Examples: pasv-hmm
pasv-hmm is one of three pasv commands used to check residues in query sequences with respect to a reference set and a key reference sequence.
Note: for a lot more examples of using this and other pasv commands, see here.
Required arguments
pasv hmm has four required arguments:
- queries: the query sequences
- references: the reference HMM. This should be the output of HMMER's
hmmbuildprogram - key reference sequence: a fasta file with the key reference sequence
- key residues positions: a comma-separated list of key positions to check
For full CLI usage info, run pasv hmm --help.
Set up environment variables
These are some environment variables that we will use in the example scripts. I am assuming you are running this from the following directory with respect to the pasv source directory: ./_examples/pasv_hmm. (If you are not, you can download the data files on GitHub.)
$ export QUERIES=amk_queries.fa
$ export REFS=P00582.refs.aln.hmm
$ export MAIN_REF=amk_main_ref.fa
$ export OUTDIR=apple
$ export RESIDUES=50,52,54
Basic usage
# Clean up outdir if it exists.
$ [ -d "${OUTDIR}" ] && rm -r "${OUTDIR}"
# Run pasv-hmm.
$ pasv hmm --outdir="${OUTDIR}" "${QUERIES}" "${REFS}" "${MAIN_REF}" "${RESIDUES}"
The output file will be apple/amk_queries.pasv_signatures.tsv. Here are the contents.
| name | pos_50 | pos_52 | pos_54 | signature | spans_start | spans_end | spans |
|---|---|---|---|---|---|---|---|
| AMK99662_spans_start_20_60_IQK | I | Q | K | IQK | NA | NA | NA |
| AMK99662_spans_start_19_60_IQK | I | Q | K | IQK | NA | NA | NA |
| AMK99662_21_60_IQK | I | Q | K | IQK | NA | NA | NA |
| AMK99662_spans_end_40_80_IQK | I | Q | K | IQK | NA | NA | NA |
| AMK99662_spans_end_40_81_IQK | I | Q | K | IQK | NA | NA | NA |
| AMK99662_40_79_IQK | I | Q | K | IQK | NA | NA | NA |
| AMK99662_spans_both_20_80_IQK | I | Q | K | IQK | NA | NA | NA |
| AMK99662_spans_both_19_81_IQK | I | Q | K | IQK | NA | NA | NA |
| AMK99662_21_79_IQK | I | Q | K | IQK | NA | NA | NA |
| AMK99662_full_length_IQK | I | Q | K | IQK | NA | NA | NA |
| AMK99662_real_seq_IQK | I | Q | K | IQK | NA | NA | NA |
| AMK99662_full_length_extra_IQK | I | Q | K | IQK | NA | NA | NA |
| AMK99662_spans_start_20_60_ABC | A | B | C | ABC | NA | NA | NA |
| AMK99662_spans_start_19_60_ABC | A | B | C | ABC | NA | NA | NA |
| AMK99662_21_60_ABC | A | B | C | ABC | NA | NA | NA |
| AMK99662_spans_end_40_80_ABC | A | B | C | ABC | NA | NA | NA |
| AMK99662_spans_end_40_81_ABC | A | B | C | ABC | NA | NA | NA |
| AMK99662_40_79_ABC | A | B | C | ABC | NA | NA | NA |
| AMK99662_spans_both_20_80_ABC | A | B | C | ABC | NA | NA | NA |
| AMK99662_spans_both_19_81_ABC | A | B | C | ABC | NA | NA | NA |
| AMK99662_21_79_ABC | A | B | C | ABC | NA | NA | NA |
| AMK99662_full_length_ABC | A | B | C | ABC | NA | NA | NA |
| AMK99662_real_seq_ABC | A | B | C | ABC | NA | NA | NA |
| AMK99662_full_length_extra_ABC | A | B | C | ABC | NA | NA | NA |
For a detailed explanation of this file's format, see here.
One thing to note is that there are a lot of NA values present in the output. This is because we didn't provide a region of interest. Let's see how to do that.
With region of interest
You can also use pasv to check if query sequences span a region of interest with respect to the key reference sequence.
# Clean up outdir if it exists.
$ [ -d "${OUTDIR}" ] && rm -r "${OUTDIR}"
# Run pasv-hmm.
$ pasv hmm \
--roi-start=20 \
--roi-end=80 \
--outdir="${OUTDIR}" \
"${QUERIES}" \
"${REFS}" \
"${MAIN_REF}" \
"${RESIDUES}"
The output file will be here: "${OUTDIR}/aln.pasv_signatures.tsv". Here are the contents:
| name | pos_50 | pos_52 | pos_54 | signature | spans_start | spans_end | spans |
|---|---|---|---|---|---|---|---|
| AMK99662_spans_start_20_60_IQK | I | Q | K | IQK | Yes | No | Start |
| AMK99662_spans_start_19_60_IQK | I | Q | K | IQK | Yes | No | Start |
| AMK99662_21_60_IQK | I | Q | K | IQK | No | No | Neither |
| AMK99662_spans_end_40_80_IQK | I | Q | K | IQK | No | Yes | End |
| AMK99662_spans_end_40_81_IQK | I | Q | K | IQK | No | Yes | End |
| AMK99662_40_79_IQK | I | Q | K | IQK | No | No | Neither |
| AMK99662_spans_both_20_80_IQK | I | Q | K | IQK | Yes | Yes | Both |
| AMK99662_spans_both_19_81_IQK | I | Q | K | IQK | Yes | Yes | Both |
| AMK99662_21_79_IQK | I | Q | K | IQK | No | No | Neither |
| AMK99662_full_length_IQK | I | Q | K | IQK | Yes | Yes | Both |
| AMK99662_real_seq_IQK | I | Q | K | IQK | Yes | Yes | Both |
| AMK99662_full_length_extra_IQK | I | Q | K | IQK | Yes | Yes | Both |
| AMK99662_spans_start_20_60_ABC | A | B | C | ABC | Yes | No | Start |
| AMK99662_spans_start_19_60_ABC | A | B | C | ABC | Yes | No | Start |
| AMK99662_21_60_ABC | A | B | C | ABC | No | No | Neither |
| AMK99662_spans_end_40_80_ABC | A | B | C | ABC | No | Yes | End |
| AMK99662_spans_end_40_81_ABC | A | B | C | ABC | No | Yes | End |
| AMK99662_40_79_ABC | A | B | C | ABC | No | No | Neither |
| AMK99662_spans_both_20_80_ABC | A | B | C | ABC | Yes | Yes | Both |
| AMK99662_spans_both_19_81_ABC | A | B | C | ABC | Yes | Yes | Both |
| AMK99662_21_79_ABC | A | B | C | ABC | No | No | Neither |
| AMK99662_full_length_ABC | A | B | C | ABC | Yes | Yes | Both |
| AMK99662_real_seq_ABC | A | B | C | ABC | Yes | Yes | Both |
| AMK99662_full_length_extra_ABC | A | B | C | ABC | Yes | Yes | Both |
See how there is data about whether queries span the region of interest?