From 527f6dc5f30f1b3642d985cb3382e8a604d09a99 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E2=80=98ens-ftricomi=E2=80=99?= Date: Fri, 6 Oct 2023 11:02:48 +0100 Subject: [PATCH] fixed directory paths --- .../ensembl/tools/anno/transcriptomic_annotation/star.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/python/ensembl/tools/anno/transcriptomic_annotation/star.py b/src/python/ensembl/tools/anno/transcriptomic_annotation/star.py index 33f9ad6..ec736c5 100644 --- a/src/python/ensembl/tools/anno/transcriptomic_annotation/star.py +++ b/src/python/ensembl/tools/anno/transcriptomic_annotation/star.py @@ -98,8 +98,8 @@ def run_star( star_dir = create_dir(output_dir, "star_output") for output_file in [ - output_dir / "stringtie_output" / "annotation.gtf", - output_dir / "scallop_output" / "annotation.gtf", + Path(f"{output_dir}/stringtie_output/annotation.gtf"), + Path(f"{output_dir}/scallop_output/annotation.gtf"), ]: if output_file.exists(): transcript_count = check_gtf_content(output_file, "transcript") # check a gtf @@ -253,7 +253,7 @@ def _create_paired_paths(fastq_file_paths: List) -> List[Path]: path_dict = {} # final_list = [] for fastq_file in fastq_file_paths: - paired_name = re.search(r"(.+)_\d+\.(fastq|fq)", fastq_file) + paired_name = re.search(r"(.+)_\d+\.(fastq|fq)", str(fastq_file)) if not paired_name: logging.exception( "Could not find _1 or _2 at the end of the prefix \