From 3031847f7ac73f61355685371c77cff0d745b1b4 Mon Sep 17 00:00:00 2001
From: Niko <nikolaos.papadopoulos@univie.ac.at>
Date: Wed, 27 Nov 2024 15:44:48 +0100
Subject: [PATCH] re-organising submission folder
---
08-submission/gff-01-compose_gff.sh | 23 ++
08-submission/gff-02-functional_annot.ipynb | 220 ++++++++++++++++++
...t_to_embl.sh => gff-03-convert_to_embl.sh} | 5 +-
08-submission/gff-04-submit_to_ENA.sh | 1 +
...me_manifest.py => tx-01-txome_manifest.py} | 0
5 files changed, 247 insertions(+), 2 deletions(-)
create mode 100644 08-submission/gff-01-compose_gff.sh
create mode 100644 08-submission/gff-02-functional_annot.ipynb
rename 08-submission/{convert_to_embl.sh => gff-03-convert_to_embl.sh} (90%)
create mode 100644 08-submission/gff-04-submit_to_ENA.sh
rename 08-submission/{txome_manifest.py => tx-01-txome_manifest.py} (100%)
diff --git a/08-submission/gff-01-compose_gff.sh b/08-submission/gff-01-compose_gff.sh
new file mode 100644
index 0000000..a2c9b89
--- /dev/null
+++ b/08-submission/gff-01-compose_gff.sh
@@ -0,0 +1,23 @@
+#!/usr/bin/env bash
+
+# compose the GFF3 file to prepare for ENA submission
+
+# first gather the various input sources
+BASE=/lisc/scratch/zoology/pycnogonum/genome/draft/annot_merge
+ISOSEQ=$BASE/isoseq.gff
+BRAKER_R1=$BASE/braker.gff
+BRAKER_R2=$BASE/braker2_unique_renamed_nocodon_intron.gff3
+DENOVO=$BASE/overlap_translated.gff3
+
+ls ISOSEQ
+ls BRAKER_R1
+ls BRAKER_R2
+ls DENOVO
+
+# cat isoseq.gff > merged.gff3
+# cat braker.gff >> merged.gff3
+# cat braker2_unique_renamed_nocodon_intron.gff3 >> merged.gff3
+# cat denovo_txomes/overlap_translated.gff3 >> merged.gff3
+# cat ../trnascan/trnascan.gff3 >> merged.gff3
+# module load genometools/
+# gt gff3 -tidy -retainids -o merged_sorted.gff3 -force merged.gff3
\ No newline at end of file
diff --git a/08-submission/gff-02-functional_annot.ipynb b/08-submission/gff-02-functional_annot.ipynb
new file mode 100644
index 0000000..ba2eba6
--- /dev/null
+++ b/08-submission/gff-02-functional_annot.ipynb
@@ -0,0 +1,220 @@
+{
+ "cells": [
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "# Adding functional annotation from EggNOG-mapper\n",
+ "\n"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 1,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "import pandas as pd\n",
+ "import numpy as np"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "best_per_gene = '/Users/npapadop/Documents/data/pycnogonum/draft/out.emapper.best.annotations'\n",
+ "emapper = pd.read_csv(best_per_gene, sep='\\t', header=0)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "def parse_gene_id(x):\n",
+ " if 'PB' in x:\n",
+ " parts = x.split('.')\n",
+ " return '.'.join(parts[:2])\n",
+ " elif x.startswith('r2') or x.startswith('g') or x.startswith('at'):\n",
+ " return x.split('.')[0]\n",
+ " else:\n",
+ " return ValueError('Unknown gene ID format')"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "apply the parsing on each row..."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "emapper['gene'] = emapper['#query'].apply(parse_gene_id)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "emapper.set_index('gene', inplace=True)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 6,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "#query PB.3.1.p1\n",
+ "seed_ortholog 136037.KDR12978\n",
+ "evalue 0.0\n",
+ "score 570.0\n",
+ "eggNOG_OGs COG0462@1|root,KOG1503@2759|Eukaryota,38F3E@33...\n",
+ "max_annot_lvl 33208|Metazoa\n",
+ "COG_category EF\n",
+ "Description ribose phosphate diphosphokinase activity. It ...\n",
+ "Preferred_name PRPSAP1\n",
+ "GOs GO:0001501,GO:0002189,GO:0003674,GO:0004857,GO...\n",
+ "EC -\n",
+ "KEGG_ko -\n",
+ "KEGG_Pathway -\n",
+ "KEGG_Module -\n",
+ "KEGG_Reaction -\n",
+ "KEGG_rclass -\n",
+ "BRITE -\n",
+ "KEGG_TC -\n",
+ "CAZy -\n",
+ "BiGG_Reaction -\n",
+ "PFAMs Pribosyl_synth,Pribosyltran_N\n",
+ "Name: PB.3, dtype: object"
+ ]
+ },
