GetGeneLength Package
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Extract gene length based on featureCount calculation gene nonredundant exon length method.
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If you want to calculate TPM/FPKM/RPKM to visualize results and for other downstream analysis with only count matrix, you can use this GetGeneLength function to get gene length information and get normalized values.
Install
$ pip install GetGeneLength
# for lattest version
$ pip install GetGeneLength==0.0.3
Usage
help infomation:
$ GetGeneLength -h
usage: GetGeneLength --database ensembl --gtffile gencode.v38.annotation_human.gtf --lengthfile gene_length.txt
Get gene length from GTF annotation file.
optional arguments:
-h, --help show this help message and exit
-v, --version show program's version number and exit
-d {ucsc,ensembl,gencode}, --database {ucsc,ensembl,gencode}
which annotation database you choose. (default="ensembl")
-g GTFFILE, --gtffile GTFFILE
input your GTF file. (ucsc/ensembl/gencode)
-l LENGTH_INFO, --lengthfile LENGTH_INFO
output your gene lenth file. (gene_length.txt)
Thank your for your support, if you have any questions or suggestions please contact me: [email protected].
for ucsc gtf file:
$ GetGeneLength -d ucsc -g hg38.ncbiRefSeq.gtf -l ucsc_gene_length.txt
Your job is running, please wait...
Your job is done!
$ head -n 3 ucsc_gene_length.txt
TRNP TRNP 68
TRNT TRNT 66
CYTB CYTB 1141
for gencode/ensembl gtf file:
$ GetGeneLength -d gencode -g gencode.v38.annotation_human.gtf -l gene_length.txt
Your job is running, please wait...
Your job is done!
$ head -n 3 gene_length.txt
DDX11L1 ENSG00000223972.5 transcribed_unprocessed_pseudogene 1735
WASH7P ENSG00000227232.5 unprocessed_pseudogene 1351
MIR6859-1 ENSG00000278267.1 miRNA 68
2 Jul 30, 2022
9 Dec 28, 2022
3 Jun 7, 2022
276 Dec 30, 2022
133 Nov 13, 2022
26 Dec 5, 2022
1 Dec 21, 2021
1 Nov 27, 2021
1 Jan 23, 2022
3 Oct 27, 2022
16 Oct 13, 2022
22 Mar 17, 2022
1 Dec 24, 2021
0 Aug 24, 2022
2 Jan 18, 2022
4 May 16, 2022
2 Mar 19, 2022
8 Oct 14, 2022
4 Nov 28, 2021