From b387ad91c548b23f6b2265f1fb72abdd501373e2 Mon Sep 17 00:00:00 2001
From: Niko <nikolaos.papadopoulos@univie.ac.at>
Date: Wed, 27 Nov 2024 22:13:52 +0100
Subject: [PATCH] fixed paths, added validate script
---
08-submission/Makefile | 13 ++++++++-----
08-submission/gff-03-ENA_conform.sh | 19 ++++++++++++-------
08-submission/gff-04-convert_to_embl.sh | 8 +++++---
08-submission/gff-05-submit_to_ENA.sh | 13 +++++++++++++
4 files changed, 38 insertions(+), 15 deletions(-)
diff --git a/08-submission/Makefile b/08-submission/Makefile
index 273236f..a5c23d3 100644
--- a/08-submission/Makefile
+++ b/08-submission/Makefile
@@ -4,10 +4,7 @@ compose:
bash gff-01-compose_gff.sh
annotate:
- module load conda
- # a conda environment that has pandas and can run jupyter notebooks
- conda activate jupyterhub-5.1.0
- jupyter nbconvert --to notebook --execute gff-02-annotate.ipynb
+ bash gff-02-functional_annot.sh
conform:
bash gff-03-ENA_conform.sh
@@ -16,4 +13,10 @@ embl:
bash gff-04-convert_to_embl.sh
validate:
- bash gff-05-submit_to_ENA.sh validate
\ No newline at end of file
+ bash gff-05-submit_to_ENA.sh -validate
+
+submit:
+ bash gff-05-submit_to_ENA.sh -submit
+
+all: compose annotate conform embl validate 2>&1 | tee log.txt
+ @echo Done.
\ No newline at end of file
diff --git a/08-submission/gff-03-ENA_conform.sh b/08-submission/gff-03-ENA_conform.sh
index 4a3249d..398fec2 100644
--- a/08-submission/gff-03-ENA_conform.sh
+++ b/08-submission/gff-03-ENA_conform.sh
@@ -13,15 +13,16 @@ 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=$BASE/kill_list.tsv
+GFF=./merged_sorted_named.gff3
+DEDUP=./merged_sorted_named_dedup.gff3
+SHORT_INTRONS=./short_introns.tsv
+KILL_LIST=./kill_list.tsv
-FILTERED_GFF=$BASE/merged_sorted_named_dedup_filtered.gff3
+FILTERED_GFF=./merged_sorted_named_dedup_filtered.gff3
+FILTERED_mRNA=./short_introns.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
+KILLSCRIPT=/lisc/user/papadopoulos/repos/plit-genome/08-submission/gff-03-build_kill_list.py
# first remove duplicate features
agat_sp_fix_features_locations_duplicated.pl --gff "$GFF" -o "$DEDUP"
@@ -31,7 +32,11 @@ 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
+# this was written in Python 3.12 but Python >3 should be fine; we only use default libraries
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 "$FILTERED_GFF"
\ No newline at end of file
+agat_sp_filter_feature_from_kill_list.pl --gff "$DEDUP" --kill_list "$KILL_LIST" -p mRNA -o "$FILTERED_GFF"
+
+# also make a supplementary GFF with only the short introns:
+agat_sp_filter_feature_from_keep_list.pl --gff "$DEDUP" --keep_list "$KILL_LIST" -p mRNA -o "$FILTERED_mRNA"
\ No newline at end of file
diff --git a/08-submission/gff-04-convert_to_embl.sh b/08-submission/gff-04-convert_to_embl.sh
index 8447494..bbe13d8 100644
--- a/08-submission/gff-04-convert_to_embl.sh
+++ b/08-submission/gff-04-convert_to_embl.sh
@@ -3,8 +3,8 @@
module load conda
conda activate emblmygff3
-GENOME=/lisc/project/zoology/pycnogonum/paper/results/draft.fasta
-GFF=/lisc/project/zoology/pycnogonum/paper/results/merged_sorted_dedup.gff3
+GENOME=/lisc/project/zoology/pycnogonum/paper/zenodo/results/draft.fasta
+GFF=/lisc/scratch/zoology/pycnogonum/genome/submission/merged_sorted_named_dedup_filtered.gff3
RESDIR=/lisc/scratch/zoology/pycnogonum/genome/submission
cd $RESDIR || exit
@@ -19,4 +19,6 @@ EMBLmyGFF3 $GFF $GENOME \
--locus_tag VPG \
--project_id PRJEB80537 \
-vvv \
- -o result.embl
\ No newline at end of file
+ -o result.embl
+
+gzip result.embl
\ No newline at end of file
diff --git a/08-submission/gff-05-submit_to_ENA.sh b/08-submission/gff-05-submit_to_ENA.sh
index f1f641a..947b173 100644
--- a/08-submission/gff-05-submit_to_ENA.sh
+++ b/08-submission/gff-05-submit_to_ENA.sh
@@ -1 +1,14 @@
#!/usr/bin/env bash
+
+# submit the GFF3 file to ENA. Assumes we are in the submission directory
+# and the genome manifest file is present and valid.
+module load java
+
+MODE=$1 # either -validate or -submit
+
+java -jar ~/bin/webin-cli-8.0.0.jar \
+ -context genome \
+ -userName Webin-68127 \
+ -passwordFile ~/webin.pwd \
+ -manifest genome.manifest \
+ "$MODE"
\ No newline at end of file
--
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