camlhmp-blast-targets¶
camlhmp-blast-targets is a command that allows users to type their samples using a provided
schema with BLAST algorithms. This command is useful when a schema is looking at full length
genes or proteins.
Usage¶
Usage: camlhmp-blast-targets [OPTIONS]
🐪 camlhmp-blast-targets 🐪 - Classify assemblies using BLAST against individual
genes or proteins
╭─ Options ───────────────────────────────────────────────────────────────────────────╮
│ * --input -i TEXT Input file in FASTA format to classify [required] │
│ * --yaml -y TEXT YAML file documenting the targets and types │
│ [required] │
│ * --targets -t TEXT Query targets in FASTA format [required] │
│ --outdir -o PATH Directory to write output [default: ./] │
│ --prefix -p TEXT Prefix to use for output files [default: camlhmp] │
│ --min-pident INTEGER Minimum percent identity to count a hit │
│ [default: 95] │
│ --min-coverage INTEGER Minimum percent coverage to count a hit │
│ [default: 95] │
│ --force Overwrite existing reports │
│ --verbose Increase the verbosity of output │
│ --silent Only critical errors will be printed │
│ --version Print schema and camlhmp version │
│ --help Show this message and exit. │
╰─────────────────────────────────────────────────────────────────────────────────────╯
Example Usage¶
To run camlhmp-blast-targets, you will need a FASTA file of your input sequences, a YAML
file with the schema, and a FASTA file with the targets. Below is an example of how to run
camlhmp-blast-targets using available test data.
camlhmp-blast-targets \
--yaml tests/data/blast/targets/sccmec-partial.yaml \
--targets tests/data/blast/targets/sccmec-partial.fasta \
--input tests/data/blast/targets/sccmec-i.fasta
Running camlhmp with following parameters:
--input tests/data/blast/targets/sccmec-i.fasta
--yaml tests/data/blast/targets/sccmec-partial.yaml
--targets tests/data/blast/targets/sccmec-partial.fasta
--outdir ./
--prefix camlhmp
--min-pident 95
--min-coverage 95
Starting camlhmp for SCCmec Typing...
Running blastn...
Processing hits...
Final Results...
SCCmec Typing
┏━━━━━━━━━┳━━━━━━┳━━━━━━━━━━━┳━━━━━━━━━━━┳━━━━━━━━━━━┳━━━━━━━━━━┳━━━━━━━━━━━┳━━━━━━━━━┓
┃ sample ┃ type ┃ targets ┃ schema ┃ schema_v… ┃ camlhmp… ┃ params ┃ comment ┃
┡━━━━━━━━━╇━━━━━━╇━━━━━━━━━━━╇━━━━━━━━━━━╇━━━━━━━━━━━╇━━━━━━━━━━╇━━━━━━━━━━━╇━━━━━━━━━┩
│ camlhmp │ I │ ccrA1,cc… │ sccmec_p… │ 0.0.1 │ 0.3.1 │ min-cove… │ │
└─────────┴──────┴───────────┴───────────┴───────────┴──────────┴───────────┴─────────┘
Writing outputs...
Final predicted type written to ./camlhmp.tsv
Results against each type written to ./camlhmp.details.tsv
blastn results written to ./camlhmp.blastn.tsv
Note
The table printed to STDOUT by camlhmp-blast-targets has been purposefully truncated
for viewing on the docs. It is the same information that that is in {PREFIX}.tsv.
