Scripts to type and compare assemblies based off of Enterobase schemes
Project description
EnteroTyper
This is a set of scripts to type assemblies according to schemes retrieved from Enterobase.
Enterobase databases can be manually retrieved with EnterobasePull. Database files retrieved from Enterobase can be automatically formatted via makeblastdb by the typer script.
Requirements
- Python >= 3.6
- ncbi-blast+ (makeblastdb and blastn must be in your $PATH)
- MUSCLE (muscle must be in your $PATH)
Installation
pip install EnteroTyper
Usage
Calling EnteroTyper
Usage: enterotyper [OPTIONS] COMMAND [ARGS]...
EnteroTyper is a suite of tools to type and evaluate assemblies with
Enterobase typing schemes.
Options:
--help Show this message and exit.
Commands:
bulk Runs typer on many samples simultaneously
compare Compares sequence types across samples processed by typer
concatenate Concatenate sequences from report files generated by typer
typer Types an assembly based on a given Enterobase scheme
Single-sample Usage
Usage: enterotyper typer [OPTIONS]
Types an assembly based on an Enterobase scheme
Options:
-i, --input_assembly PATH Path to input assembly in FASTA format
[required]
-db, --database PATH Path to your MLST database [required]
-o, --outdir PATH Root directory to store all output files
[required]
--create_db Set this flag to create the blastDB files using
makeblastdb in the specified database
directory.Will re-create the database files if
they are already present.
-v, --verbose Set this flag to enable more verbose logging.
--version Specify this flag to print the version and exit.
--help Show this message and exit.
Multi-sample Usage
Usage: enterotyper bulk [OPTIONS]
Runs typer on many samples simultaneously
Options:
-i, --input_dir PATH Path to directory containing FASTA assemblies
[required]
-db, --database PATH Path to your MLST database [required]
-o, --outdir PATH Root directory to store all output files [required]
--create_db Set this flag to create the blastDB files using
makeblastdb in the specified database directory.Will
re-create the database files if they are already
present.
-v, --verbose Set this flag to enable more verbose logging.
--version Specify this flag to print the version and exit.
--help Show this message and exit.
Sequence Concatenation
Usage: enterotyper concatenate [OPTIONS] [TARGETS]...
Takes a list of target *.BLASTn_Detailed_Report.tsv files, followed by
several options. Extracts sequences from the BLASTn report files as FASTA
files, aligns them all with MUSCLE, and then concatenates all sequences
into a single FASTA.
Options:
-o, --outdir PATH Root directory to store all output files [required]
-db, --database PATH Path to your MLST database [required]
-v, --verbose Set this flag to enable more verbose logging.
--help Show this message and exit.
Sequence Comparison
Usage: enterotyper compare [OPTIONS] [TARGETS]...
Takes a list of target *.cgMLST_Allele_Report.tsv files as input.
Number of mismatches will be indicated in output files -
a zero means no mismatches between types.
Options:
-o, --outdir PATH Root directory to store all output files [required]
-v, --verbose Set this flag to enable more verbose logging.
--help Show this message and exit.
Project details
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