Offline curation tools

Automated offline sequence tagging

Sequence tagging is the process of identifying alleles by scanning the sequence bin linked to an isolate record. Loci need to be defined in an external sequence definition database that contains the sequences for known alleles. The tagging function uses BLAST to identify sequences and will tag the specific sequence region with locus information and an allele designation if a matching allele is identified by reference to an external database.

There is a script called ‘autotag.pl’ in the BIGSdb package. This can be used to tag genome sequences from the command line.

Before autotag.pl can be run for the first time, a log file needs to be created. This can be created if it doesn’t already exist with the following:

sudo touch /var/log/bigsdb_scripts.log
sudo chown bigsdb /var/log/bigsdb_scripts.log

The autotag.pl script should be installed in /usr/local/bin. It is run as follows:

autotag.pl --database <database configuration>

where <database configuration> is the name used for the argument ‘db’ when using the BIGSdb application.

If you have multiple processor cores available, use the –threads option to set the number of jobs to run in parallel. Isolates for scanning will be split among the threads.

The script must be run by a user that can both write to the log file and access the databases, e.g. the ‘bigsdb’ user (see ‘Setting up the offline job manager’).

A full list of options can be found by typing:

autotag.pl --help

NAME
    autotag.pl - BIGSdb automated allele tagger

SYNOPSIS
    autotag.pl --database NAME [options]

OPTIONS
-0, --missing
   Marks missing loci as provisional allele 0. Sets default word size to 15.

-d, --database NAME
    Database configuration name.

-h, --help
    This help page.

-i, --isolates LIST
    Comma-separated list of isolate ids to scan (ignored if -p used).

-I, --exclude_isolates LIST
    Comma-separated list of isolate ids to ignore.

-l, --loci LIST
    Comma-separated list of loci to scan (ignored if -s used).

-L, --exclude_loci LIST
    Comma-separated list of loci to exclude

-m, --min_size SIZE
    Minimum size of seqbin (bp) - limit search to isolates with at least this
    much sequence.

-n, --new_only
    New (previously untagged) isolates only.

-o, --order
    Order so that isolates last tagged the longest time ago get scanned first
    (ignored if -r used).

-p, --projects LIST
    Comma-separated list of project isolates to scan.

-P, --exclude_projects LIST
    Comma-separated list of projects whose isolates will be excluded.

-q, --quiet
    Only error messages displayed.

-r, --random
    Shuffle order of isolate ids to scan.

-R, --locus_regex REGEX
    Regex for locus names.

-s, --schemes LIST
    Comma-separated list of scheme loci to scan.

-t, --time MINS
    Stop after t minutes.

--threads THREADS
    Maximum number of threads to use.

-T, --already_tagged
    Scan even when sequence tagged (no designation).

-w, --word_size SIZE
    BLASTN word size.

-x, --min ID
    Minimum isolate id.

-y, --max ID
    Maximum isolate id.

Automated offline allele definition

There is a script called ‘scannew.pl’ in the BIGSdb scripts/automation directory. This can be used to identify new alleles from the command line. This can (optionally) upload these to a sequence definition database.

Before scannew.pl can be run for the first time, a log file needs to be created. This can be created if it doesn’t already exist with the following:

sudo touch /var/log/bigsdb_scripts.log
sudo chown bigsdb /var/log/bigsdb_scripts.log

The autotag.pl script should be installed in /usr/local/bin. It is run as follows:

scannew.pl --database <database configuration>

where <database configuration> is the name used for the argument ‘db’ when using the BIGSdb application.

If you have multiple processor cores available, use the –threads option to set the number of jobs to run in parallel. Loci for scanning will be split among the threads.

The script must be run by a user that can both write to the log file and access the databases, e.g. the ‘bigsdb’ user (see ‘Setting up the offline job manager’).

A full list of options can be found by typing:

scannew.pl --help

NAME
  scannew.pl - BIGSdb automated allele definer

SYNOPSIS
  scannew.pl --database NAME [options]

OPTIONS
-a, --assign
     Assign new alleles in definitions database.

-A, --alignment INT
    Percentage alignment (default: 100).

-B, --identity INT
    Percentage identity (default: 99).

-c, --coding_sequences
    Only return complete coding sequences.

-d, --database NAME
    Database configuration name.

-h, --help
    This help page.

-i, --isolates LIST
    Comma-separated list of isolate ids to scan (ignored if -p used).

-I, --exclude_isolates LIST
    Comma-separated list of isolate ids to ignore.

-l, --loci LIST
    Comma-separated list of loci to scan (ignored if -s used).

-L, --exclude_loci LIST
    Comma-separated list of loci to exclude.

-m, --min_size SIZE
    Minimum size of seqbin (bp) - limit search to isolates with at least this
    much sequence.

-n, --new_only
    New (previously untagged) isolates only.

-o, --order
    Order so that isolates last tagged the longest time ago get scanned first
    (ignored if -r used).

-p, --projects LIST
    Comma-separated list of project isolates to scan.

-P, --exclude_projects LIST
    Comma-separated list of projects whose isolates will be excluded.

-r, --random
    Shuffle order of isolate ids to scan.

-R, --locus_regex REGEX
    Regex for locus names.

-s, --schemes LIST
    Comma-separated list of scheme loci to scan.

-t, --time MINS
    Stop after t minutes.

--threads THREADS
    Maximum number of threads to use.

-T, --already_tagged
    Scan even when sequence tagged (no designation).

-w, --word_size SIZE
    BLASTN word size.

-x, --min ID
    Minimum isolate id.

-y, --max ID
    Maximum isolate id.

Cleanly interrupting offline curation

Sometimes you may wish to stop running autotagger or allele autodefiner jobs as they can be run for a long time and as CRON jobs. If these are running in single threaded mode, the easiest way is to simply send a kill signal to the process, i.e. identify the process id using ‘top’, e.g. 23232 and then

kill 23232

The scripts should respond to this signal within a couple of seconds, clean up all their temporary files and write the history log (where appropriate). Do not use ‘kill -9’ as this will terminate the processes immediately and not allow them to clean up.

If these scripts are running using multiple threads, then you need to cleanly kill each of these. The simplest way to terminte all autotagger jobs is to, type

pkill autotag

The parent process will wait for all forked processes to cleanly terminate and then exit itself.

Similarly, to terminate all allele autodefiner jobs, type

pkill scannew