| Name | HIV-Isoform-filter JSON |
| Version |
1.0.2
JSON |
| download |
| home_page | |
| Summary | Filters .gtf file of suspected HIV isoforms and confirms the isoform identities |
| upload_time | 2023-12-26 20:34:16 |
| maintainer | |
| docs_url | None |
| author | Jessica Lauren ALbert |
| requires_python | >=3.11 |
| license | MIT License Copyright (c) 2023 Jessica Lauren Albert Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. |
| keywords |
hiv
isoforms
splicing
ont sequencing
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
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| coveralls test coverage |
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|
# 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
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"description": "# HIV Isoform Filter\n\nThis package takes a .gtf file of preliminarily filtered HIV transcripts from ONT sequencing\nand filters them to include only correctly assigned transcripts using the\nfollowing filters.\n- FILTER 1: only include class codes =, J, and m\n- FILTER 2: only include samples with end values >= min_end_bp and\n start values <= max_start_bp\n- FILTER 3: get rid of any samples with read errors/small gaps\n- FILTER 4: keep only correct Env samples\n- FILTER 5: keep only correct Nef samples(long samples added to possible_misassigned) \n- FILTER 6: keep only correct Rev samples(long samples added to possible_misassigned) \n- FILTER 7: keep only correct Tat samples(long samples added to possible_misassigned) \n- FILTER 8: keep only correct Vif samples\n- FILTER 9: keep only correct Vpr samples\n- FILTER 10: check possible_misassigned for partial splice compatibility\n (vif -> vpr -> unslpiced_tat -> env)\n\n> 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 [].\ntranscript 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]\n>exon entry = ref genome, analysis_pathway, exon, start, end, \".\", \"+\", \".\", [transcript id; gene id; exon number]\n\n## Installation\nFast install:\n\n pip install HIV_Isoform_Filter\n \n\n## Usage\n HIV Isoform Filter [options] input_file_name output_file_prefix ref_file_name\n\npositional arguments:\n input_file_name Designates input file to be filtered. This is required.\n output_file_prefix Designates output file prefix. This is required.\n 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.\n\noptions:\n| Arguement | Function |\n| ------ | ------ |\n|-h, --help | show this help message and exit |\n|-g value, --gap value|Sets gap tolerance. Default is 15.\n|-a value, --startBP value|Sets maximum starting bp. Default is 700.\n|-z value, --endBP value|Sets minimum ending bp. Default is 9500.\n|-l value, --lengthFS value|Sets maximum fully spliced transcript length. Default is 2100.\n|-n value, --NCE value|When set to True, csv file will have y/n columns for the precence of NCEs. Default is False.\n\n## License\n\nMIT - Copyright (c) 2023 Jessica Lauren Albert\n\n# HIV_Isoform_filter\n",
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