Editing FASTA files sporadically does not have effect.

[sfbrunner]

Hi there,
First of, thanks for writing pyfaidx, it's really useful to my work.
I am currently experiencing an issue where I try to replace a sequence fragment of a FASTA file and the replacement only takes place sporadically. Ie. I do the following:

fasta_connxn = pyfaidx.Fasta(fasta_path, mutable=True)
fasta_connxn[chrom][start:end] = 'NNNNNNNNNN'

Now if I check the file on disk, it does not contain the 'N's. If I then execute the same command again, it now does. Just appears as if the changes do not always take effect. Have you ever seen a similar error? Do you know a fix for this?
I am using bioconda pyfaidx version 0.4.8.1 py27_0.

Thanks!

[mdshw5]

This is expected behavior for the current version, since writes are not immediately flushed to disk and instead may be buffered. There shouldn't be much of a performance penalty to change this and make MutableFastaRecord flush writes. I'll make the change and release 0.4.8.4 shortly.

[mdshw5]

Thanks for reporting this, by the way!

[mdshw5]

The new version is available and hopefully meets your needs: https://pypi.python.org/pypi/pyfaidx

[sfbrunner]

Thanks for the rapid response, I'll give the new version a try!

[sfbrunner]

Btw: are you going to attend the Abcam Mutational Signatures conference in Boston this week?

[mdshw5]

No, but that looks like a worthwhile conference. I'll have to check it out for next year!