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ypriverol merged 2 commits into from
Feb 3, 2026
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Dev #84

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1937ff7
Fix CLI command names in README to match actual implementation
claude Feb 2, 2026
7ae198d
Merge pull request #83 from PRIDE-Archive/claude/verify-readme-cli-ex…
ypriverol Feb 3, 2026
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23 changes: 10 additions & 13 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -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.
Expand Down Expand Up @@ -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).
Expand Down Expand Up @@ -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
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