Metadata-Version: 2.4
Name: tRNAdecoder
Version: 1.1.2
Summary: Isodecoder level analysis for Nano-tRNAseq runs
Project-URL: Homepage, https://github.com/novoalab/tRNAdecoder
Project-URL: Issues, https://github.com/novoalab/tRNAdecoder/issues
Author-email: Leszek Pryszcz <lpyszcz@crg.es>
License-Expression: MIT
License-File: LICENSE
Keywords: Nano-tRNAseq,nanopore,tRNA
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Requires-Python: >=3.9
Requires-Dist: mappy==2.30
Requires-Dist: numpy
Requires-Dist: pysam
Description-Content-Type: text/markdown

# tRNAdecoder

Isodecoder level analysis for Nano-tRNAseq runs. 


## Installation

```bash
pip install tRNAdecoder
```

## Running it

### align
It accepts both, FastQ (can be gzippped) and SAM/BAM/CRAM files.
If SAM/BAM/CRAM is provided, it'll output all tags. 

It outputs sorted BAM.
Unmapped reads are not reported. 

```bash
s=sacCer3
ref=/no_backup/enovoa/reference_fasta/app/v1.1/$s.fa.gz
for f in /no_backup/enovoa/data/app/1.1/Laia_tRNA_sacCer3_rna004_fast_b13_10/AV_yeast_RAPPL_pilot/RNA260326_total/reads.bc_*.bam; do
    bc=$(basename $f|cut -f2 -d'.')
    runid=$(basename $(dirname $f))
    echo `date` $runid $bc
    tRNAdecoder align -v -f $ref -i $f -o test/$s/$runid/$bc.bam
done; date
```
