Create a conda environment with all dependencies:
conda create -n nif-finder_env -c conda-forge pandas numpy biopython joblib tqdm bioservices -y
$ python nif_finder.py --help
usage: nif_finder.py [-h] [-p PATH_PREMRNA] [-c PATH_CDS] [-o OUT_DIR]
[-n PROJECT_NAME] [-k KOZAK_TYPE]
[--tol_min_codons TOL_MIN_CODONS] [--tol_dej TOL_DEJ]
[--tol_window TOL_WINDOW] [--tol_long3utr TOL_LONG3UTR]
optional arguments:
-h, --help show this help message and exit
-p PATH_PREMRNA, --path_premrna PATH_PREMRNA
pre-mRNA .fasta filepath where exons are upper case and introns are lower case
-c PATH_CDS, --path_cds PATH_CDS
CDS .fasta filepath of upper case CDS sequences
-o OUT_DIR, --out_dir OUT_DIR
Path/to/existing-directory-for-output. Warning: Do not
use `~` to specify /home/[user]/. [Default: Current
directory]
-n PROJECT_NAME, --project_name PROJECT_NAME
Project name for files (no spaces). [Default: Date]
-k KOZAK_TYPE, --kozak_type KOZAK_TYPE
Stringency of kozak sequences ranging from 0 - 3. 0:
`ATG`; 1: `[A|G]..ATG or ATG[G]; 2: `[A|G]..ATG[G]; 3:
`[A|G].[C]ATG[G]. [Default: 1]
--tol_min_codons TOL_MIN_CODONS
Mimumum codons considered in output (not including
STOP) [Default: 10 codons]
--tol_dej TOL_DEJ Minimum distance between dEJ and termination codon
[Default: 55 nts]
--tol_window TOL_WINDOW
Number of nucleotides at the end of CDS to check GC-
Content
--tol_long3utr TOL_LONG3UTR
Minimum number of nucleotides to be considered a long
3'utr
- pre-mRNA sequences: Use
get_premrna_sequences_from_gtf.pyto generate a pre-mRNA fasta file with exons as upper case and introns as lower case.
python get_premrna_sequences_from_gtf.py -h
usage: get_premrna_sequences_from_gtf.py -a <assembly.fa[.gz]> -g <gene_models.gtf[.gz]> -o <output.fa>
Running: get_premrna_sequences_from_gtf.py v2022.01.05 via Python v3.8.5
optional arguments:
-h, --help show this help message and exit
-a ASSEMBLY, --assembly ASSEMBLY
path/to/assembly.fa[.gz]
-g GTF, --gtf GTF path/to/gene_models.gtf[.gz]
-o OUTPUT, --output OUTPUT
path/to/pre-mRNA.fa
# Usage:
python get_premrna_sequences_from_gtf.py -a Mus_musculus.GRCm39.dna.primary_assembly.fa.gz -g Mus_musculus.GRCm39.105.gtf.gz > Mus_musculus.GRCm39.105.gtf.premrna.fa
Reading: /Users/jespinoz/Documents/NMD/Mus_musculus.GRCm39/Mus_musculus.GRCm39.dna.primary_assembly.fa.gz: 61 sequence [00:33, 1.84 sequence/s]
Reading: /Users/jespinoz/Documents/NMD/Mus_musculus.GRCm39/Mus_musculus.GRCm39.105.gtf.gz: 100%|███████████████████████████████████████████████████████████████████████████████████████████████████████| 1866443/1866443 [00:08<00:00, 230844.77 line/s]
Merging exon sequences: 100%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 142435/142435 [00:22<00:00, 6230.19 transcript/s]
Writing pre-mRNA sequences: 100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 142435/142435 [00:06<00:00, 21961.93 sequence/s]
- CDS sequences: Download this from Ensemble and make sure it's the same build as the GTF used for pre-mRNA sequences.
BSD-3
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Espinoza, Josh L. (2022): NIF Finder. figshare. Software. https://doi.org/10.6084/m9.figshare.17775977.v1
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