`auto_process_ngs.indexes`

Provides a utility class IndexBuilder with methods for building indexes for various aligners:

There are also functions for constructing Command instances to run the appropriate index building commands:

class auto_process_ngs.indexes.IndexBuilder(runner, use_conda=False, conda_env_dir=None)

Utility class for building aligner indexes

Provides the following methods:

Parameters:

runner (JobRunner) – JobRunner instance that will be used to run the index command
use_conda (bool) – if True then try to use Conda to resolve the dependencies for building the indexes
conda_env_dir (str) – explicitly specify the directory to look for/create Conda environments in

STAR(fasta, annotation, out_dir, memory_limit=None, overhang=100, nthreads=None, star_version=None)

Build index for STAR

Parameters:

fasta (str) – path to Fasta file
annotation (str) – path to annotation file
out_dir (str) – path to output directory for index files
memory_limit (int) – specify memory limit (optional; default: no limit specified)
overhang (int) – specify overhang (default: 100)
nthreads (int) – specify number of threads to use when making index (defaults to the number defined in the job runner)
star_version (str) – specify the version of STAR to use (only if conda dependency resolution being used)

bowtie(fasta, out_dir, ebwt_basename=None, bowtie_version=None)

Build index for bowtie

Parameters:

fasta (str) – path to Fasta file
out_dir (str) – path to output directory for index files
ebwt_basename (str) – optional base name for the output index (.ebwt) files
bowtie_version (str) – specify the version of Bowtie to use (only if conda dependency resolution being used)

bowtie2(fasta, out_dir, bt2_basename=None, nthreads=None, bowtie2_version=None)

Build index for bowtie2

Parameters:

fasta (str) – path to Fasta file
out_dir (str) – path to output directory for index files
bt2_basename (str) – optional base name for the output index (.bt2) files
nthreads (int) – specify number of threads to use when making index (defaults to the number defined in the job runner)
bowtie2_version (str) – specify the version of Bowtie2 to use (only if conda dependency resolution being used)

auto_process_ngs.indexes.bowtie2_build_cmd(fasta, bt2_basename, nthreads=None)

Return command to run ‘bowtie2-build’

Argument:

fasta (str): path to input Fasta file bt2_basename (str): basename for output

‘bt2’ index files (can include a leading path)

nthreads (int): optional, specify the: number of threads to run ‘bowtie2-build’ with

Returns:

Return type:

Command

auto_process_ngs.indexes.bowtie_build_cmd(fasta, ebwt_basename)

Return command to run ‘bowtie-build’

Argument:: fasta (str): path to input Fasta file ebwt_basename (str): basename for output

‘ebwt’ index files (can include a leading path)

Returns:

Return type:

Command

auto_process_ngs.indexes.star_genome_generate_cmd(fasta, annotation, out_dir, overhang=None, nthreads=None, memory_limit=None)

Return command to run ‘STAR’ to build an index

Argument:

fasta (str): path to input Fasta file annotation (str): path to input annotation file out_dir (str): path to directory to write index

files into

auto_process_ngs.indexes