Examples: pasv-check
Of the three commands for checking residues, pasv-check is the simplest.
It takes two input files: a multiple sequence alignment file in fasta format, and a comma separated list of key residue positions to check.
Note: for a lot more examples of using this and other pasv commands, see here.
Input files
aln.fa
A multiple sequence alignment in fasta format.
The first sequence in the alignment file is treated as the key reference sequence.
You can download the aln.fa file from GitHub.
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_check. (If you are not, you can download the data files on GitHub.)
$ export ALN=aln.fa
$ export OUTDIR=apple
Basic usage
# Clean up outdir if it exists.
$ [ -d "${OUTDIR}" ] && rm -r "${OUTDIR}"
# Run pasv-check.
$ pasv check --outdir="${OUTDIR}" "${ALN}" 50,52,54
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 | 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-check.
$ pasv check \
--roi-start=20 \
--roi-end=80 \
--outdir="${OUTDIR}" \
"${ALN}" \
50,52,54
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?