python3 -> python in GENERATE.sh
@@ -45,7 +45,7 @@ cp $SCRIPT_ABSOLUTE_PATH .
# pseudosequences but have associated training data
TRAINING_DATA="$(mhcflurry-downloads path data_curated)/curated_training_data.csv.bz2"
-python3 select_alleles_to_disambiguate.py \
+python select_alleles_to_disambiguate.py \
"$TRAINING_DATA" \
--min-count 1000 \
--out training_data.alleles.txt
@@ -76,17 +76,17 @@ wget -q https://www.uniprot.org/uniprot/Q31151.fasta # H-2 Lq
# Various
wget -q ftp://ftp.ebi.ac.uk/pub/databases/ipd/mhc/MHC_prot.fasta
-python3 filter_sequences.py *.fasta --out class1.fasta
+python filter_sequences.py *.fasta --out class1.fasta
time clustalo -i class1.fasta -o class1.aligned.fasta
-time python3 make_allele_sequences.py \
+time python make_allele_sequences.py \
class1.aligned.fasta \
--recapitulate-sequences class1_pseudosequences.csv \
--differentiate-alleles training_data.alleles.txt \
--out-csv allele_sequences.csv
-time python3 make_allele_sequences.py \
+time python make_allele_sequences.py \
class1.aligned.fasta \
--recapitulate-sequences class1_pseudosequences.csv \
--out-csv allele_sequences.no_differentiation.csv
