From ba1d59d5965c23e395e22b0b36698a19d1388e44 Mon Sep 17 00:00:00 2001 From: Yaobo Xu Date: Mon, 26 Nov 2018 11:49:57 +0000 Subject: [PATCH 1/2] ignore hidden folder of vscode --- .gitignore | 1 + 1 file changed, 1 insertion(+) diff --git a/.gitignore b/.gitignore index 97b2970..20c9383 100644 --- a/.gitignore +++ b/.gitignore @@ -10,3 +10,4 @@ htmlcov/ /build /dist /cgp_seq_input_val.egg-info +.vscode \ No newline at end of file From 80b94b928e64460afe2e49e616c8d9f529f10fdb Mon Sep 17 00:00:00 2001 From: Yaobo Xu Date: Mon, 26 Nov 2018 11:50:54 +0000 Subject: [PATCH 2/2] made validator fastq extentsion checks consistent with manifest.py --- CHANGES.md | 4 ++++ cgp_seq_input_val/seq_validator.py | 3 ++- setup.py | 2 +- 3 files changed, 7 insertions(+), 2 deletions(-) diff --git a/CHANGES.md b/CHANGES.md index a3c6bce..ecf5dcf 100644 --- a/CHANGES.md +++ b/CHANGES.md @@ -1,5 +1,9 @@ # CHANGES +## 1.4.1 + +* `validator` now allows upper case in FastQ file name extensions + ## 1.4.0 * Correct base config for file types accepted. File_2 should only accept `f(?:ast)q.gz` (upper/lower) diff --git a/cgp_seq_input_val/seq_validator.py b/cgp_seq_input_val/seq_validator.py index 0bf48e1..0be426d 100644 --- a/cgp_seq_input_val/seq_validator.py +++ b/cgp_seq_input_val/seq_validator.py @@ -94,7 +94,8 @@ def _prep(self): full_ext = ext (base, ext) = os.path.splitext(base) - if ext not in ('.fastq', '.fq'): + if ext.lower() not in ('.fastq', '.fq'): + # This check should be consistent with FastQ file extension restrictions in manifest.py raise SeqValidationError("Input files must be fastq|fq[.gz]") full_ext = ext + full_ext diff --git a/setup.py b/setup.py index 210c8c5..649d9fb 100755 --- a/setup.py +++ b/setup.py @@ -9,7 +9,7 @@ 'url': 'https://github.com/cancerit/cgp_seq_input_val', 'download_url': '', 'author_email': 'cgphelp@sanger.ac.uk', - 'version': '1.4.0', + 'version': '1.4.1', 'python_requires': '>= 3.6', 'setup_requires': ['pytest'], 'install_requires': ['progressbar2', 'xlrd', 'xopen'],