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read_seqs() function not working for me #171
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This is strange. Can you confirm that this returns a tibble with 6 rows: read_seqs(ex("emales/emales.fna")) If so, can you share your fasta file so I can have a look what's going wrong? |
I am having the same issue using the emales example data. The resulting tibble has no information in it:
Reading * file_id: emales [C:/Users/Dean Mckeown/AppData/Local/R/win-library/4.2/gggenomes/extdata/emales/emales.fna] |
Dear Markus,
Thank you so much for your reply. When I run
read_seqs(ex("emales/emales.fna")) the result is an empty tibble with four
columns. Same thing happens when I run the function on my fasta. I instead
managed to create a sequence track using read_fai(myfile.fasta.fai).
I have attached my fasta file.
Best,
Rikki
…On Thu, Dec 14, 2023 at 10:32 PM Markus J. Ankenbrand < ***@***.***> wrote:
This is strange. Can you confirm that this returns a tibble with 6 rows:
read_seqs(ex("emales/emales.fna"))
If so, can you share your fasta file so I can have a look what's going
wrong?
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Thank you for checking. I can reproduce the problem on my Windows machine. On Linux it works as expected. My first guess, line endings, does not seem to cause the issue. I'll dig into it. |
Sequences from fasta are internally processed by |
I think that I found a way around it.
# A tibble: 33 × 3 |
See my earlier post for the same solution :) |
|
I have attempted to create a seq track using the function read_seqs() with either my .fna or .gff3 file as argument. But in any case get an empty tibble as object. Meanwhile, using read_gff3() function with my .gff3 file works just fine.
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