Archived - Please use https://github.com/rpetit3/sccmec
staphopia-sccmec reads Staphopia results or assembly to assign a SCCmec type.
Staphopia includes a primer based SCCmec Typing scheme. Unfortunately there was a disconnect between running the ananlysis and making the call. The primers are aligned by BLAST in the Staphopia Anlaysis Pipeline but the logic making the type and subtype calls was in the Staphopia Website.
staphopia-sccmec has taken this process and merged into a single command.
You can either provide results already produced by Staphopia or give an assembly and a path to SCCmec data (included in this repo).
conda create -n staphopia-sccmec -c conda-forge -c bioconda staphopia-sccmec
git clone [email protected]:staphopia/staphopia-sccmec.git
cd staphopia-sccmec
./bin/staphopia-sccmec.py
usage: staphopia-sccmec [-h] [--assembly ASSEMBLY|ASSEMBLY_DIR|STAPHOPIA_DIR] [--staphopia STAPHOPIA_DIR] [--sccmec SCCMEC_DATA] [--ext STR] [--evalue EVALUE] [--hamming] [--json]
[--debug] [--depends] [--test] [--citation] [--version]
Determine SCCmec Type/SubType
optional arguments:
-h, --help show this help message and exit
Options:
--assembly ASSEMBLY|ASSEMBLY_DIR|STAPHOPIA_DIR
Input assembly (FASTA format), directory of assemblies to predict SCCmec. (Cannot be used with --staphopia)
--staphopia STAPHOPIA_DIR
Input directory of samples processed by Staphopia. (Cannot be used with --assembly)
--sccmec SCCMEC_DATA Directory where SCCmec reference data is stored (Default: /home/yaopeng/staphopia-sccmec/share/staphopia-sccmec/data).
--ext STR Extension used by assemblies. (Default: fna)
--evalue EVALUE evalue required by blast
--hamming Report the hamming distance of each type.
--json Report the output as JSON (Default: tab-delimited)
--debug Print debug related text.
--depends Verify dependencies are installed/found.
--test Run with example test data.
--citation Print citation information for using Staphopia SCCmec
--version show program's version number and exit
staphopia-sccmec has two ways of being used, with Staphopia results or with an assembly.
Part of the Staphopia Anlaysis Pipeline is to BLAST the SCCmec primers against your assembly. As mentioned previously, the logic to actually use those results and make a type call was included on the database side.
staphopia-sccmec allows you to type using your existing Staphopia results. You just need to provide
the path to a set of samples processed by staphopia and use the --staphopia parameter.
Below is an example of typing the Staphopia results for SRX085180.
staphopia-sccmec --staphopia /data/storage/semaphore/staphopia-v1/staphopia/ | head
sample I II III IV V VI VII VIII IX meca Ia IIa IIb IIIa IVa IVb IVc IVd IVg IVh
S.200218.00785 False False False False False False False False False False False False False False False False False False False False
S.200218.00787 False False False False False False False False False False False False False False False False False False False False
S.200218.00789 False False False False False False False False False False False False False False False False False False False False
S.200218.00791 False False False False False False False False False False False False False False False False False False False False
S.200218.00793 False False False False False False False False False False False False False False False False False False False False
S.200218.00795 False True False True False False False False False True False True False False False False False False False False
S.200218.00797 False False False False False False False False False False False False False False False False False False False False
S.200218.00824 False False False False False False False False False False False False False False False False False False False False
S.200218.00827 False False False False False False False False False False False False False False False False False False False False
As an alternative to Staphopia results, you can provide an assembly, or a directory of assemblies. When an assembly is provided, a BLAST database is created of the assembly and the primers are blasted against it.
Below is an example of typing the GCF_001580515 assembly, available in the test/ directory.
staphopia-sccmec --assembly test/GCF_001580515.1.fna
sample I II III IV V VI VII VIII IX meca Ia IIa IIb IIIa IVa IVb IVc IVd IVg IVh
GCF_001580515 False False False True False False False False False True False False False False True False False False False False
ls ~/bactopia-dev/test-assemblies/
ERX140798.fna ERX1711341.fna ERX204841.fna ERX3565118.fna ERX385151.fna ERX514151.fna ERX956727.fna SRX1885573.fna SRX477083.fna SRX6900463.fna
ERX1666543.fna ERX1830501.fna ERX2543896.fna ERX3837876.fna ERX3969884.fna ERX770670.fna SRX1885362.fna SRX3883084.fna SRX5659541.fna SRX7775692.fna
staphopia-sccmec --assembly ~/bactopia-dev/test-assemblies/
sample I II III IV V VI VII VIII IX meca Ia IIa IIb IIIa IVa IVb IVc IVd IVg IVh
ERX204841 False False False True False False False False False True False False False False True False False False False False
ERX2543896 False False False False False False False False False True False False False False False False False False False False
ERX3565118 False False False False False False False False False False False False False False False False False False False False
SRX3883084 False False True False True False True False False True False False False True False False False False False False
SRX6900463 False False False True False False False False False True False False False False True False False False False False
ERX956727 False False False False False False False False False False False False False False False False False False False False
SRX1885362 False False False False False False False False False False False False False False False False False False False False
SRX7775692 False False False True False False False False False True False False False False True False False False False False
ERX514151 False False False True False False False False False True False False False False False False False False False True
SRX477083 False False False True False False False False False True False False False False True False False False False False
SRX5659541 False True False False False False False False False True False True False False False False False False False False
ERX3969884 False False False False False False False False False False False False False False False False False False False False
ERX1830501 False False False False False False False False False False False False False False False False False False False False
ERX1711341 False False False False False False False False False False False False False False False False False False False False
ERX1666543 False False False False False False False False False False False False False False False False False False False False
ERX385151 False False False False False False False False False False False False False False False False False False False False
ERX3837876 False False False True False False False False False True False False False False False False True False False False
ERX140798 False False True False False False False False False True False False False True False False False False False False
SRX1885573 False False False False False False False False False False False False False False False False False False False False
ERX770670 False False False True False False False False False True False False False False False False False False False True
You can also switch from a tab-delimited output to JSON, using the --json option.
staphopia-sccmec --assembly test/GCF_001580515.fna --json
[
{
"sample": "GCF_001580515",
"I": false,
"II": false,
"III": false,
"IV": true,
"V": false,
"VI": false,
"VII": false,
"VIII": false,
"IX": false,
"meca": true,
"Ia": false,
"IIa": false,
"IIb": false,
"IIIa": false,
"IVa": true,
"IVb": false,
"IVc": false,
"IVd": false,
"IVg": false,
"IVh": false
}
]
By default, staphopia-sccmec reports True for exact primer matches and False for at least 1 base pair difference. As an alternative you can print the Hamming Distance instead. The Hamming Distance outputs the number of mismatches, with 0 being a perfect match.
staphopia-sccmec --assembly test/GCF_001580515.fna --hamming --json
[
{
"sample": "GCF_001580515",
"I": 8,
"II": 6,
"III": 14,
"IV": 0,
"V": 16,
"VI": 14,
"VII": 16,
"VIII": 20,
"IX": 8,
"meca": 0,
"Ia": 19,
"IIa": 20,
"IIb": 14,
"IIIa": 14,
"IVa": 0,
"IVb": 14,
"IVc": 12,
"IVd": 17,
"IVg": 12,
"IVh": 14
}
]
Petit III RA, Read TD, Staphylococcus aureus viewed from the perspective of 40,000+ genomes. PeerJ 6, e5261 (2018).
- Robert A. Petit III
- Twitter: @rpetit3