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Setup
$ source "$TESTDIR"/_setup.sh
Filter into two separate sets and then select sequences from the union of those sets.
First, select strains from Brazil (there should be 1).
$ ${AUGUR} filter \
> --metadata "$TESTDIR/../data/metadata.tsv" \
> --query "country == 'Brazil'" \
> --output-strains filtered_strains.brazil.txt 2>/dev/null
$ wc -l filtered_strains.brazil.txt
\s*1 .* (re)
Then, select strains from Colombia (there should be 3).
$ ${AUGUR} filter \
> --metadata "$TESTDIR/../data/metadata.tsv" \
> --query "country == 'Colombia'" \
> --output-strains filtered_strains.colombia.txt 2>/dev/null
$ wc -l filtered_strains.colombia.txt
\s*3 .* (re)
Finally, exclude all sequences except those from the two sets of strains (there should be 4).
$ ${AUGUR} filter \
> --sequences "$TESTDIR/../data/sequences.fasta" \
> --sequence-index "$TESTDIR/../data/sequence_index.tsv" \
> --metadata "$TESTDIR/../data/metadata.tsv" \
> --exclude-all \
> --include filtered_strains.brazil.txt filtered_strains.colombia.txt \
> --output filtered.fasta 2>/dev/null
$ grep "^>" filtered.fasta | wc -l
\s*4 (re)
Repeat this filter without a sequence index.
We should get the same outputs without building a sequence index on the fly, because the exclude-all flag tells us we only want to force-include strains and skip all other filters.
$ ${AUGUR} filter \
> --sequences "$TESTDIR/../data/sequences.fasta" \
> --metadata "$TESTDIR/../data/metadata.tsv" \
> --exclude-all \
> --include filtered_strains.brazil.txt filtered_strains.colombia.txt \
> --output filtered.fasta \
> --output-metadata filtered.tsv 2>/dev/null
$ grep "^>" filtered.fasta | wc -l
\s*4 (re)
Metadata should have the same number of records as the sequences plus a header.
$ wc -l filtered.tsv
\s*5 .* (re)
Alternately, exclude the sequences from Brazil and Colombia (N=4) and records without sequences (N=1) or metadata (N=1).
$ ${AUGUR} filter \
> --sequences "$TESTDIR/../data/sequences.fasta" \
> --sequence-index "$TESTDIR/../data/sequence_index.tsv" \
> --metadata "$TESTDIR/../data/metadata.tsv" \
> --exclude filtered_strains.brazil.txt filtered_strains.colombia.txt \
> --output filtered.fasta 2>/dev/null
$ grep "^>" filtered.fasta | wc -l
\s*7 (re)
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