Build multi-segment ref to simulate reads from

.github/data/reads_to_simulate.csv

@@ -1,4 +1 @@
-HQ011408.1,.github/data/assemblies/HQ011408.1.fa
-CY014984.1,.github/data/assemblies/CY014984.1.fa
-NC026423.1,.github/data/assemblies/NC_026423.1.fa
-NC026431.1,.github/data/assemblies/NC_026431.1.fa
+MK58361X-H3N2,.github/data/assemblies/MK58361X-H3N2.fa

.github/scripts/download_assemblies.sh

@@ -2,7 +2,13 @@
 
 mkdir -p .github/data/assemblies
 
-curl -o .github/data/assemblies/HQ011408.1.fa "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?retmode=text&id=HQ011408.1&db=nucleotide&rettype=fasta"
-curl -o .github/data/assemblies/CY014984.1.fa "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?retmode=text&id=CY014984.1&db=nucleotide&rettype=fasta"
-curl -o .github/data/assemblies/NC_026423.1.fa "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?retmode=text&id=NC_026423.1&db=nucleotide&rettype=fasta"
-curl -o .github/data/assemblies/NC_026431.1.fa "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?retmode=text&id=NC_026431.1&db=nucleotide&rettype=fasta"
+curl -o .github/data/assemblies/MK583610.1_segment_1_PB2_H3N2.fa "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?retmode=text&id=MK583610.1&db=nucleotide&rettype=fasta"
+curl -o .github/data/assemblies/MK583611.1_segment_2_PB1_H3N2.fa "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?retmode=text&id=MK583611.1&db=nucleotide&rettype=fasta"
+curl -o .github/data/assemblies/MK583612.1_segment_3_PA_H3N2.fa "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?retmode=text&id=MK583612.1&db=nucleotide&rettype=fasta"
+curl -o .github/data/assemblies/MK583613.1_segment_4_HA_H3N2.fa "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?retmode=text&id=MK583613.1&db=nucleotide&rettype=fasta"
+curl -o .github/data/assemblies/MK583614.1_segment_5_NP_H3N2.fa "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?retmode=text&id=MK583614.1&db=nucleotide&rettype=fasta"
+curl -o .github/data/assemblies/MK583615.1_segment_6_NA_H3N2.fa "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?retmode=text&id=MK583615.1&db=nucleotide&rettype=fasta"
+
+cat .github/data/assemblies/MK58361*.fa > .github/data/assemblies/MK58361X-H3N2.fa
+
+rm .github/data/assemblies/MK58361*.1_segment_*.fa

.github/scripts/simulate_reads.sh

@@ -13,7 +13,7 @@ while IFS=',' read -r sample_id assembly; do
     art_illumina \
 	--paired \
 	--in ${assembly} \
-	--fcov 100 \
+	--fcov 500 \
 	--len 150 \
 	--mflen 400 \
 	--sdev 100 \

.gitignore

@@ -12,5 +12,5 @@ input_test/
 output_test/
 Validation_notes.md
 .Rproj.user
-__pycache__/
+*/__pycache__/*.pyc
 assets/genoflu/GenoFLU