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View Code? Open in Web Editor NEWA python package that consists of functions that process publicly available annotated sets of genes
License: Other
A python package that consists of functions that process publicly available annotated sets of genes
License: Other
This issue was imported from the old repository in bitbucket (https://bitbucket.org/greenelab/annotation-refinery/issues).
This affects the download_from_url() function in utils.py. This is a documented issue in Python, which persists in the newest version (v2.7.13), at the time this issue was created (http://bugs.python.org/issue27973).
This is an older issue, copied from https://bitbucket.org/rzelayafavila/annotation-refinery/issues
This is a very minor issue:
When running cron_update_public_tribe.sh
initially on my desktop, I noticed that line 5:
rm -r download_files/
complained that download_files
doesn't exist. It can be fixed by either:
if [ -e download_files ]; then
rm -r download_files
fi
or simply:
rm -rf download_files
(Note that the trailing /
in download_files/
is removed too, because download_files
should be deleted regardless of whether it is a directory or not.)
This is to follow a loose-coupling model, so that certain parts of the code can be imported and called from anywhere.
This issue was imported from the old repository in bitbucket (https://bitbucket.org/greenelab/annotation-refinery/issues).
This was brought up in #8.
The ftp://ftp.geneontology.org/go/gene-associations/goa_uniprot_all_noiea.gaf.gz
URL was being used as one of the GO ASSOC_FILE_URLS
for all of the species, so we thought we could abstract it to the main_config.ini
file. It can have a name like COMMON_GO_ASSOC_URLS
or something similar, and the code in download_files.py
and process_go.py
will need to get it from this new location, instead of its old location in the .ini files.
This sounds like it is more of an issue in Tribe than the annotation-refinery. Cross-linking with Tribe issue:
greenelab/tribe#5
This would be used in the process_go.py, process_kegg.py and process_do.py files.
As per Matt's suggestion, it could look something like this:
def filename_from_url(self, folder, urlstr):
return os.path.join(folder, 'DO', os.path.basename(urlsplit(urlstr).path))
This issue was imported from the old repository in bitbucket (https://bitbucket.org/greenelab/annotation-refinery/issues).
I found a few typos in README.rst
:
Line 19: amon
should be among
.
Line 33: loaded to
probably should be uploaded to
, downloaded to
should be downloaded from
.
Line 43: this files
should be this file
.
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