Closed adamrp closed 9 years ago
:+1:
In running an analysis that was using AG.txt, PGP.txt and others, I ran into a similar issue, tried applying this script but it didn't fix my problem.
Actually looking at the mapping file + the OTU table, there seems to be a mismatch:
In [1]: from biom import load_table
In [2]: from md import load_template_to_dataframe
In [9]: mf = load_template_to_dataframe('AG.txt')
/Users/yoshikivazquezbaeza/.virtualenvs/qiime-dev/lib/python2.7/site-packages/pandas/io/parsers.py:1159: DtypeWarning: Columns (34,200) have mixed types. Specify dtype option on import or set low_memory=False.
data = self._reader.read(nrows)
In [10]: bt = load_table('AG.biom')
In [11]: mfids = set(mf.index.tolist())
In [18]: btids = set(bt.ids('sample'))
In [19]: len(mfids)
Out[19]: 4545
In [21]: len(btids)
Out[21]: 4545
In [23]: len(mfids - btids)
Out[23]: 3459
I gotta go back to the processing directory and checkout whats going on
On Fri, Mar 6, 2015 at 5:26 PM, Yoshiki Vázquez Baeza < notifications@github.com> wrote:
In running an analysis that was using AG.txt, PGP.txt and others, I ran into a similar issue, tried applying this script but it didn't fix my problem.
Actually looking at the mapping file + the OTU table, there seems to be a mismatch:
In [1]: from biom import load_table
In [2]: from md import load_template_to_dataframe
In [9]: mf = load_template_to_dataframe('AG.txt')/Users/yoshikivazquezbaeza/.virtualenvs/qiime-dev/lib/python2.7/site-packages/pandas/io/parsers.py:1159: DtypeWarning: Columns (34,200) have mixed types. Specify dtype option on import or set low_memory=False. data = self._reader.read(nrows)
In [10]: bt = load_table('AG.biom')
In [11]: mfids = set(mf.index.tolist())
In [18]: btids = set(bt.ids('sample'))
In [19]: len(mfids) Out[19]: 4545
In [21]: len(btids) Out[21]: 4545
In [23]: len(mfids - btids) Out[23]: 3459
— Reply to this email directly or view it on GitHub https://github.com/biocore/American-Gut/pull/131#issuecomment-77661060.
Were these zeroes added back in by some other fashion, or are we still investigating? If this PR is not needed any more, please close.
Regenerated, this should be safe to close
On Wed, Mar 25, 2015 at 11:02 AM, adamrp notifications@github.com wrote:
Were these zeroes added back in by some other fashion, or are we still investigating? If this PR is not needed any more, please close.
— Reply to this email directly or view it on GitHub https://github.com/biocore/American-Gut/pull/131#issuecomment-86122206.
Not sure when/why they were removed, but this adds them back in. I used the code at the following gist:
https://gist.github.com/adamrp/cc337b63e7ac33160f4b
Fixes #130