alejandrogzi/bed2gtf

A high-performance BED-to-GTF converter written in Rust

bed2gtf's Issues

TO DO: compressed input files

To be implemented in the next version.

*Also include version badge in README

isoform file not available

I don´t have an isoform.txt file, can I still convert bed to gtf?

why exon_number 0 existed/generated in gtf ?

Hi, this is a very useful tool, but i met some error here
I'm running in centos7 zsh:
bed2gtf --bed test.bed12 --isoforms test.isoform --output test.gtf
you could see many "exon_number 0" have been generated in output gtf
could you explanin why this happened?

-> % cat ./test.bed12
chrX 119786505 119791643 ENST00000361575.3 0 - 119786683 119791576 0 3 227,104,70, 0,3402,5068,
chrX 119786505 119791595 ENST00000468844.1 0 - 119791595 119791595 0 2 227,1688, 0,3402,
chrX 119786503 119787456 ENST00000477403.1 0 - 119787456 119787456 0 2 229,176, 0,777,

-> % cat test.isoform
ENSG00000198918.7 ENST00000477403.1
ENSG00000198918.7 ENST00000468844.1
ENSG00000198918.7 ENST00000361575.3

-> % cat test.gtf
#provider: bed2gtf
#version: 1.8.0
#contact: github.com/alejandrogzi/bed2gtf
#date: 2024-1-3
chrX bed2gtf gene 119786504 119791643 . - . gene_id "ENSG00000198918.7";
chrX bed2gtf transcript 119786504 119787456 . - . gene_id "ENSG00000198918.7"; transcript_id "ENST00000477403.1";
chrX bed2gtf exon 119786504 119786732 . - . gene_id "ENSG00000198918.7"; transcript_id "ENST00000477403.1"; exon_number "0"; exon_id "ENST00000477403.1.2";
chrX bed2gtf transcript 119786506 119791643 . - . gene_id "ENSG00000198918.7"; transcript_id "ENST00000361575.3";
chrX bed2gtf exon 119786506 119786732 . - . gene_id "ENSG00000198918.7"; transcript_id "ENST00000361575.3"; exon_number "0"; exon_id "ENST00000361575.3.3";
chrX bed2gtf three_prime_utr 119786506 119786683 . - 1 gene_id "ENSG00000198918.7"; transcript_id "ENST00000361575.3";
chrX bed2gtf transcript 119786506 119791595 . - . gene_id "ENSG00000198918.7"; transcript_id "ENST00000468844.1";
chrX bed2gtf exon 119786506 119786732 . - . gene_id "ENSG00000198918.7"; transcript_id "ENST00000468844.1"; exon_number "0"; exon_id "ENST00000468844.1.2";
chrX bed2gtf stop_codon 119786684 119786686 . - 0 gene_id "ENSG00000198918.7"; transcript_id "ENST00000361575.3"; exon_number "0"; exon_id "ENST00000361575.3.3";
chrX bed2gtf CDS 119786687 119786732 . - 1 gene_id "ENSG00000198918.7"; transcript_id "ENST00000361575.3"; exon_number "0"; exon_id "ENST00000361575.3.3";
chrX bed2gtf exon 119787281 119787456 . - . gene_id "ENSG00000198918.7"; transcript_id "ENST00000477403.1"; exon_number "1"; exon_id "ENST00000477403.1.1";
chrX bed2gtf exon 119789908 119790011 . - . gene_id "ENSG00000198918.7"; transcript_id "ENST00000361575.3"; exon_number "1"; exon_id "ENST00000361575.3.2";
chrX bed2gtf CDS 119789908 119790011 . - 0 gene_id "ENSG00000198918.7"; transcript_id "ENST00000361575.3"; exon_number "1"; exon_id "ENST00000361575.3.2";
chrX bed2gtf exon 119789908 119791595 . - . gene_id "ENSG00000198918.7"; transcript_id "ENST00000468844.1"; exon_number "1"; exon_id "ENST00000468844.1.1";
chrX bed2gtf exon 119791574 119791643 . - . gene_id "ENSG00000198918.7"; transcript_id "ENST00000361575.3"; exon_number "2"; exon_id "ENST00000361575.3.1";
chrX bed2gtf CDS 119791574 119791576 . - 0 gene_id "ENSG00000198918.7"; transcript_id "ENST00000361575.3"; exon_number "2"; exon_id "ENST00000361575.3.1";
chrX bed2gtf start_codon 119791574 119791576 . - 0 gene_id "ENSG00000198918.7"; transcript_id "ENST00000361575.3"; exon_number "2"; exon_id "ENST00000361575.3.1";
chrX bed2gtf five_prime_utr 119791577 119791643 . - 0 gene_id "ENSG00000198918.7"; transcript_id "ENST00000361575.3";

Output is not sorted

Even since gtfsort exists, user may want to receive an output nicely sorted. The computation cost is not that significant (~0.2 seconds).

How to do it: Implement an early ordering layer before converting lines into BedRecords.

Verbose does not include time units

In any given bed2gtf run, the logging info lacks time units:

2023-10-05T17:20:03.860Z INFO  [bed2gtf] Memory usage: 10.5582695 MB
2023-10-05T17:20:03.860Z INFO  [bed2gtf] Elapsed: 9.9935

should be:

2023-10-05T17:20:03.860Z INFO  [bed2gtf] Memory usage: 10.5582695 MB
2023-10-05T17:20:03.860Z INFO  [bed2gtf] Elapsed: 9.9935 secs

How to fix it: modify the formatted String in the logging function.