update

downloads-generation/data_curated/GENERATE.sh

@@ -18,8 +18,8 @@ rm -rf "$SCRATCH_DIR/$DOWNLOAD_NAME"
 mkdir "$SCRATCH_DIR/$DOWNLOAD_NAME"
 
 # Send stdout and stderr to a logfile included with the archive.
-#exec >  >(tee -ia "$SCRATCH_DIR/$DOWNLOAD_NAME/LOG.txt")
-#exec 2> >(tee -ia "$SCRATCH_DIR/$DOWNLOAD_NAME/LOG.txt" >&2)
+exec >  >(tee -ia "$SCRATCH_DIR/$DOWNLOAD_NAME/LOG.txt")
+exec 2> >(tee -ia "$SCRATCH_DIR/$DOWNLOAD_NAME/LOG.txt" >&2)
 
 # Log some environment info
 date
@@ -42,10 +42,6 @@ done
 
 time python curate_by_pmid.py $CURATE_BY_PMID_ARGS --out curated.by_pmid.csv --debug
 
-exit 1
-
-
-
 # No mass-spec data
 time python curate.py \
     --data-iedb \

downloads-generation/data_published/GENERATE.sh

@@ -46,6 +46,15 @@ PMID=28832583
 mkdir -p raw/$PMID
 wget -q https://doi.org/10.1371/journal.pcbi.1005725.s002 -P raw/$PMID # data generated in this work
 wget -q https://doi.org/10.1371/journal.pcbi.1005725.s003 -P raw/$PMID # data reanalyzed in this work
+cd raw/$PMID
+unzip *.s002
+unzip *.s003
+mkdir saved
+mv Dataset*/Dataset*.txt saved
+rm -rf Dataset* *.s002 *.s003 _*
+mv saved/* .
+rmdir saved
+cd ../..
 
 # Bassani-Sternberg, ..., Mann Mol Cell Proteomics 2015 [PMID 25576301]
 PMID=25576301

mhcflurry/downloads.yml

@@ -46,7 +46,7 @@ releases:
               default: false
 
             - name: data_published
-              url: https://github.com/openvax/mhcflurry/releases/download/pre-1.4.0/data_published.20190920.tar.bz2
+              url: https://github.com/openvax/mhcflurry/releases/download/pre-1.4.0/data_published.20190924.tar.bz2
               default: false
 
             - name: data_curated