smdabdoub / phylotoast Goto Github PK
View Code? Open in Web Editor NEWTools for phylogenetic data analysis including visualization and cluster-computing support.
Home Page: http://phylotoast.org
License: MIT License
Tools for phylogenetic data analysis including visualization and cluster-computing support.
Home Page: http://phylotoast.org
License: MIT License
The docs say that phylotoast in in pypi but the command pip install phylotoast
fails. A search of the pypi.org website also fails to locate the package.
While using --reverse_lookup
, OTUs not found in taxa file must raise an error and report a helpful suggestion to the user.
Either use a csv.DictReader or have the function return the header line along with existing list of entries.
List of parse_map_file occurrences:
bin/PCoA_bubble.py: imap = util.parse_map_file(args.mapping)
bin/barcode_filter.py: barcodes = util.parse_map_file(mapFN, 1).keys()
bin/iTol.py: imap = util.parse_map_file(args.mapping)
bin/transpose_biom.py: mapping = util.parse_map_file(args.mapping)
Currently, this script uses OTUIDs to get OTU genus-species identifiers. Adding the ability to get OTUIDs from genus-species identifiers (reverse option).
When calculating raw abundance (for example), if there is no overlap in sample IDs between the mapping file and the BIOM table, the output will be zero for each OTU.
While the mapping file is not strictly necessary for calculating raw abundance, it is for the other calculations. As such it is a required argument to the program. Additionally, for greater code simplicity the abundance calculation methods in the biom_calc module take a list of sample IDs. In the case of iTol.py calculating total OTU abundance, it just passes all the sample IDs in the mapping file to the abundance calculation methods. If none of those sample IDs are found in the BIOM table, nothing will be calculated and all zeroes will be output.
For these reasons, changing the code to just for the raw abundance use case would add unnecessary complexity. Instead, a warning should be output if no overlap in sample IDs is found between the mapping file and the BIOM table.
The brewer2mpl library has been replaced by Palettable. The code in PCoA.py and diversity.py should be updated to reflect this.
When attempting to run the PCoA_bubble.py script, I run into the below error:
Traceback (most recent call last): File "/usr/local/bin/PCoA_bubble.py", line 254, in <module> main() File "/usr/local/bin/PCoA_bubble.py", line 251, in main category_colors, xr, yr, args.output_dir) File "/usr/local/bin/PCoA_bubble.py", line 109, in plot_PCoA graph_util.rstyle(ax) AttributeError: 'module' object has no attribute 'rstyle'
From my googling of the issue I'm assuming this has to do with matplotlib, but beyond that I'm helpless. As an aside- there are pretty major differences in the input of this script in the documentation online and the script-as-installed... but that could be the difference between the pip installed version and the github installed version correct?
Changes to biom_calc.py file
The PCoA_bubble script was written very early on, and never updated along with the rest of the visualization scripts. The code needs to be cleaned up in general, but a few specific things need to be addressed:
Move biom_summary() function from otu_calc.py to biom_calc.py.
Changes to otu_calc.py
Hello,
Is there any option to move or remove legend while making PCoA plots? My legend box is inside the plot and it is covering some plot points.
--input_data_type
parameter.
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