diff test-data/reproduce_test_data.sh @ 0:b7b1c8bf7ae0 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/reproduce_test_data.sh	Wed Oct 16 16:57:55 2019 -0400
@@ -0,0 +1,29 @@
+#!/bin/bash
+
+# This script produces a small kraken2 database containing only a ~1kb portion each of a salmonella and ecoli genome
+# It requires kraken2, art and entrez-direct (all available on bioconda)
+kraken2-build --db test_db --download_taxonomy
+mv test_db/taxonomy/nucl_gb.accession2taxid test_db/taxonomy/nucl_gb.accession2taxid_full
+grep -e 'NC_003198.1' -e 'NC_011750.1' test_db/taxonomy/nucl_gb.accession2taxid_full > test_db/taxonomy/nucl_gb.accession2taxid
+esearch -db nucleotide -query "NC_003198.1" | efetch -format fasta > NC_003198.1.fasta
+esearch -db nucleotide -query "NC_011750.1" | efetch -format fasta > NC_011750.1.fasta
+head -n 14 NC_003198.1.fasta > NC_003198.1_1kb.fasta
+head -n 14 NC_011750.1.fasta > NC_011750.1_1kb.fasta
+kraken2-build --db test_db --add-to-library NC_003198.1_1kb.fasta
+kraken2-build --db test_db --add-to-library NC_011750.1_1kb.fasta
+kraken2-build --db test_db --build
+
+# Simulate 100bp reads from ~1kb portions of genomes
+art_illumina -sam -i NC_011750.1_1kb.fasta -p -m 300 -f 10 -s 10 -l 100 -o NC_011750.1_simulated_R
+art_illumina -sam -i NC_003198.1_1kb.fasta -p -m 300 -f 10 -s 10 -l 100 -o NC_003198.1_simulated_R
+
+# Generate kraken reports
+kraken2 --db test_db --report NC_011750.1_simulated_kraken_report.txt --paired NC_011750.1_simulated_R1.fastq NC_011750.1_simulated_R2.fastq
+kraken2 --db test_db --report NC_003198.1_simulated_kraken_report.txt --paired NC_003198.1_simulated_R1.fastq NC_003198.1_simulated_R2.fastq
+
+# Build bracken kmer distribution files using default kmer-len=35 and read-len=100
+bracken-build -d test_db
+
+# 
+# est_abundance.py --kmer_distr test_db/database100mers.kmer_distrib --level S -i NC_003198.1_simulated_kraken_report.txt -o NC_003198.1_simulated_bracken_report.txt
+# est_abundance.py --kmer_distr test_db/database100mers.kmer_distrib --level S -i NC_011750.1_simulated_kraken_report.txt -o NC_011750.1_simulated_bracken_report.txt