shenwei356/bio

A lightweight and high-performance bioinformatics package in Golang

Wei Shen 沈 伟

Bioinformatician
Institute for Viral Hepatitis, The Second Affiliated Hospital of Chongqing Medical University, China

Github | Twitter | Biostars | Google Scholar | ORCID

• 🔬 I’m currently working on microbial genomics and metagenomics.
• 🔭 I'm passionate about reproducible research and open-source software.

Learn more: http://shenwei.me

I'm grateful to users who have greatly helped to report bugs and suggest new features.
I may respond to issues or fix bugs quickly, but I usually implement new features periodically (two or more weeks).

bio's Issues

Support FASTA with both ">" and ";" label

add frameShiftingOptions to protein translation (seq.DNAToProtein)

see transeq as a reference

Six-frame_translation

add the ability to translate from rna to protein based on ncbi standards

https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=tgencodes#SG1

GuessQualityEncoding Panic issue.

Hello I'm running into an issue while creating a fastq validator using your fastx package. I've narrowed it down to my call to GuessQualityEncoding

panic: runtime error: index out of range

goroutine 1 [running]:
github.com/shenwei356/bio/seq.GuessQualityEncoding(0xc4207536d0, 0x4a, 0x4a, 0xc4205e0140, 0xc4205d0fc0, 0x31)
	/Users/srynobio1/go/src/github.com/shenwei356/bio/seq/qual.go:225 +0x308
main.main()
	/Users/srynobio1/Projects/goFqValidator/goFqValidator.go:61 +0x427
exit status 2

bio/seq/qual.go

Line 225 in 61346d8

if countSorted[i].Key == 'B' {

And here's the fastq record that the error occurs:

@HWI-ST0831_0238:5:1109:13365:88075#CTTGTACTTGTA/2
GGGGGCAGAACGGCCGACCGCCACCACAAGACATCCTGGGGGACAGAGGCCCTGGGCACAGCCCAGTCCCCATC
+
CCFFDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDCCD

Unable to parse protein fasta file.

I'm guessing your original design was focused on DNA sequence. Do you plan on supporting amino acid encoded fasta files?

panic: error when parsing seq: NP_000572.2 (seq: invalid Protein letter: U)

goroutine 1 [running]:
main.digestFasta(0x7ffeefbffb17, 0x2b, 0x18)
	/Users/srynobio1/go/src/github.com/srynobio/vmccl/vmccl.go:80 +0x38c
main.main()
	/Users/srynobio1/go/src/github.com/srynobio/vmccl/vmccl.go:28 +0x531

建.fai索引的时候，将 XM_005682112.1 处理为 XM_005682112，有意漏掉版本号？

https://github.com/shenwei356/bio/blob/master/seqio/fai/fai.go#L110

我发现建.fai索引的时候，将 XM_005682112.1 处理为 XM_005682112，是否有意这样？