From 5028f2cade99fc68a479f52fc265253db174d545 Mon Sep 17 00:00:00 2001 From: Yancong Zhang Date: Sat, 10 Sep 2022 13:30:04 -0400 Subject: [PATCH] Updated demo results --- readme.md | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/readme.md b/readme.md index aa94a5e..2a386fe 100644 --- a/readme.md +++ b/readme.md @@ -278,7 +278,7 @@ Bacteroides_thetaiotaomicron Cluster_1024034 GO:0004673 GO 0.8 ... ``` -* The finalized prediction results using integrated evidence per taxon are in the file: `$OUTPUT_DIR/main/$TAXONNAME/prediction/finalized/$BASENAME.$TAXONNAME.finalized_ML.prediction.tsv`. +* The finalized prediction results using integrated evidence per taxon are in the file: `$OUTPUT_DIR/main/$TAXONNAME/$BASENAME.$TAXONNAME.finalized_ML.prediction.tsv`. * `$OUTPUT_DIR` = the output folder * `$TAXONNAME ` = taxon name * `$BASENAME` = the basename of output files @@ -373,14 +373,15 @@ Escherichia_coli Cluster_100559 GO:0003979 GO 0.34 0 * Predictions of each taxon * FUGAsseM predicts functions based on input evidence data. - * The finalized prediction results using integrated evidence per taxon are in the file: `$OUTPUT_DIR/main/$TAXONNAME/prediction/finalized/$BASENAME.$TAXONNAME.finalized_ML.prediction.tsv`. - * The prediction results by using individual evidence per taxon are in the file: `$OUTPUT_DIR/$TAXONNAME/prediction/$EVIDENCE_TYPE/$BASENAME.$TAXONNAME.$EVIDENCE_TYPE_ML.prediction.tsv` (where `$EVIDENCE_TYPE` = the basename of each evidence). + * The finalized prediction results using integrated evidence per taxon are in the file: `$OUTPUT_DIR/main/$TAXONNAME/$BASENAME.$TAXONNAME.finalized_ML.prediction.tsv`. + * The prediction results by using individual evidence per taxon are in the file: `$OUTPUT_DIR/$TAXONNAME/$BASENAME.$TAXONNAME.$EVIDENCE_TYPE_ML.prediction.tsv` (where `$EVIDENCE_TYPE` = the basename of each evidence). **4. Intermediate output files** * Preprocessing features of each taxon - * FUGAsseM preprocesses input evidence data and prepare feature tables for machine learning per taxon. Each type of features will be used to build a ML classifier. - * All intermediate results are in the folder per taxon: `$OUTPUT_DIR/main/$TAXONNAME/preprocessing/`. + * FUGAsseM preprocesses input evidence data and prepare feature tables for machine learning per taxon. Each type of features will be used to build a ML classifier. These input data are in the folder: `$OUTPUT_DIR/main/$TAXONNAME/data/`. + * All intermediate preprocessing results are in the folder: `$OUTPUT_DIR/main/$TAXONNAME/preprocessing/`. + * All intermediate prediction results are in the folder per taxon: `$OUTPUT_DIR/main/$TAXONNAME/prediction/`.