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runEVM.sh
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runEVM.sh
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#!/bin/bash
GFF1=$1
GFF2=$2
weights=$3
genome=TAIR10_chr_all.fas
cat ${GFF1} <( grep -v "^#" ${GFF2}) > gene_predictions.gff3
partition_EVM_inputs.pl \
--genome ${genome} \
--gene_predictions gene_predictions.gff3 \
--segmentSize 100000 \
--overlapSize 10000 \
--partition_listing partitions_list.out
write_EVM_commands.pl \
--genome ${genome} \
--weights $weights \
--gene_predictions gene_predictions.gff3 \
--output_file_name evm.out \
--partitions partitions_list.out > commands.list
execute_EVM_commands.pl commands.list | tee run.log
recombine_EVM_partial_outputs.pl \
--partitions partitions_list.out \
--output_file_name evm.out
convert_EVM_outputs_to_GFF3.pl \
--partitions partitions_list.out \
--output evm.out \
--genome ${genome}
find . -regex ".*evm.out.gff3" -exec cat {} \; > EVM.all.gff3