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FindPHIBaseCandidates.md

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FindPHIBaseCandidates

Bio::EnsEMBL::EGPipeline::PipeConfig::FindPHIBaseCandidates_conf

Adding pathogen-host interactions data from PHI-base as xrefs to fungal, oomycete and bacterial pathogen genes

Prerequisites

A registry file with the locations of the core database server(s) and the production database (or -production_db $PROD_DB_URL specified).

PHI-base csv file (see below).

How to run

init_pipeline.pl Bio::EnsEMBL::EGPipeline::PipeConfig::FindPHIBaseCandidates_conf \
    $($CMD details script) \
    -hive_force_init 1\
    -registry $REG_FILE \
    -blast_db_dir $BLAST_DB_DIRECTORY \
    -input_file $INPUT_ROTHAMSTED_FILE \
    ${OTHER_OPTIONS} \
    2> $OUT_DIR/init.stderr \
    1> $OUT_DIR/init.stdout

SYNC_CMD=$(cat $OUT_DIR/init.stdout | grep -- -sync'$' | perl -pe 's/^\s*//; s/"//g')
# should get something like
#   beekeeper.pl -url $url -sync

LOOP_CMD=$(cat $OUT_DIR/init.stdout | grep -- -loop | perl -pe 's/^\s*//; s/\s*#.*$//; s/"//g')
# should get something like
#   beekeeper.pl -url $url -reg_file $REG_FILE -loop

$SYNC_CMD 2> $OUT_DIR/sync.stderr 1> $OUT_DIR/sync.stdout
$LOOP_CMD 2> $OUT_DIR/loop.stderr 1> $OUT_DIR/loop.stdout

Parameters / Options

option default value meaning
-species species to process, several -species options are possible
-input_file path to the prepared PHI-base current snapshot
-blast_db_dir cache with species-specific (generated from cores) peptide files
-skip_blast_update 0 skip verifying and updating cached BLAST DBs; 1 -- to skip
-write 0 remove old and update with new xrefs; 1 -- to actually run (recommended), 0 -- for debugging
-phi_release PHI_base release version (i.e. 4.6)

Notes

N.B. The pipeline does not support collections at the moment

PHI-base data preparation steps

The pipeline works with slightly modified version of phi-base_current.csv file.

We need a header and unused colums to be removed from the file.

A typical flow for creating such file is:

  1. Get the raw phi-base_current.csv file
wget -c https://github.com/PHI-base/data/raw/master/releases/phi-base_current.csv
  1. Remove headers and unused columns using helper script.
# TODO
  > phi_base.filtered.csv
  1. Normalise ontology terms, using phi_ontology/phi-base_ontologies.pl script and ontology maps within phi_ontology dir.
PHIBO_DIR=${ENS_ROOT_DIR}/ensembl-production-imported/scripts/phi_ontology

cp phi_base.filtered.csv phi_base.filtered.csv.orig # creating a back up

perl ${PHIBO_DIR}/phi-base_ontologies.pl \
  -phenotype_dictionary ${PHIBO_DIR}/ontologies_phenotypes.pl \
  -conditions_dictionary ${PHIBO_DIR}/ontologies_conditions.pl \
  -input_file phi_base.filtered.csv \
  -obo_file_destination PHIbase_ontology.${VERSION}.obo

Params:

  • -phenotype_dictionary -- Perl file with phenotype (%mapped_phenotypes) dictionary
  • -conditions_dictionary -- Perl file with conditions (%mapped_conditions) dictionary
  • -input_file -- previous stage result (no header, subset of columns); input file is replaced with the normalised vesrion
  • -obo_file_destination -- optional arg to store .obo file

If the script can't solve all the entries in the file, it outputs the list of terms that need to be added to the dictionaries in phi_ontology dir.

There are few things to be aware of when running this script:

  • The sript replaces the input_file with the normalized version. Please, have a copy if you need one.
  • The script will create (and remove on success) Ontologies_temp_files temporary directory, in the directory, the -input_file is taken from. Thus this recent directory needs to be writable.
  1. Now you can use phi_base.filtered.csv to initialize -input_file option of your pipeline.

Parts

A few generic from Common::RunnableDB.

A few from PHIBase.