update allele_sequences download

downloads-generation/allele_sequences/GENERATE.sh

@@ -43,7 +43,10 @@ cp $SCRIPT_ABSOLUTE_PATH .
 # pseudosequences but have associated training data
 TRAINING_DATA="$(mhcflurry-downloads path data_curated)/curated_training_data.csv.bz2"
 
-python select_alleles_to_disambiguate.py "$TRAINING_DATA" --out training_data.alleles.txt
+python select_alleles_to_disambiguate.py \
+    "$TRAINING_DATA" \
+    --min-count 50 \
+    --out training_data.alleles.txt
 
 # Human
 wget -q ftp://ftp.ebi.ac.uk/pub/databases/ipd/imgt/hla/fasta/A_prot.fasta

downloads-generation/allele_sequences/select_alleles_to_disambiguate.py

@@ -17,7 +17,6 @@ parser.add_argument(
 parser.add_argument(
     "--min-count",
     type=int,
-    default=50,
     metavar="N",
     help="Keep only alleles with at least N measurements")
 parser.add_argument(

mhcflurry/downloads.yml

@@ -74,7 +74,7 @@ releases:
               default: false
 
             - name: allele_sequences
-              url: http://github.com/openvax/mhcflurry/releases/download/pan-dev1/allele_sequences.20190506.tar.bz2
+              url: https://github.com/openvax/mhcflurry/releases/download/1.4.0/allele_sequences.20191231.tar.bz2
               default: false
 
             - name: random_peptide_predictions