From 0bdd277c2b3820c57df53c9a4ccc0991cef30036 Mon Sep 17 00:00:00 2001
From: Niko <nikolaos.papadopoulos@univie.ac.at>
Date: Wed, 27 Nov 2024 21:07:50 +0100
Subject: [PATCH] wrapper for functional input notebook; fixed double/missing
semicolons
---
08-submission/gff-02-functional_annot.ipynb | 10 ++++++----
08-submission/gff-02-functional_annot.sh | 10 ++++++++++
2 files changed, 16 insertions(+), 4 deletions(-)
create mode 100644 08-submission/gff-02-functional_annot.sh
diff --git a/08-submission/gff-02-functional_annot.ipynb b/08-submission/gff-02-functional_annot.ipynb
index c26e7eb..98a24f3 100644
--- a/08-submission/gff-02-functional_annot.ipynb
+++ b/08-submission/gff-02-functional_annot.ipynb
@@ -148,7 +148,7 @@
},
{
"cell_type": "code",
- "execution_count": 7,
+ "execution_count": null,
"metadata": {},
"outputs": [],
"source": [
@@ -162,6 +162,8 @@
" # for line in tqdm(gff.readlines()):\n",
" for line in gff.readlines():\n",
" line = line.strip()\n",
+ " if line[-1] == ';':\n",
+ " line = line[:-1]\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",
@@ -170,13 +172,13 @@
" gene = attributes['ID']\n",
" name = find_protein(gene, emapper)\n",
" name = f'{name} (predicted)'\n",
- " line = f'{line}name={name}'\n",
+ " line = f'{line};name={name}'\n",
" if feature_type == 'mRNA':\n",
" mRNA = attributes['ID']\n",
" isoform = mRNA.split('.')[-1]\n",
- " line = f'{line}name={name} isoform {isoform};gene_name={name}'\n",
+ " line = f'{line};name={name} isoform {isoform};gene_name={name}'\n",
" if feature_type == 'CDS' or feature_type == 'exon':\n",
- " line = f'{line}gene_name={name}'\n",
+ " line = f'{line};gene_name={name}'\n",
" named.write(line + '\\n')"
]
}
diff --git a/08-submission/gff-02-functional_annot.sh b/08-submission/gff-02-functional_annot.sh
new file mode 100644
index 0000000..ff226d6
--- /dev/null
+++ b/08-submission/gff-02-functional_annot.sh
@@ -0,0 +1,10 @@
+#!/usr/bin/env bash
+
+# wrapper script for the functional annotation of the GFF3 file, which is a jupyter notebook
+
+module load conda
+
+conda activate jupyterhub-5.2.1
+# a conda environment that has pandas and can run jupyter notebooks
+
+jupyter execute gff-02-functional_annot.ipynb
\ No newline at end of file
--
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