From 1937ff702ea26357ba7f7495f46960989e475757 Mon Sep 17 00:00:00 2001 From: Claude Date: Mon, 2 Feb 2026 21:38:20 +0000 Subject: [PATCH] Fix CLI command names in README to match actual implementation - Update help output block to show correct commands: - Remove non-existent: get-files-by-filter, get-files-by-project-accession, get-private-files, get-projects, get-projects-by-accession - Add missing: download-all-public-category-files, download-px-raw-files, list-private-files - Fix download-files-by-category -> download-all-public-category-files - Use consistent 'pridepy' command instead of 'python -m pridepy.pridepy' Fixes #82 https://claude.ai/code/session_017TpGVPTK44DCWtaSpVHaVj --- README.md | 23 ++++++++++------------- 1 file changed, 10 insertions(+), 13 deletions(-) diff --git a/README.md b/README.md index 6a8f38a..71a88c0 100644 --- a/README.md +++ b/README.md @@ -49,17 +49,14 @@ Options: --help Show this message and exit. Commands: - download-all-public-raw-files Download all public raw files... - download-file-by-name Download a single file from a... - get-files-by-filter get paged files :return: - get-files-by-project-accession get files by project accession... - get-private-files Get private files by project... - get-projects get paged projects :return: - get-projects-by-accession get projects by accession... - stream-files-metadata Stream all files metadata in... - stream-projects-metadata Stream all projects metadata... - search-projects-by-keywords-and-filters Search all projects by keywords... - + download-all-public-raw-files Download all public raw files... + download-all-public-category-files Download all public files of specific category... + download-file-by-name Download a single file from a... + download-px-raw-files Download all raw files referenced by a ProteomeXchange... + list-private-files List private files by project accession... + search-projects-by-keywords-and-filters Search all projects by keywords... + stream-files-metadata Stream all files metadata in... + stream-projects-metadata Stream all projects metadata... ``` > [!NOTE] > Please make sure you are using Python3, not Python 2.7 version. @@ -118,7 +115,7 @@ Users may be interested in downloading files by category. Here is how to downloa - FASTA: FASTA files ```bash -$ pridepy download-files-by-category -a PXD022105 -o /Users/yourname/Downloads/foldername/ -c RAW -p ftp +$ pridepy download-all-public-category-files -a PXD022105 -o /Users/yourname/Downloads/foldername/ -c RAW -p ftp ``` Please be aware that the additional parameters are the same as the previous command [Downloading a project from PRIDE Archive](#downloading-a-project-from-pride-archive). @@ -173,7 +170,7 @@ $ pridepy stream-files-metadata -o PXD005011_files.json -a PXD005011 Get the Project metadata by keywords and filters ```bash -$ python -m pridepy.pridepy search-projects-by-keywords-and-filters -f projectTags==Proteometools,organismsPart==Pancreas -k human -sd DESC -sf accession -sf submissionDate +$ pridepy search-projects-by-keywords-and-filters -f projectTags==Proteometools,organismsPart==Pancreas -k human -sd DESC -sf accession -sf submissionDate ``` # White paper