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Clarify fasta header naming with uc to biom #3
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Hi, good question. You need a string in the fasta header that includes:
where ‘cp83’ is the sample ID. This formatting comes from the Jon On Aug 22, 2016, at 1:25 PM, sacha schutz <notifications@github.com mailto:notifications@github.com> wrote:
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Hi, I have an .uc file that is in the format below:
I get the following error: Error in uc file formating. Check for spaces in sample IDs and to make sure there is a semicolon after sample IDs. I'm finding it hard to convert the .uc file to otu table txt file. Would you be please able to modify the script, create_otu_table_from_uc_file.py for user-specific needs? Any help will be much appreciated, thanks in advance. |
I trying to do a simple test , but I don't understand how fasta header are proccess.
For exemple, I have One sample test.fa with the following reads :
I cluster them using :
vsearch --cluster_fast test.fa --id 0.97 --centroids centroids.fa --sizeout --uc test.uc --relabel_sha1 --relabel_keep
Now I want to convert them to biom using your script :
python create_otu_table_from_uc_file.py -i test.uc -o test.biom
I get the following error :
I thinks fasta header should keep a rule, but I don't know how... Could you make me a simple exemple to make me understand ?
Thanks
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