Commit b793818e authored by Valentina Galata's avatar Valentina Galata
Browse files

fixed bug in test/set-up.sh and updated test/test_sample.contig: excl FASTA...

fixed bug in test/set-up.sh and updated test/test_sample.contig: excl FASTA content from GFF before creating contig table (issue #30)
parent af1f20dc
#!/bin/bash -l
# modify *.faa: rm record descriptions
sed -i '/^>/ s/ .*//' test_sample.faa
#sed -i '/^>/ s/ .*//' test/test_sample.faa
# *.gff to *.contig: contig ID, feature ID
grep -v '^#' test_sample.gff | cut -f1,9 | cut -d';' -f1 | sed 's/ID=//' > test_sample.contig
sed -n '/^##gff/,/^##FASTA/p' test/test_sample.gff | grep -v '^#' | cut -f1,9 | cut -d';' -f1 | sed 's/ID=//' > test/test_sample.contig
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