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leffj / helper-code-for-uparse

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errors #1

Closed locon833 closed 9 years ago

locon833 commented 9 years ago

First, Can I directly enter the command "create_otu_table_from_uc_file.py' into the python terminal? It does not recognize it. Or do I enter the script under the document, if so, I get this error:

args = parser.parse_args() usage: [-h] -i INPUT_FP -o OUTPUT_FP : error: argument -i/--input_fp is required

I am new to this could you please help. I did not get the uc2otutable.py to work and this is my only option.

Thanks for your time

Nidhi

leffj commented 9 years ago

Hi Nidhi,

This should work, but you need to specify an input file path and an output file path. It should look something like this:

create_otu_table_from_uc_file.py -i readmap.uc -o otu_table.txt

It will also depend on how you demultiplexed your raw sequences. This script is meant to be used with another script in the package (prep_fast_for_uparse_paired.py).

Best, Jon

On Mar 3, 2015, at 2:28 PM, locon833 notifications@github.com wrote:

First, Can I directly enter the command "create_otu_table_from_uc_file.py' into the python terminal? It does not recognize it. Or do I enter the script under the document, if so, I get this error:

args = parser.parse_args() usage: [-h] -i INPUT_FP -o OUTPUT_FP : error: argument -i/--input_fp is required

I am new to this could you please help. I did not get the uc2otutable.py to work and this is my only option.

Thanks for your time

Nidhi

— Reply to this email directly or view it on GitHub https://github.com/leffj/helper-code-for-uparse/issues/1.