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Normalize by median pct #133

Open tshori opened 9 years ago

tshori commented 9 years ago

Hi,

I am trying to compare assemblies normalized with the regular normalize by median and the trinity like normalize by median-pct. However for the later I get the following error from khmer.counting_arg import build_construct_args Import error.

I notice that the most recent version of normalize by median, that particular module is not used anymore, rather it imports khmer.khmer.args. Is the trinity like normalization script completely deprecated or can substitute the model imported and it will work?

T.

ctb commented 9 years ago

On Wed, Sep 24, 2014 at 11:39:20AM -0700, tshori wrote:

I am trying to compare assemblies normalized with the regular normalize by median and the trinity like normalize by median-pct. However for the later I get the following error from khmer.counting_arg import build_construct_args Import error.

I notice that the most recent version of normalize by median, that particular module is not used anymore, rather it imports khmer.khmer.args. Is the trinity like normalization script completely deprecated or can substitute the model imported and it will work?

Good question! If you can get it to run w/o obvious it will be fine, but I'm not sure exactly what will work to do that. I will take a look at it this weekend if I can.

best,

--titus

C. Titus Brown, ctb@msu.edu

tshori commented 9 years ago

Thanks, Titus.

I will give it a try tomorrow.

T. Ultimate stresses sportsmanship and fair play. Competitive play is encouraged, but NEVER AT THE EXPENSE OF RESPECT BETWEEN PLAYERS, adherence to the rules and the BASIC JOY OF PLAY.

On Sep 24, 2014, at 04:10 PM, "C. Titus Brown" notifications@github.com wrote:

On Wed, Sep 24, 2014 at 11:39:20AM -0700, tshori wrote:

I am trying to compare assemblies normalized with the regular normalize by median and the trinity like normalize by median-pct. However for the later I get the following error from khmer.counting_arg import build_construct_args Import error.

I notice that the most recent version of normalize by median, that particular module is not used anymore, rather it imports khmer.khmer.args. Is the trinity like normalization script completely deprecated or can substitute the model imported and it will work?

Good question! If you can get it to run w/o obvious it will be fine, but I'm not sure exactly what will work to do that. I will take a look at it this weekend if I can.

best,

--titus

C. Titus Brown, ctb@msu.edu — Reply to this email directly or view it on GitHub.=