+ "execution_count": 6,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "emapper.loc['PB.3']"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "def parse_attributes(x):\n",
+ " '''Parses a semi-colon separated string into a dictionary\n",
+ "\n",
+ " Parameters\n",
+ " ----------\n",
+ " x : str\n",
+ " a semicolon-separated string that holds attributes\n",
+ " '''\n",
+ " attributes = x.split(';')\n",
+ " if attributes[-1] == '':\n",
+ " attributes.pop()\n",
+ " return {attr.split('=')[0]: attr.split('=')[1] for attr in attributes}"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "'-'"
+ ]
+ },
+ "execution_count": 8,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "emapper.loc['PB.1']['Preferred_name']"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "def find_protein(gene_id, lookup): # expects a protein-coding gene as input\n",
+ " if gene_id in lookup.index:\n",
+ " name = lookup.loc[gene_id]['Preferred_name']\n",
+ " if name != '-':\n",
+ " return name\n",
+ " return f'Uncharacterised protein {gene_id}'"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "gff_loc = '/Volumes/scratch/pycnogonum/genome/submission/merged_sorted.gff'\n",
+ "named_loc = '/Volumes/scratch/pycnogonum/genome/submission/merged_sorted_named.gff'\n",
+ "\n",
+ "with open(gff_loc, 'r') as gff:\n",
+ " with open(named_loc, 'w') as named:\n",
+ " gene = ''\n",
+ " mRNA = ''\n",
+ " for line in gff:\n",
+ " line = line.strip()\n",
+ " conditions_skip = line.startswith('#') or 'tRNA' in line or 'name=' in line\n",
+ " if not conditions_skip:\n",
+ " seq_id, source, feature_type, start, end, score, strand, phase, attributes = line.split('\\t')\n",
+ " attributes = parse_attributes(attributes)\n",
+ " if feature_type == 'gene':\n",
+ " gene = attributes['ID']\n",
+ " name = find_protein(gene, emapper)\n",
+ " line = f'{line}name={name} (predicted)'\n",
+ " if feature_type == 'mRNA':\n",
+ " mRNA = attributes['ID']\n",
+ " isoform = mRNA.split('.')[-1]\n",
+ " line = f'{line}name={name} (predicted) isoform {isoform}'\n",
+ "\n",
+ " named.write(line + '\\n')"
+ ]
+ }
+ ],
+ "metadata": {
+ "kernelspec": {
+ "display_name": "ascc24",
+ "language": "python",
+ "name": "python3"
+ },
+ "language_info": {
+ "codemirror_mode": {
+ "name": "ipython",
+ "version": 3
+ },
+ "file_extension": ".py",
+ "mimetype": "text/x-python",
+ "name": "python",
+ "nbconvert_exporter": "python",
+ "pygments_lexer": "ipython3",
+ "version": "3.9.19"
+ }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}
diff --git a/08-submission/convert_to_embl.sh b/08-submission/gff-03-convert_to_embl.sh
similarity index 90%
rename from 08-submission/convert_to_embl.sh
rename to 08-submission/gff-03-convert_to_embl.sh
index 892017c..8447494 100644
--- a/08-submission/convert_to_embl.sh
+++ b/08-submission/gff-03-convert_to_embl.sh
@@ -4,12 +4,13 @@ module load conda
conda activate emblmygff3
GENOME=/lisc/project/zoology/pycnogonum/paper/results/draft.fasta
-GFF=/lisc/project/zoology/pycnogonum/paper/results/merged_sorted.gff3
+GFF=/lisc/project/zoology/pycnogonum/paper/results/merged_sorted_dedup.gff3
RESDIR=/lisc/scratch/zoology/pycnogonum/genome/submission
cd $RESDIR || exit
EMBLmyGFF3 $GFF $GENOME \
+ --expose_translations \
--topology linear \
--molecule_type 'genomic DNA' \
--transl_table 1 \
@@ -17,5 +18,5 @@ EMBLmyGFF3 $GFF $GENOME \
--taxonomy INV \
--locus_tag VPG \
--project_id PRJEB80537 \
- --verbose \
+ -vvv \
-o result.embl
\ No newline at end of file
diff --git a/08-submission/gff-04-submit_to_ENA.sh b/08-submission/gff-04-submit_to_ENA.sh
new file mode 100644
index 0000000..f1f641a
--- /dev/null
+++ b/08-submission/gff-04-submit_to_ENA.sh
@@ -0,0 +1 @@
+#!/usr/bin/env bash
diff --git a/08-submission/txome_manifest.py b/08-submission/tx-01-txome_manifest.py
similarity index 100%
rename from 08-submission/txome_manifest.py
rename to 08-submission/tx-01-txome_manifest.py
--
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