geneCutterParser

Parses results HIV LANL Database Gene Cutter tool to get coordinates for potential alignments

Requirements:

• Check requirements.txt for installation dependencies
• Python 3+
• Requires BioPython=1.79

Steps:

1. Procure a fasta file of HIV sequences. Each fasta record should have an unique name. Fasta file should not be pre-aligned.
2. Submit fasta file to the (HIV LANL Gene Cutter tool)[https://www.hiv.lanl.gov/content/sequence/GENE_CUTTER/cutter.html] for HIV with the following settings:

• Uncheck "Input sequences are pre-aligned"
• Check "Do not translate"
• Keep all other default settings

3. After Gene Cutter is finished, download the compressed results.
4. Unzip/decompress the results file.
5. Run geneCutterParser (see below for arguments)

Example run

python parser.py --subjectSequences my.fasta --runID="A01" --geneCutterResults geneCutterResultsDirectory

Arguments

--subjectSequences

(required) Fasta file. HIV sequences used for input into Gene Cutter. Fasta record names must match original input. Fasta record IDs should not contain "HXB2" in its name.

--runID

(required) Run ID used to name output file.

--geneCutterResults

(required) Directory containing Gene Cutter Results (should be multiple .na.fasta files present).

--outputDir

(optional) Output folder. [defaults to current directory]

Output

TSV file (example shown below) with the following information:

• annotation: HIV gene/region
• startPos: start position on subject genome (0-indexing)
• endPos: end position on subject genome (0-indexing; inclusive)
• genome: name of genome as derived from --subjectSequences

annotation	startPos	endPos	genome
Pol	1311	4323	testGenome1
Pol	1311	4323	testGenome2
Genome	0	8917	testGenome1
Genome	0	8938	testGenome2
Genome	0	2616	testGenome3
Genome	0	2595	testGenome4