There seems to be a bug with getof where it will not preserve the full identifier. This does not occur with fastq files from what I can see.
For example
==> my.fasta <==
>M02261:10:000000000-A648D:1:1101:15313:1016
==> test.fasta <==
>1021_1 [1 - 114]
This results in orf_filter breaking down as it cannot find the original sequence identifier to extract from the input read file.
This usually is not an issue as step1 converts all identifiers into sequential integers, but it is a case that needs to be fixed so the tests run as well as allowing for orf_filter to run by itself.
There seems to be a bug with getof where it will not preserve the full identifier. This does not occur with fastq files from what I can see.
For example
This results in orf_filter breaking down as it cannot find the original sequence identifier to extract from the input read file.
This usually is not an issue as step1 converts all identifiers into sequential integers, but it is a case that needs to be fixed so the tests run as well as allowing for orf_filter to run by itself.