WGA2GenesDirect.md

WGA2GenesDirect

Bio::EnsEMBL::EGPipeline::PipeConfig::WGA2GenesDirect_conf

Project transripts and create genes based on compara lastz mappings

Prerequisites

Prepared compara database with LASTZ aligments of the source and target species.

How to run

init_pipeline.pl Bio::EnsEMBL::EGPipeline::PipeConfig::WGA2GenesDirect_conf \
    -hive_force_init 1 \
    -pipeline_tag "_${asm_from}2${asm_to}" \
    $($CMD details script) \
    $($CMD details script_compara_) \
    $($CMD details script_source_) \
    $($CMD details script_target_) \
    $($CMD details script_result_) \
    -compara_dbname $LASTZ_DBNAME \
    -source_dbname $FROM_DBNAME \
    -target_dbname $TO_DBNAME \
    -result_dbname $RES_DBNAME \
    -result_force_rewrite 1 \
    -result_clone_mode 'dna_db' \
    -reg_conf 'none' \
    ${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
-pipeline_name	wga2genes_${ENS_VERSION}_${pipeline_tag}	The hive database name will be ${USER}_${pipeline_name}
-pipeline_tag		Tag to append to the default -pipeline_name
-source_{host,port,user,pass,dbname}		projection source DB connection parameters
-target_{host,port,user,pass,dbname}		projection target DB connection parameters
-compara_{host,port,user,pass,dbname}		compara DB with genome alignments (LASTZ) between source and target
-result_{host,port,user,pass,dbname}		connection details of the DB to store results of the projection

Notes

N.B. UTRs are usually lost

Parts

A few from Bio::EnsEMBL::Analysis.