tagcount with --genemap option about umis HOT 8 CLOSED

Hi Maria,

Sorry for the problem. Hm. You have a pretty old version of umis, it looks like v1.0.3. If you update to 1.0.6 do you still run into this problem?

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Thanks for the suggestion. I've updated to v.1.0.6 but I'm still having the same problem. The error output is:

INFO:umis.umis:Reading optional files
INFO:umis.umis:Tallying evidence
INFO:umis.umis:Processed 1000000 alignments, kept 791808.
INFO:umis.umis:208192 were filtered for being unmapped.
INFO:umis.umis:Processed 2000000 alignments, kept 1584028.
INFO:umis.umis:415972 were filtered for being unmapped.
INFO:umis.umis:Processed 3000000 alignments, kept 2379834.
INFO:umis.umis:620166 were filtered for being unmapped.
INFO:umis.umis:Processed 4000000 alignments, kept 3174835.
INFO:umis.umis:825165 were filtered for being unmapped.
INFO:umis.umis:Processed 5000000 alignments, kept 3969309.
INFO:umis.umis:1030691 were filtered for being unmapped.
INFO:umis.umis:Processed 6000000 alignments, kept 4760607.
INFO:umis.umis:1239393 were filtered for being unmapped.
INFO:umis.umis:Processed 7000000 alignments, kept 5552449.
INFO:umis.umis:1447551 were filtered for being unmapped.
INFO:umis.umis:Processed 8000000 alignments, kept 6349186.
INFO:umis.umis:1650814 were filtered for being unmapped.
INFO:umis.umis:Processed 9000000 alignments, kept 7143504.
INFO:umis.umis:1856496 were filtered for being unmapped.
INFO:umis.umis:Processed 10000000 alignments, kept 7937942.
INFO:umis.umis:2062058 were filtered for being unmapped.
INFO:umis.umis:Tally done - 1.04e+02s, 5,772,446 alns/min
INFO:umis.umis:Collapsing evidence
INFO:umis.umis:Writing evidence
Traceback (most recent call last):
File "/usr/local/bin/python3.6/umis", line 11, in
load_entry_point('umis==1.0.6', 'console_scripts', 'umis')()
File "/usr/lib/python3/dist-packages/click/core.py", line 722, in call
return self.main(*args, **kwargs)
File "/usr/lib/python3/dist-packages/click/core.py", line 697, in main
rv = self.invoke(ctx)
File "/usr/lib/python3/dist-packages/click/core.py", line 1066, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/usr/lib/python3/dist-packages/click/core.py", line 895, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/usr/lib/python3/dist-packages/click/core.py", line 535, in invoke
return callback(*args, **kwargs)
File "/usr/local/lib/python3.6/dist-packages/umis-1.0.6-py3.6-linux-x86_64.egg/umis/umis.py", line 656, in tagcount
genes = expanded.ix[genes.index]
File "/usr/local/lib/python3.6/dist-packages/pandas/core/indexing.py", line 126, in getitem
return self._getitem_axis(key, axis=axis)
File "/usr/local/lib/python3.6/dist-packages/pandas/core/indexing.py", line 1088, in _getitem_axis
return self._getitem_iterable(key, axis=axis)
File "/usr/local/lib/python3.6/dist-packages/pandas/core/indexing.py", line 1205, in _getitem_iterable
raise_missing=False)
File "/usr/local/lib/python3.6/dist-packages/pandas/core/indexing.py", line 1161, in _get_listlike_indexer
raise_missing=raise_missing)
File "/usr/local/lib/python3.6/dist-packages/pandas/core/indexing.py", line 1252, in _validate_read_indexer
raise KeyError("{} not in index".format(not_found))
KeyError: "[] not in index"

from umis.

from umis.

You can download the files from here: https://www.dropbox.com/sh/3c5yilft3ts27o2/AAB_4vahMS2ZttOhEjFEETnNa?dl=0

Thanks for taking a look!

from umis.

Hi Maria!

So sorry, I am dumb-- I asked for the wrong thing. Could you send me around 40k lines of the BAM/SAM file you are looking at.

from umis.

Sorry, for the delayed reply; I somehow missed your last message. I put my sam file with 40k lines in the Dropbox folder above.
Thanks!

from umis.

haha, ok last thing: I also need the header for that file-- when you grab the small subset, could you put that up with samtools view -H?

from umis.

I've updated the sam file so that it contains all of the original header, as well as the first 40k read alignment lines.

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