diff --git a/downloads-generation/allele_sequences/GENERATE.sh b/downloads-generation/allele_sequences/GENERATE.sh index d320ed9ab13b2ace1e65f12a5151ff99bd063df9..8b9f49292278906fdbca01e6259ace711d811a96 100755 --- a/downloads-generation/allele_sequences/GENERATE.sh +++ b/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 diff --git a/downloads-generation/allele_sequences/select_alleles_to_disambiguate.py b/downloads-generation/allele_sequences/select_alleles_to_disambiguate.py index 649df45b31d860df42d0d1275b6979b4cd811de1..cbee4a19a345e9b89a56413bddfaa9bae1eeadef 100644 --- a/downloads-generation/allele_sequences/select_alleles_to_disambiguate.py +++ b/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( diff --git a/mhcflurry/downloads.yml b/mhcflurry/downloads.yml index 16a4d83e5228119c5ae9078d02c5201f38709a9a..940e0a40baaea001a49cb8cb6639ed61b19ffbd1 100644 --- a/mhcflurry/downloads.yml +++ b/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