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It is not clear from specification whether the GFF3 file should be sorted by seqid or not if multiple seqid present in a file.
I received a file where it is not the case, e.g. first there are lines of type gene for multiple seqids and then multiple nRNA lines with the same set of seqids and with parents of the genes described above.
The reader I use (Sci-Kit Bio read function) reads each occurrence of seqid as new name. If specific sequence ID it provided, it reads only the first record (I presume because it encounters different seqid after that).
So, my problem is that because it is not specified, I cannot understand is it reader's behaviour incorrect or it is being strict and correct and the file itself is formatted incorrectly?
Thank you very much for clarification.
The text was updated successfully, but these errors were encountered:
Hello!
It is not clear from specification whether the GFF3 file should be sorted by
seqid
or not if multipleseqid
present in a file.I received a file where it is not the case, e.g. first there are lines of type
gene
for multipleseqid
s and then multiple nRNA lines with the same set ofseqid
s and with parents of the genes described above.The reader I use (Sci-Kit Bio
read
function) reads each occurrence ofseqid
as new name. If specific sequence ID it provided, it reads only the first record (I presume because it encounters differentseqid
after that).So, my problem is that because it is not specified, I cannot understand is it reader's behaviour incorrect or it is being strict and correct and the file itself is formatted incorrectly?
Thank you very much for clarification.
The text was updated successfully, but these errors were encountered: