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annotate test-data/generate_test_data.sh @ 2:98099e4da1fd draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kma commit 812bb0a31f030096bf1b0836f64e76b820c8e2c2
author iuc
date Fri, 14 Jun 2024 21:15:44 +0000
parents 2595c27071c2
children
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2595c27071c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kma commit 43bbde4f8f8671284b2acb21dfd2657de4ba967f"
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1 #!/usr/bin/bash
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2595c27071c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kma commit 43bbde4f8f8671284b2acb21dfd2657de4ba967f"
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3 # E. coli locus b0842 (b0842.fasta.gz) downloaded from Enterobase E. coli cgMLST scheme
2595c27071c2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kma commit 43bbde4f8f8671284b2acb21dfd2657de4ba967f"
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4 # requires: wget, kma, bwa, samtools, bedtools
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6 gunzip b0842.fasta.gz
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8 # Take first 5 alleles to reduce size of test data
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9 mkdir ecoli_cgMLST
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10 head -n 10 b0842.fasta > ecoli_cgMLST/ecoli_b0842_1to5.fasta
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12 kma index -k 8 -i ecoli_cgMLST/ecoli_b0842_1to5.fasta -o ecoli_cgMLST/ecoli_b0842_1to5
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14 wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR884/ERR884056/ERR884056_1.fastq.gz
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16 # Use bwa to map reads to reduced E. coli locus b0842
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17 # and extract only mapped reads (to reduce size of test dataset)
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18 bwa index ecoli_cgMLST/ecoli_b0842_1to5.fasta
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20 bwa mem ecoli_cgMLST/ecoli_b0842_1to5.fasta ERR884056_1.fastq.gz -o ERR884056_1_ecoli_b0842_1to5.sam
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22 samtools view ERR884056_1_ecoli_b0842_1to5.sam -bo ERR884056_1_ecoli_b0842_1to5.bam
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24 # Select mapped reads
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25 samtools view -b -F 4 ERR884056_1_ecoli_b0842_1to5.bam > ERR884056_1_ecoli_b0842_1to5.mapped.bam
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27 samtools sort -n ERR884056_1_ecoli_b0842_1to5.mapped.bam -o ERR884056_1_ecoli_b0842_1to5.mapped.sort.bam
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29 bedtools bamtofastq -i ERR884056_1_ecoli_b0842_1to5.mapped.sort.bam -fq ERR884056_ecoli_b0842.mapped_R1.fastq
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