checks and balances for ENA submission

08-submission/gff-03-ENA_conform.sh

+#!/usr/bin/env bash
+
+# modify the sorted GFF3 file to conform to ENA requirements.
+# this means: 
+# - remove duplicate features
+# - remove short introns (<10nt)
+
+module load conda
+conda activate agat-1.4.1
+
+# switch to the submission directory
+RESULT=/lisc/scratch/zoology/pycnogonum/genome/submission
+cd $RESULT || exit
+
+# define inputs and outputs
+GFF=$BASE/merged_sorted_named.gff3
+DEDUP=$BASE/merged_sorted_named_dedup.gff3
+SHORT_INTRONS=$BASE/short_introns.tsv
+KILL_LIST=$BASE/kill_list.tsv
+
+FILTERED_GFF=$BASE/merged_sorted_named_dedup_filtered.gff3
+
+# the python script that will generate the kill list
+KILLSCRIPT=/lisc/user/papadopoulos/repos/plit-genome/08-submission/gff-04-build_kill_list.py
+
+# first remove duplicate features
+agat_sp_fix_features_locations_duplicated.pl --gff "$GFF" -o "$DEDUP"
+
+# now find short introns
+agat_sp_list_short_introns.pl --gff "$DEDUP" --size 10 --out "$SHORT_INTRONS"
+
+# this table contains the locus (chromosome), gene, start position, and length of 
+# map the short introns to mRNAs in the GFF3 file
+python $KILLSCRIPT "$SHORT_INTRONS" "$DEDUP" > "$KILL_LIST"
+
+# use the kill list to filter the offending mRNAs out of the GFF3
+agat_sp_filter_feature_from_kill_list.pl --gff "$DEDUP" --kill_list "$KILL_LIST" -p mRNA -o "$FILTERED_GFF"
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