HIV-Isoform-filter 1.0.2

Filters .gtf file of suspected HIV isoforms and confirms the isoform identities

HIV Isoform Filter

This package takes a .gtf file of preliminarily filtered HIV transcripts from ONT sequencing and filters them to include only correctly assigned transcripts using the following filters.

• FILTER 1: only include class codes =, J, and m
• FILTER 2: only include samples with end values >= min_end_bp and start values <= max_start_bp
• FILTER 3: get rid of any samples with read errors/small gaps
• FILTER 4: keep only correct Env samples
• FILTER 5: keep only correct Nef samples(long samples added to possible_misassigned)
• FILTER 6: keep only correct Rev samples(long samples added to possible_misassigned)
• FILTER 7: keep only correct Tat samples(long samples added to possible_misassigned)
• FILTER 8: keep only correct Vif samples
• FILTER 9: keep only correct Vpr samples
• FILTER 10: check possible_misassigned for partial splice compatibility (vif -> vpr -> unslpiced_tat -> env)

Note: This code currently relies on a very specific setup of the gtf file to work properly. The note must be in the order designated in the []. transcript entry = ref genome, analysis_pathway, transcript, start, end, ".", "+", ".", [transcript id; gene id; gene_name; xloc; ref_gene_id; contained_in; cmp_ref; class_code; tss_id] exon entry = ref genome, analysis_pathway, exon, start, end, ".", "+", ".", [transcript id; gene id; exon number]

Installation

Fast install:

pip install HIV_Isoform_Filter

Usage

HIV Isoform Filter [options] input_file_name output_file_prefix ref_file_name

positional arguments: input_file_name Designates input file to be filtered. This is required. output_file_prefix Designates output file prefix. This is required. ref_file_name Designates reference CDS file name. This should be a python file with only a dictionary with the splice donor sites, splice acceptor sites and gene CDS regions defined. This is required. An example is available in the test data set.

options:

Arguement	Function
-h, --help	show this help message and exit
-g value, --gap value	Sets gap tolerance. Default is 15.
-a value, --startBP value	Sets maximum starting bp. Default is 700.
-z value, --endBP value	Sets minimum ending bp. Default is 9500.
-l value, --lengthFS value	Sets maximum fully spliced transcript length. Default is 2100.
-n value, --NCE value	When set to True, csv file will have y/n columns for the precence of NCEs. Default is False.

License

MIT - Copyright (c) 2023 Jessica Lauren Albert

HIV_Isoform_filter