autometa.common.external package

Submodules

autometa.common.external.bedtools module

autometa.common.external.bowtie module

# License: GNU Affero General Public License v3 or later # A copy of GNU AGPL v3 should have been included in this software package in LICENSE.txt. Script containing wrapper functions for bowtie2.

autometa.common.external.bowtie.align(db: str, sam: str, fwd_reads: Optional[List[str]] = None, rev_reads: Optional[List[str]] = None, se_reads: Optional[List[str]] = None, cpus: int = 0, **kwargs) → str

Align reads to bowtie2-index db (at least one *_reads argument is required).

Parameters

  • db (str) – </path/to/prefix/bowtie2/database>. I.e. db.{#}.bt2

  • sam (str) – </path/to/out.sam>

  • fwd_reads (list, optional) – [</path/to/forward_reads.fastq>, …]

  • rev_reads (list, optional) – [</path/to/reverse_reads.fastq>, …]

  • se_reads (list, optional) – [</path/to/single_end_reads.fastq>, …]

  • cpus (int, optional) – Num. processors to use (the default is 0).

  • **kwargs (dict, optional) – Additional optional args to supply to bowtie2. Must be in format: key = flag value = flag-value

Returns

</path/to/out.sam>

Return type

str

Raises

ChildProcessError – bowtie2 failed

autometa.common.external.bowtie.build(assembly: str, out: str) → str

Build bowtie2 index.

Parameters

  • assembly (str) – </path/to/assembly.fasta>

  • out (str) – </path/to/output/database> Note: Indices written will resemble </path/to/output/database.{#}.bt2>

Returns

</path/to/output/database>

Return type

str

Raises

ChildProcessError – bowtie2-build failed

autometa.common.external.bowtie.main()
autometa.common.external.bowtie.run(cmd: str) → bool

Run cmd via subprocess.

Parameters

cmd (str) – Executable input str

Returns

True if no returncode from subprocess.call else False

Return type

bool

autometa.common.external.diamond module

autometa.common.external.hmmscan module

autometa.common.external.hmmsearch module

autometa.common.external.prodigal module

autometa.common.external.samtools module

Script containing wrapper functions for samtools

autometa.common.external.samtools.main()
autometa.common.external.samtools.sort(sam, bam, cpus=2)

Views then sorts sam file by leftmost coordinates and outputs to bam.

Parameters

  • sam (str) – </path/to/alignment.sam>

  • bam (str) – </path/to/output/alignment.bam>

  • cpus (int, optional) – Number of processors to be used. By default uses all the processors of the system

Raises

  • TypeError – cpus must be an integer greater than zero

  • FileNotFoundError – Specified path is incorrect or the file is empty

  • ExternalToolError – Samtools did not run successfully, returns subprocess traceback and command run

Module contents