From 1b37309b84a850a9a29ea61e945794f2ab2135ac Mon Sep 17 00:00:00 2001 From: Yasset Perez-Riverol Date: Thu, 16 Oct 2025 15:32:29 +0100 Subject: [PATCH] add to README --- README.md | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/README.md b/README.md index 5d80d8c..1b0419b 100644 --- a/README.md +++ b/README.md @@ -84,6 +84,17 @@ Additional options: - `--aspera_maximum_bandwidth` flag is used to specify the maximum bandwidth for the Aspera download. The default value is 100M. - `--checksum_check` flag is used to check the checksum of the downloaded files. The default value is False. +## Downloading raw files from ProteomeXchange (PX) + +You can download all raw files referenced by a ProteomeXchange dataset by passing only the accession: + +```bash +$ pridepy download-px-raw-files -a PXD039236 -o /Users/yourname/Downloads/foldername/ +``` + +- The tool resolves the ProteomeXchange XML and downloads via FTP when available, otherwise HTTP(S). +- Resume and skip-if-already-downloaded are supported by default. + ## Download single file by name Users instead of downloading an entire project files may be interested in downloading a single file if they know it by name. Here is how to download a single file by name.