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edgraham / PhylogenomicsWorkflow

A workflow to generate a phylogentic tree with your Genomes
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Issues with identityHMM #1

Open arghya1611 opened 4 years ago

arghya1611 commented 4 years ago

Hi, Came across identityHMM quite accidentally. Very handy tool!! I faced few issues which I am listing below:

  1. identityHMM had trouble importing biopython in a conda environment. My guess is it was calling the default python of the system. Specifying the conda environment python solved the issue. You may add a note for future users. Ex. /conda/your/environment/bin/python identityHMM --markerdb .....

  2. Line 62: if arg_dict["cut_tc"] == "True" should be if arg_dict["cut_tc"] == True Keeps the --cut_tc option of identityHMM from working.

  3. Typo in Line 61. viz. hmmer_log = open("hmmsearhc-log.txt","w")

I was also wondering if the ribosomal protein HMM file provided has been updated since the Hug et al publication?

edgraham commented 4 years ago

Hello,

I’m glad you found it useful! Thanks for these comments, I’ll fix these issues for future use (I do think the latter two issues may are python versioning as those two latter functions had worked previously).

In terms of conda it seems odd that you’d have to specify the biopython conda location. If you’ve activated your conda environment it should by default call the conda versions of everything preferentially and only call the system version if there is not one installed via conda. I’ll have to check this out and see what’s going on there.

Just for a quick bit of info what version of conda/python are you using?

-Elaina

On Dec 30, 2019, at 4:00 PM, Arghya Mukherjee notifications@github.com wrote:

 Hi, Came across identityHMM quite accidentally. Very handy tool!! I faced few issues which I am listing below:

identityHMM had trouble importing biopython in a conda environment. My guess is it was calling the default python of the system. Specifying the conda environment python solved the issue. You may add a note for future users. Ex. /conda/your/environment/bin/python identityHMM --markerdb .....

Line 62: if arg_dict["cut_tc"] == "True" should be if arg_dict["cut_tc"] == True Keeps the --cut_tc option of identityHMM from working.

Typo in Line 61. viz. hmmer_log = open("hmmsearhc-log.txt","w")

I was also wondering if the ribosomal protein HMM file provided has been updated since the Hug et al publication?

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arghya1611 commented 4 years ago

Hi, Sorry for the very late reply. The conda version is 4.7.12.

arghya1611 commented 4 years ago

Hi, I also wanted to add that if possible you could add some lines to the code to output a tab-delimited file giving us a matrix of number of copies of ribosomal proteins found in the genomes. Genomes in Rows and ribosomal proteins in columns. Just a suggestion. Cheers,