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trf_split_run.bash

A trf wrapper with chunking support to be used with ensembl-production-imported DNAFeatures pipeline Compatible compatible with input/output format of trf invocation from Bio::EnsEMBL::Analysis::Runnable::TRF. And can be used as a hack to allow TRF stage to be accomplished at the cost of splitting long repeat into several adjacent ones (with possible losses).

Prerequisites

You should have Biopython installed and available in your environment. You may check this with

python -c 'from Bio import SeqIO' || echo "no biopython" >> /dev/stderr

Options

Use environment variable to control script run

  • DNA_FEATURES_TRF_SPLIT_NO_SPLITTING -- set to YES to skip splitting stage
  • DNA_FEATURES_TRF_SPLIT_NO_TRF -- set to YES to skip trf stage
  • DNA_FEATURES_TRF_SPLIT_SPLITTER_CHUNK_SIZE -- chunk size [1_000_000]
  • DNA_FEATURES_TRF_SPLIT_SPLITTER_OPTIONS -- for a finer control [--n_seq 1 --chunk_tolerance 10 --chunk_size ${DNA_FEATURES_TRF_SPLIT_SPLITTER_CHUNK_SIZE}]
  • DNA_FEATURES_TRF_SPLIT_TRF_EXE -- trf executable (or abs path to be used) [trf]
  • DNA_FEATURES_TRF_SPLIT_TRF_OPTIONS -- additional options for TRF (like -l 10) []

Usage examples

A standalone run

trf_split_run.bash /writable/path_to/dna.fasta 2 5 7 80 10 40 500 -d -h

As a substitution for the "trf_exe" to be used with the TRF stage of the DNAFeatures pipeline:

# change TRF "program" parameter, you should have ENSEMBL_ROOT_DIR env defined
tweak_pipeline.pl -url "$DNA_FEATURES_EHIVE_DB_URL" -tweak 'analysis[TRF].param[parameters_hash]={program=>"'${ENSEMBL_ROOT_DIR}'/ensembl-genomio/scripts/trf_split_run.bash"}'

# set environment variables if you need to, i.e.
export DNA_FEATURES_TRF_SPLIT_TRF_EXE=trf.4.09.1 
export DNA_FEATURES_TRF_SPLIT_TRF_OPTIONS='-l 10' # N.B. "l" correlated with the chunk size (-l chunk_size / 10^6)
export DNA_FEATURES_TRF_SPLIT_SPLITTER_CHUNK_SIZE=10_000_000'

runWorker.pl ... 
# or
beekeeper.pl ... -loop

# revert back (if you need to)
tweak_pipeline.pl -url $DNA_FEATURES_EHIVE_DB_URL  -tweak 'analysis[TRF].param[parameters_hash]={}'

# revert env settings
unset DNA_FEATURES_TRF_SPLIT_SPLITTER_CHUNK_SIZE
unset DNA_FEATURES_TRF_SPLIT_SPLITTER_OPTIONS
unset DNA_FEATURES_TRF_SPLIT_TRF_EXE
unset DNA_FEATURES_TRF_SPLIT_TRF_OPTIONS
#   script stages
unset DNA_FEATURES_TRF_SPLIT_NO_SPLITTING
unset DNA_FEATURES_TRF_SPLIT_NO_TRF