From 41718853eebf408b9ab10597bb9c4e10535c8cab Mon Sep 17 00:00:00 2001 From: Ekaterina Sakharova Date: Mon, 1 Apr 2024 13:50:24 +0100 Subject: [PATCH] fix generate_samplesheet script --- download_data/generate_samplesheet.py | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/download_data/generate_samplesheet.py b/download_data/generate_samplesheet.py index bba29a40a..6a7010951 100644 --- a/download_data/generate_samplesheet.py +++ b/download_data/generate_samplesheet.py @@ -24,7 +24,7 @@ def main(assembly_dir, run_dir, rename_file, output): accession = run_file.split('.')[0].split('_')[0] runs.setdefault(accession, []) runs[accession].append(run_file) - # double check for 2 fastq files or other starnge cases + # double check for 2 fastq files or other strange cases for run_accession in runs: se, pe_forward, pe_reversed = False, False, False if len(runs[run_accession]) > 2: @@ -43,8 +43,14 @@ def main(assembly_dir, run_dir, rename_file, output): file_out.write(','.join(['id', 'assembly', 'fastq_1', 'fastq_2', 'assembly_accession']) + '\n') for run_accession in accessions: list_values = [] + if run_accession not in accessions: + print(f'No {run_accession} in fetched assemblies') + continue assembly_accession = accessions[run_accession] list_values.extend([run_accession, os.path.join(assembly_dir, assemblies[run_accession])]) + if run_accession not in runs: + print(f'No {run_accession} in fetched runs') + continue if len(runs[run_accession]) == 2: if len(runs[run_accession][0].split('_1')) >= 2: run1 = os.path.join(run_dir, runs[run_accession][0])