Closed dswan closed 5 years ago
That's odd. Do you mind sending the fasta sequences for particular query sequence and database hits to us (qunfengd@gmail.com). We'd like to repeat it. The only reason I can think of now is that the other hits do not have good alignment coverage as in the top hits.
On Wed, May 29, 2019 at 6:57 AM Dr. Daniel Swan notifications@github.com wrote:
I don't know if this is a feature of my dataset or not. I have a dataset of ~100k sequences from various sources.
I'm getting an identification from a particular sequence:
Consensus superkingdom:Bacteria;100.0;phylum:Firmicutes;100.0;class:Bacilli;100.0;order:Bacillales;100.0;family:Bacillaceae;100.0;genus:Bacillus;100.0;species:Bacillus zhangzhouensis;100.0;
But actually this is a very short sequence which matches equally well:
Top 2 hits from blast file:
Consensus 1ef276d07f3045c7293275c749dc254a 100.000 599 0 0 1 599 20 618 0.0 1107 599 plus 1513 599 Consensus a6cf5d187e2a898b1f278069046fef6d 100.000 599 0 0 1 599 20 618 0.0 1107 599 plus 1529 599
Bottom 2 hits from blast file:
Consensus dd9a3ce113e3dc10a53045dcce4682fb 100.000 598 0 0 2 599 1 598 0.0 1105 598 plus 1474 599 Consensus ba471a3dc4742f1e5440a0d9de8e9283 100.000 598 0 0 2 599 1 598 0.0 1105 598 plus 1474 599
This is a sequence I would have expected more 'uncertainty' over and potentially not to be reporting back "100" values at the full taxonomy (I would expect this back to Bacillus genus).
Am I misinterpreting the scoring, and is there anything I'm missing with regards to the analysis?
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I have included some files to you via email - thanks!
OK some further digging, this issue isn't present in fb2bd12 - using python2.7 and muscle. It appears in 32c8cf7 with clustalo and python3. I'm using the same input file (the standard test.fasta) and NCBI database, and only in release fb2bd12 do I get scores <100 at the species level
There may have been some unintended consequences of the move to python3. The python2.7 "release" that shares the core code with the python3 release still has issue #13 (or similar) on the default NCBI database run with python2.7 but fb2bd12 runs fine.
Hi Dr. Swan,
Thanks for taking the effort to dig into this. I found out this python version problem too, and I am in the process of fixing it. It seems to be a python 3 dictionary issue. I am thinking to use the defaultdict from collections package. I am still in the process of testing and implementing.
Thanks again for your help, I will keep you posted when this bug is resolved.
Best,
Eddi
On Mon, Jun 3, 2019 at 5:14 AM Dr. Daniel Swan notifications@github.com wrote:
There may have been some unintended consequences of the move to python3. The python2.7 "release" that shares the core code with the python3 release still has issue #13 https://github.com/qunfengdong/BLCA/issues/13 or similar when run with python2.7 but fb2bd12 https://github.com/qunfengdong/BLCA/commit/fb2bd12afc1dbf2c67c82a9c9d5aad91783034b5 runs fine.
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Hi Daniel - thanks so much for your efforts. We have fixed the hidden bug and github is now updated.
On Mon, Jun 3, 2019 at 5:14 AM Dr. Daniel Swan notifications@github.com wrote:
There may have been some unintended consequences of the move to python3. The python2.7 "release" that shares the core code with the python3 release still has issue #13 https://github.com/qunfengdong/BLCA/issues/13 or similar when run with python2.7 but fb2bd12 https://github.com/qunfengdong/BLCA/commit/fb2bd12afc1dbf2c67c82a9c9d5aad91783034b5 runs fine.
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@yingeddi2008 @qunfengdong - I can confirm that this is fixed at my end too and it now works with python 2.7 and 3.6 - thanks so much for your prompt attention!
There might be a little issue with some of the floating point maths:
Bacillus_test superkingdom:Bacteria;100.00000000000001;phylum:Firmicutes;100.00000000000001;class:Bacilli;100.00000000000001;order:Bacillales;100.00000000000001;family:Bacillaceae;100.00000000000001;genus:Bacillus;100.00000000000001;species:Bacillus subtilis;92.00000000000001;
But I can certainly work around that for now!
I don't know if this is a feature of my dataset or not. I have a dataset of ~100k sequences from various sources.
I'm getting an identification from a particular sequence:
Consensus superkingdom:Bacteria;100.0;phylum:Firmicutes;100.0;class:Bacilli;100.0;order:Bacillales;100.0;family:Bacillaceae;100.0;genus:Bacillus;100.0;species:Bacillus zhangzhouensis;100.0;
But actually this is a very short sequence which matches equally well:
Top 2 hits from blast file:
Bottom 2 hits from blast file:
This is a sequence I would have expected more 'uncertainty' over and potentially not to be reporting back "100" values at the full taxonomy (I would expect this back to Bacillus genus).
Am I misinterpreting the scoring, and is there anything I'm missing with regards to the analysis?
Are there any concerns with using a full length gene database with a shorter input query?