Open jolo2486 opened 1 year ago
I have loaded a few example gzipped fasta files, e.g. the following one: hgdownload.cse.ucsc.edu/goldenPath/dm6/bigZips/dm6.fa.gz
hgdownload.cse.ucsc.edu/goldenPath/dm6/bigZips/dm6.fa.gz
I can load it, iterate and so on, and:
fasta = pyfastx.Fasta(./data/genomes/dm6.fa.gz) fasta[0] Out[49]: <Sequence> chr2L with length of 23513712
but
fasta['chr2L'] KeyError: 'chr2L does not exist in fasta file'
Also:
keys = fasta.keys() keys[0] Out[57]: 'chr2L'
fasta[keys[0]] KeyError: 'chr2L does not exist in fasta file'
I sincerely hope that I have not misunderstood anything, I went by what was listed in the docs:
>>> # get sequence like dictionary >>> s1 = fa['JZ822577.1'] >>> s1 <Sequence> JZ822577.1 with length of 333
I am in a conda environment, and installed pyfastx 0.9.1 using pip.
Try the latest version 1.0.0. We have fixed this issue.
I have loaded a few example gzipped fasta files, e.g. the following one:
hgdownload.cse.ucsc.edu/goldenPath/dm6/bigZips/dm6.fa.gz
I can load it, iterate and so on, and:
but
Also:
but
I sincerely hope that I have not misunderstood anything, I went by what was listed in the docs:
I am in a conda environment, and installed pyfastx 0.9.1 using pip.