Update by aswathyseb on Tue Oct 24 21:36:16 EDT 2017 from MacBook-Air.local
@@ -18,11 +18,9 @@ RESULT_DIR=results
# Create reference sequence file.
mkdir -p $REF_DIR
blastdbcmd -entry 'all' -db ${FISH_DB}/fish -outfmt '%f' >${REF_DIR}/$REF_SEQ
-#python -m biostar.tools.classify.reference --ids $ACCESSION_LIST --sequence >${REF_DIR}/$REF_SEQ
# Create accession-taxid map.
blastdbcmd -entry 'all' -db ${FISH_DB}/fish -outfmt '%a,%T' |tr ',' '\t' >${REF_DIR}/$TAXA_MAP
-#python -m biostar.tools.classify.reference --ids $ACCESSION_LIST --taxid >${REF_DIR}/$TAXA_MAP
# Build centrifuge index.
cd $REF_DIR
@@ -33,7 +31,6 @@ cd ..
mkdir -p $RESULT_DIR
centrifuge -x ${REF_DIR}/$INDEX -U $INPUT_DATA --report-file ${RESULT_DIR}/report.txt -S ${RESULT_DIR}/classification.txt
-
# Register results to settings.index.
cp ${RESULT_DIR}/report.txt ${RESULT_VIEW}
