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README.postprocessing_partitions.txt
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README.postprocessing_partitions.txt
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### This is for the partitions, for the main results see (first) README.postprocessing.txt.
### First ensure you have done everything in README.preprocessing.txt (this one is not specific to the paritions).
### And of course you need to run the code [TED, can you please make README.processing_partitions.txt like this one with how you created the partitions and the partitions results?]
## Assuming you've already done the prep in README.postprocessing.txt
### First we need to gather the identify_founders results. We do this using the postProcessIdentifyFounders.sh script, which essetntially just concatenates all of the identify_founders.tab files from the subdirectories, but retains only one header.
## caprisa_002 v3:
./postProcessIdentifyFounders.sh /fh/fast/edlefsen_p/bakeoff/gold_standard/caprisa_002/v3/ /fh/fast/edlefsen_p/bakeoff/analysis_sequences/raw_edited_20160216/v3_edited_20160216/1m/partitions /fh/fast/edlefsen_p/bakeoff_analysis_results/raw_edited_20160216/v3_edited_20160216/1m/partitions 1 caprisa002 1M V3
./postProcessIdentifyFounders.sh /fh/fast/edlefsen_p/bakeoff/gold_standard/caprisa_002/v3/ /fh/fast/edlefsen_p/bakeoff/analysis_sequences/raw_edited_20160216/v3_edited_20160216/6m/partitions /fh/fast/edlefsen_p/bakeoff_analysis_results/raw_edited_20160216/v3_edited_20160216/6m/partitions 1 caprisa002 6M V3
./postProcessIdentifyFounders.sh /fh/fast/edlefsen_p/bakeoff/gold_standard/caprisa_002/v3/ /fh/fast/edlefsen_p/bakeoff/analysis_sequences/raw_edited_20160216/v3_edited_20160216/1m6m/partitions /fh/fast/edlefsen_p/bakeoff_analysis_results/raw_edited_20160216/v3_edited_20160216/1m6m/partitions 1 caprisa002 1M6M V3
## ERE I AM. TODO: evaluateAllFoundersCap, etc. FOR NOW JUST LOOKING AT TIMING RESULTS OF THE PARTITIONS.
### To evaluate the ancestral sequence calls, we use evaluateAllFounders.sh and evaluateAllFoundersCap.sh, and see below for Infer results.
## caprisa_002 v3:
./evaluateAllFoundersCap.sh /fh/fast/edlefsen_p/bakeoff/gold_standard/caprisa_002/v3/ /fh/fast/edlefsen_p/bakeoff/analysis_sequences/raw_edited_20160216/v3_edited_20160216/1m/ /fh/fast/edlefsen_p/bakeoff_analysis_results/raw_edited_20160216/v3_edited_20160216/1m/ 1
./evaluateAllFoundersCap.sh /fh/fast/edlefsen_p/bakeoff/gold_standard/caprisa_002/v3/ /fh/fast/edlefsen_p/bakeoff/analysis_sequences/raw_edited_20160216/v3_edited_20160216/6m/ /fh/fast/edlefsen_p/bakeoff_analysis_results/raw_edited_20160216/v3_edited_20160216/6m/ 1
./evaluateAllFoundersCap.sh /fh/fast/edlefsen_p/bakeoff/gold_standard/caprisa_002/v3/ /fh/fast/edlefsen_p/bakeoff/analysis_sequences/raw_edited_20160216/v3_edited_20160216/1m6m/ /fh/fast/edlefsen_p/bakeoff_analysis_results/raw_edited_20160216/v3_edited_20160216/1m6m/ 1
### To evaluate PREAST's ancestral sequence calls, we use evaluateAllFoundersFromInfer.sh and evaluateAllFoundersFromInferCap.sh.
## caprisa_002 v3:
./evaluateAllFoundersFromInferCap.sh /fh/fast/edlefsen_p/bakeoff/gold_standard/caprisa_002/v3/ /fh/fast/edlefsen_p/bakeoff/analysis_sequences/raw_edited_20160216/v3_edited_20160216/1m/ /fh/fast/edlefsen_p/bakeoff_analysis_results/raw_edited_20160216/v3_edited_20160216/1m/infer/ 1
./evaluateAllFoundersFromInferCap.sh /fh/fast/edlefsen_p/bakeoff/gold_standard/caprisa_002/v3/ /fh/fast/edlefsen_p/bakeoff/analysis_sequences/raw_edited_20160216/v3_edited_20160216/6m/ /fh/fast/edlefsen_p/bakeoff_analysis_results/raw_edited_20160216/v3_edited_20160216/6m/infer/ 1
./evaluateAllFoundersFromInferCap.sh /fh/fast/edlefsen_p/bakeoff/gold_standard/caprisa_002/v3/ /fh/fast/edlefsen_p/bakeoff/analysis_sequences/raw_edited_20160216/v3_edited_20160216/1m6m/ /fh/fast/edlefsen_p/bakeoff_analysis_results/raw_edited_20160216/v3_edited_20160216/1m6m/infer/ 1
### