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tobiasgf / lulu

r package for post-clustering curation of amplicon next generation sequencing data (metabarcoding)
GNU Lesser General Public License v3.0
63 stars 17 forks source link

buildOTUtable_simple.sh missing from repo #3

Closed Talitrus closed 4 years ago

Talitrus commented 4 years ago

Hi Tobias,

I can't seem to find the script buildOTUtable_simple.sh in the provided CLI scripts. Am I missing something?

Best, Bryan

tobiasgf commented 4 years ago

Hi. Sorry. For some reason I cannot push my updates to GitHub at the moment. So I post the lines of code here. Just put it in a text file named buildOTUtable_simple.sh

!/bin/bash

FASTA=$1 SCRIPT="OTU_contingency_table_simple.py" STATS="${FASTA/.fas/.stats}" SWARMS="${FASTA/.fas/.swarms}" REPRESENTATIVES="${FASTA/.fas/.centroids}" UCHIME="${FASTA/.fas/.uchime}" OTU_TABLE="${FASTA/.fas/.otutable}"

"${SCRIPT}" \
"${REPRESENTATIVES}" \
"${STATS}" \
"${SWARMS}" \
"${UCHIME}" \
S[0-9][0-9][0-9]*.fas > "${OTU_TABLE}"