Sequence compostion

[kullrich]

Hi,

I am using angsd to produce fasta sequences, these are automatically gzipped fasta files.

If I open the fasta file with R-Biostrings the sequence compositon looks like this:

dna<-readDNAStringSet("WSBg.asm5.fa.gz")
> alphabetFrequency(dna[1])
            A        C        G        T M R W S Y K V H D B        N - + .
[1,] 53974765 37689595 37636633 53870814 0 0 0 0 0 0 0 0 0 0 11982472 0 0 0

However, for the same fasta.gz file the sequence composition with pyfastx looks like this:

fa=pyfastx.Fasta("WSBg.asm5.fa.gz")
s1=fa['chr1']
s1.composition
{'\x00': 162258284,
 'A': 8774131,
 'C': 5629514,
 'G': 5628512,
 'N': 4131093,
 'T': 8732745}

Could you please indicate what the '\x00' would mean?

Can it be that pyfastx can not correctly index read these gzipped files?

Thank you in anticipation

Best regards

Kristian

[lmdu]

Thanks. I will fix this bug

[lmdu]

Fixed in v2.1.0