
    Int? sequence
    Int? skipLines
    Boolean? printHeader
    Boolean? onlyHeader
    Boolean? listChroms
    File? reheader
    File? regions
    File? targets
  }
  command <<<
    set -e
    cp -f '~{inp}' '.'
    tabix \
      ~{if (defined(zeroBased) && select_first([zeroBased])) then "--zero-based" else ""} \
      ~{if (defined(csi) && select_first([csi])) then "--csi" else ""} \
      ~{if (defined(force) && select_first([force])) then "--force" else ""} \
      ~{if defined(minShift) then ("--min-shift " + minShift) else ''} \
      ~{if (defined(printHeader) && select_first([printHeader])) then "--print-header" else ""} \
      ~{if (defined(onlyHeader) && select_first([onlyHeader])) then "--only-header" else ""} \
      ~{if (defined(listChroms) && select_first([listChroms])) then "--list-chroms" else ""} \
      ~{if defined(reheader) then ("--reheader '" + reheader + "'") else ""} \
      ~{if defined(select_first([preset, "vcf"])) then ("--preset '" + select_first([preset, "vcf"]) + "'") else ""} \
      ~{if defined(sequence) then ("--sequence " + sequence) else ''} \
      ~{if defined(begin) then ("--begin " + begin) else ''} \
      ~{if defined(end) then ("--end " + end) else ''} \
      ~{if defined(skipLines) then ("--skip-lines " + skipLines) else ''} \
      ~{if defined(comment) then ("--comment '" + comment + "'") else ""} \
      '~{basename(inp)}' \
      ~{if defined(regions) then ("--regions '" + regions + "'") else ""} \
      ~{if defined(targets) then ("--targets '" + targets + "'") else ""}
  >>>
  runtime {
    cpu: select_first([runtime_cpu, 1])
    disks: "local-disk ~{select_first([runtime_disks, 20])} SSD"
    docker: "quay.io/biocontainers/htslib:1.9--ha228f0b_7"
    duration: select_first([runtime_seconds, 86400])
    memory: "~{select_first([runtime_memory, 4])}G"
    preemptible: 2
  }
  output {
    File out = basename(inp)
    File out_tbi = basename(inp) + ".tbi"
  }
}

Common Workflow Language¶

#!/usr/bin/env cwl-runner
class: CommandLineTool
cwlVersion: v1.2
label: Tabix
doc: |-
  tabix – Generic indexer for TAB-delimited genome position files

  Tabix indexes a TAB-delimited genome position file in.tab.bgz and creates an index file (in.tab.bgz.tbi or
  in.tab.bgz.csi) when region is absent from the command-line. The input data file must be position sorted
  and compressed by bgzip which has a gzip(1) like interface.

  After indexing, tabix is able to quickly retrieve data lines overlapping regions specified in the format
  "chr:beginPos-endPos". (Coordinates specified in this region format are 1-based and inclusive.)

  Fast data retrieval also works over network if URI is given as a file name and in this case the
  index file will be downloaded if it is not present locally.

requirements:
- class: ShellCommandRequirement
- class: InlineJavascriptRequirement
- class: InitialWorkDirRequirement
  listing:
  - entry: $(inputs.inp)
- class: DockerRequirement
  dockerPull: quay.io/biocontainers/htslib:1.9--ha228f0b_7

inputs:
- id: inp
  label: inp
  doc: |-
    File from which to create the index. The input data file must be position sorted and compressed by bgzip which has a gzip(1) like interface.
  type: File
  inputBinding:
    position: 8
- id: preset
  label: preset
  doc: |-
    -p: Input format for indexing. Valid values are: gff, bed, sam, vcf. This option should not be applied together with any of -s, -b, -e, -c and -0; it is not used for data retrieval because this setting is stored in the index file. [gff]
  type: string
  default: vcf
  inputBinding:
    prefix: --preset
    position: 2
- id: zeroBased
  label: zeroBased
  doc: |-
    -0: Specify that the position in the data file is 0-based (e.g. UCSC files) rather than 1-based.
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --zero-based
    position: 1
- id: begin
  label: begin
  doc: '-b: Column of start chromosomal position. [4]'
  type:
  - int
  - 'null'
  inputBinding:
    prefix: --begin
    position: 4
- id: comment
  label: comment
  doc: '-c: Skip lines started with character CHAR. [#]'
  type:
  - string
  - 'null'
  inputBinding:
    prefix: --comment
    position: 7
- id: csi
  label: csi
  doc: '-C: Produce CSI format index instead of classical tabix or BAI style indices.'
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --csi
    position: 1
- id: end
  label: end
  doc: |-
    -e: Column of end chromosomal position. The end column can be the same as the start column. [5]
  type:
  - int
  - 'null'
  inputBinding:
    prefix: --end
    position: 5
- id: force
  label: force
  doc: '-f: Force to overwrite the index file if it is present.'
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --force
    position: 1
- id: minShift
  label: minShift
  doc: '-m: set minimal interval size for CSI indices to 2^INT [14]'
  type:
  - int
  - 'null'
  inputBinding:
    prefix: --min-shift
    position: 1
- id: sequence
  label: sequence
  doc: |-
    -s: Column of sequence name. Option -s, -b, -e, -S, -c and -0 are all stored in the index file and thus not used in data retrieval. [1]
  type:
  - int
  - 'null'
  inputBinding:
    prefix: --sequence
    position: 3
- id: skipLines
  label: skipLines
  doc: '-S: Skip first INT lines in the data file. [0]'
  type:
  - int
  - 'null'
  inputBinding:
    prefix: --skip-lines
    position: 6
- id: printHeader
  label: printHeader
  doc: '-h: Print also the header/meta lines.'
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --print-header
    position: 1
- id: onlyHeader
  label: onlyHeader
  doc: '-H: Print only the header/meta lines.'
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --only-header
    position: 1
- id: listChroms
  label: listChroms
  doc: '-l: List the sequence names stored in the index file.'
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --list-chroms
    position: 1
- id: reheader
  label: reheader
  doc: '-r: Replace the header with the content of FILE'
  type:
  - File
  - 'null'
  inputBinding:
    prefix: --reheader
    position: 1
- id: regions
  label: regions
  doc: |-
    -R: Restrict to regions listed in the FILE. The FILE can be BED file (requires .bed, .bed.gz, .bed.bgz file name extension) or a TAB-delimited file with CHROM, POS, and, optionally, POS_TO columns, where positions are 1-based and inclusive. When this option is in use, the input file may not be sorted.
  type:
  - File
  - 'null'
  inputBinding:
    prefix: --regions
    position: 11
- id: targets
  label: targets
  doc: |-
    -T: Similar to -R but the entire input will be read sequentially and regions not listed in FILE will be skipped
  type:
  - File
  - 'null'
  inputBinding:
    prefix: --targets
    position: 11

outputs:
- id: out
  label: out
  type: File
  secondaryFiles:
  - pattern: .tbi
  outputBinding:
    glob: $(inputs.inp.basename)
    loadContents: false
stdout: _stdout
stderr: _stderr

baseCommand: tabix
arguments: []

hints:
- class: ToolTimeLimit
  timelimit: |-
    $([inputs.runtime_seconds, 86400].filter(function (inner) { return inner != null })[0])
id: tabix