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‎.gitignore

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# egg-info
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src/swissisoform.egg-info
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# pycache
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src/swissisoform/__pycache__
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# data
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data/genome_data/hg38.fa
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data/genome_data/hg38.ncbiRefSeq.gtf
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data/ribosome_profiling

‎LICENSE

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MIT License
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Copyright (c) 2019, Massachusetts Institute of Technology All rights reserved.
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.

‎README.md

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# swissisoform
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# SwissIsoform
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Tool for analyzing and visualizing alternative protein isoforms from ribosome profiling data.
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## Installation
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```bash
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# Clone repository
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git clone https://github.com/cheeseman-lab/swissisoform.git
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cd swissisoform
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# Create conda environment
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conda env create --file=environment.yml
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# Activate environment
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conda activate swissisoform
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```
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## Data Requirements
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1. Reference genome (FASTA)
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2. Gene annotations (GTF)
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```bash
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# Move into genome_data folder
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cd data/genome_data
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# Download genome data
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sh download_genome.sh
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```
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3. Alternative start sites (BED)
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## Usage
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See `notebooks/visualize_isoforms.ipynb` for example usage.

‎data/genome_data/download_genome.sh

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#!/bin/bash
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UCSC_BASE="https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips"
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wget ${UCSC_BASE}/hg38.fa.gz
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wget ${UCSC_BASE}/genes/hg38.ncbiRefSeq.gtf.gz
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gunzip *.gz

‎environment.yml

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name: swissisoform
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channels:
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- conda-forge
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- bioconda
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- anaconda
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dependencies:
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- python=3.10
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- numpy
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- pandas
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- biopython
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- pip
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- matplotlib
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- pip:
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- -e .

‎notebooks/naxe_5utr_NM_144772.3_2.png

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‎notebooks/naxe_features.csv

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chromosome,source,feature_type,start,end,score,strand,frame,gene_id,transcript_id,,exon_number,exon_id,gene_name
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chr1_MU273335v1_fix,ncbiRefSeq.2022-10-28,exon,150333,150543,.,+,.,NAXE,NM_144772.3,,1,NM_144772.3.1,NAXE
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chr1_MU273335v1_fix,ncbiRefSeq.2022-10-28,5UTR,150333,150361,.,+,.,NAXE,NM_144772.3,,1,NM_144772.3.1,NAXE
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chr1_MU273335v1_fix,ncbiRefSeq.2022-10-28,CDS,150362,150543,.,+,0,NAXE,NM_144772.3,,1,NM_144772.3.1,NAXE
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chr1_MU273335v1_fix,ncbiRefSeq.2022-10-28,exon,150658,150766,.,+,.,NAXE,NM_144772.3,,2,NM_144772.3.2,NAXE
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chr1_MU273335v1_fix,ncbiRefSeq.2022-10-28,CDS,150658,150766,.,+,1,NAXE,NM_144772.3,,2,NM_144772.3.2,NAXE
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chr1_MU273335v1_fix,ncbiRefSeq.2022-10-28,exon,150922,151032,.,+,.,NAXE,NM_144772.3,,3,NM_144772.3.3,NAXE
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chr1_MU273335v1_fix,ncbiRefSeq.2022-10-28,CDS,150922,151032,.,+,0,NAXE,NM_144772.3,,3,NM_144772.3.3,NAXE
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chr1_MU273335v1_fix,ncbiRefSeq.2022-10-28,exon,151114,151227,.,+,.,NAXE,NM_144772.3,,4,NM_144772.3.4,NAXE
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chr1_MU273335v1_fix,ncbiRefSeq.2022-10-28,CDS,151114,151227,.,+,0,NAXE,NM_144772.3,,4,NM_144772.3.4,NAXE
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chr1_MU273335v1_fix,ncbiRefSeq.2022-10-28,exon,151965,152112,.,+,.,NAXE,NM_144772.3,,5,NM_144772.3.5,NAXE
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chr1_MU273335v1_fix,ncbiRefSeq.2022-10-28,CDS,151965,152112,.,+,0,NAXE,NM_144772.3,,5,NM_144772.3.5,NAXE
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chr1_MU273335v1_fix,ncbiRefSeq.2022-10-28,exon,152439,152856,.,+,.,NAXE,NM_144772.3,,6,NM_144772.3.6,NAXE
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chr1_MU273335v1_fix,ncbiRefSeq.2022-10-28,CDS,152439,152638,.,+,2,NAXE,NM_144772.3,,6,NM_144772.3.6,NAXE
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chr1_MU273335v1_fix,ncbiRefSeq.2022-10-28,3UTR,152642,152856,.,+,.,NAXE,NM_144772.3,,6,NM_144772.3.6,NAXE
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chr1_MU273335v1_fix,ncbiRefSeq.2022-10-28,start_codon,150362,150364,.,+,0,NAXE,NM_144772.3,,1,NM_144772.3.1,NAXE
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chr1_MU273335v1_fix,ncbiRefSeq.2022-10-28,stop_codon,152639,152641,.,+,0,NAXE,NM_144772.3,,6,NM_144772.3.6,NAXE

‎notebooks/naxe_transcript_NM_144772.3_2.png

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‎notebooks/test_line.gtf

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chr1_MU273335v1_fix ncbiRefSeq.2022-10-28 transcript 150333 152856 . + . gene_id "NAXE"; transcript_id "NM_144772.3"; gene_name "NAXE";

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