ROTLA (Reader of the Lost Arcs)

ROTLA (Reader of the Lost Arcs) is a Python package that applies a split-read approach to detect deletions in mitochondrial genomes.

Requirements

ROTLA was developed using Python 2.7.13. In addition to requirements specified in setup.py, ROTLA requires installation of the BLAT command-line alignment utility. BLAT binaries may be downloaded from the UCSC Genome Browser here:

• UCSC Utilities Download Page

Installation

The location of the BLAT executable must be specified prior to installation. To do this, manually edit the path in paths.cfg using a text editor.

After the path has been set, install ROTLA using:

python setup.py install

Users without administrative privileges may install ROTLA in their home directories by appending '--user' to the command above. The ROTLA package can then be executed as ${HOME}/.local/bin/ROTLA, or simply, ROTLA, provided the user adds the location ${HOME}/.local/bin to their PATH environment variable.

Usage

Muliple functions are accessible using ROTLA's command line interface. General usage is as follows:

ROTLA COMMAND [OPTIONS] [ARGS]...

Available commands:

• compile_breakpoint_results
• find_breakpoints
• get_aligned_bases

compile_breakpoint_results

ROTLA compile_breakpoint_results [OPTIONS] LIST_FILE_NAME OUTPUT_FILE_NAME

Given a list of breakpoint files, create a composite table containing counts for all observed breakpoints in all files. The input list file must contain two tab-separated columns with no header line. Entries in column 1 should identify the name of a breakpoint file and entries in column 2 should specify the corresponding name to be written to the header line in the output file. See example_list.txt in the docs folder for an illustration of this format.

find_breakpoints

ROTLA find_breakpoints [OPTIONS] READ_1_FASTQ_FILE READ_2_FASTQ_FILE REFERENCE_SEQUENCE OUTPUT_PREFIX

Given a set of paired-end FASTQ files and FASTA reference sequence, identify breakpoint coordinates and determine count of supporting reads. This command will produce the following output files, with each name below preceded by the provided OUTPUT_PREFIX:

• OUTPUT_PREFIX.read_1.psl

Output of Read 1 FASTQ blat alignment in psl format

• OUTPUT_PREFIX.read_2.psl

Output of Read 2 FASTQ blat alignment in psl format

• OUTPUT_PREFIX.read_1.blat.out

Content written to STDOUT during Read 1 blat alignment

• OUTPUT_PREFIX.read_2.blat.out

Content written to STDOUT during Read 2 blat alignment

• OUTPUT_PREFIX.breakpoints.txt

Tab-delimited table of breakpoint start coordinates, end coordinates, and counts of supporting reads

Options

• --length INTEGER

Minimum required alignment length, default = 25

get_aligned_bases

ROTLA get_aligned_bases [OPTIONS] INPUT_FILE_PREFIX REFERENCE_SEQUENCE

Given a pair of PSL files produced using find_breakpoints and the FASTA reference sequence, this command will determine the total count of aligned bases and print this value to an output file named INPUT_PREFIX.aligned_bases.txt. To allow aligned base counts of many samples to be easily combined, this output file utlizes a two-column tab-delimited format where the first contains the input file prefix and the second contains the count itself.

Authors

ROTLA was conceptualized by Christopher Lavender and Scott Lujan. ROTLA was written by Christopher Lavender and Adam Burkholder.

License

This project is licensed under the MIT License. See LICENSE for details.