Output Files¶
camlhmp-blast-targets will generate three output files:
| File Name | Description |
|---|---|
{PREFIX}.tsv |
A tab-delimited file with the predicted type |
{PREFIX}.blast.tsv |
A tab-delimited file of all blast hits |
{PREFIX}.details.tsv |
A tab-delimited file with details for each type |
{PREFIX}.tsv¶
The {PREFIX}.tsv file is a tab-delimited file with the predicted type. The columns are:
| Column | Description |
|---|---|
| sample | The sample name as determined by --prefix |
| type | The predicted type |
| targets | The targets for the given type that had a hit |
| schema | The schema used to determine the type |
| schema_version | The version of the schema used |
| camlhmp_version | The version of camlhmp used |
| params | The parameters used for the analysis |
| comment | A small comment about the result |
Below is an example of the {PREFIX}.tsv file:
sample type targets schema schema_version camlhmp_version params comment
camlhmp I ccrA1,ccrB1,IS431,IS1272,mecA,mecR1 sccmec_partial 0.0.1 0.2.1 min-coverage=95;min-pident=95
{PREFIX}.blast.tsv¶
The {PREFIX}.blast.tsv file is a tab-delimited file of the raw output for all blast hits.
The columns are the standard BLAST output with -outfmt 6.
Here is an example of the {PREFIX}.blast.tsv file:
qseqid sseqid pident qcovs qlen slen length nident mismatch gapopen qstart qend sstart send evalue bitscore
ccrA1 AB033763.2 100.000 100 1350 39332 1350 1350 0 0 1 1350 23692 25041 0.0 2494
ccrB1 AB033763.2 100.000 100 1152 39332 1152 1152 0 0 1 1152 25063 26214 0.0 2128
IS1272 AB033763.2 100.000 100 1659 39332 1659 1659 0 0 1 1659 28423 30081 0.0 3064
mecR1 AB033763.2 100.000 100 987 39332 987 987 0 0 1 987 30304 31290 0.0 1823
mecA AB033763.2 99.950 100 2007 39332 2007 2006 1 0 1 2007 31390 33396 0.0 3701
mecA AB033763.2 99.950 100 2007 39332 2007 2006 1 0 1 2007 31390 33396 0.0 3701
IS431 AB033763.2 99.873 100 790 39332 790 789 1 0 1 790 35958 36747 0.0 1454
IS431 AB033763.2 100.000 100 792 39332 792 792 0 0 1 792 35957 36748 0.0 1463
{PREFIX}.details.tsv¶
The {PREFIX}.details.tsv file is a tab-delimited file with details for each type. This file
can be useful for seeing how a sample did against all other types in a schema.
The columns in this file are:
| Column | Description |
|---|---|
| sample | The sample name as determined by --prefix |
| type | The predicted type |
| status | The status of the type (True if passed thresholds, False if failed to exceed thresholds) |
| targets | The targets for the given type that had a match |
| missing | The targets for the given type that were not found |
| schema | The schema used to determine the type |
| schema_version | The version of the schema used |
| camlhmp_version | The version of camlhmp used |
| params | The parameters used for the analysis |
| comment | A small comment about the result |
Below is an example of the {PREFIX}.details.tsv file:
sample type status targets missing schema schema_version camlhmp_version params comment
camlhmp I True ccrA1,ccrB1,IS431,mecA,mecR1,IS1272 sccmec_partial 0.0.1 0.2.1 min-coverage=95;min-pident=95
camlhmp II False IS431,mecA,mecR1 ccrA2,ccrB2,mecI sccmec_partial 0.0.1 0.2.1 min-coverage=95;min-pident=95
camlhmp III False IS431,mecA,mecR1 ccrA3,ccrB3,mecI sccmec_partial 0.0.1 0.2.1 min-coverage=95;min-pident=95
camlhmp IV False IS431,mecA,mecR1,IS1272 ccrA2,ccrB2 sccmec_partial 0.0.1 0.2.1 min-coverage=95;min-pident=95
Example Implementation¶
If you would like to see how camlhmp-blast-targets can be used, please see
sccmec. In sccmec the schema is set up
to directly use camlhmp-blast-targets to classify samples without any extra
logic.
This allows for a simple wrapper like the following:
#!/usr/bin/env bash
sccmec_dir=$(dirname $0)
CAML_YAML="${sccmec_dir}/../data/sccmec.yaml" \
CAML_TARGETS="${sccmec_dir}/../data/sccmec.fasta" \
camlhmp-blast-targets \
"${@:1}"
This script will run camlhmp-blast-targets with the sccmec schema and targets.