Create the test files for 'regtools junctions annotate'

create_annotate_files.sh

#Generate the FASTA
rm -f test.fa; samtools faidx ../../regtools-test/chr22.fa 22:41475000-41585000 > test.fa
sed "1s/.*/>22/" test.fa > new_test.fa; rm -f test.fa; mv new_test.fa test.fa #fix the header
samtools faidx test.fa

#Generate the GTF
rm -f test.gtf; awk -F"\t" '$4> 41480000 && $5 < 41580000 { OFS = "\t"; $4 = $4 - 41475000 + 1; $5 = $5 - 41475000 + 1; print }'  ../../regtools-test/genes_chr22.gtf > test.gtf

#Create the junctions.bed
rm -f test_junctions.bed; awk '$1==22 && $2> 41480000 && $3 < 41580000 { OFS = "\t"; $2=$2 - 41475000 + 1; $3 = $3 - 41475000 + 1; $7=$2; $8=$3; print }'  hcc1395_junctions.bed > test_junctions.bed

#Run regtools on these
./regtools junctions annotate test_junctions.bed test.fa test.gtf 2>/dev/null