cirtap
A command-line utility to handle PATRIC data from their FTP
Check out the wiki page for more info.
Installation
$ pip install cirtap
Usage
Usage: cirtap [OPTIONS] COMMAND [ARGS]...
Run `cirtap COMMAND -h` for subcommand help
Options:
--version Show the version and exit.
--help Show this message and exit.
Commands:
best Select best genomes based on stats retrieved from genome_summary
collect Create sequence sets based on the installed files
index Create an index of contents for all directories
mirror Mirror all data from ftp.patricbrc.org in the specified DB_DIR
pack Create a gzipped tar archive from a list of genome ids in a file
Quickstart
mirror
- Start a new mirror of all data in a local path, wiht 8 parallel downloads
$ cirtap mirror -j 8 some/path
- Resume a failing job
$ cirtap mirror -j 8 -r some/path
- Archive previous release notes and send notification emails when a mirror job launches or fails to some users
$ cirtap mirror -j 8 --notify user1@example.com,user2@gmail.com --archive-notes some/path
The rest of the commands assume a mirror is set up
index
- Create a presence/absence index of files installed
$ cirtap index -j 16 path/to/genomes index.tsv
This is useful for selecting genomes based on file presence
collect
- Collect all proteins for e.g. building a
blastpdatabase
$ cirtap collect -t proteins -j 4 -i path/to/index.tsv path/to/genomes all_proteins.fa.gz
- Collect all 16S SSU sequences
$ cirtap collect -t SSU -j 4 -i path/to/index.tsv path/to/genomes SSU.fa.gz
best
- Make a selection of best genomes based on completeness, consistency, fine/coarse consistency.
$ cirtap best -i path/to/index.tsv -d path/to/local/patric best_genomes
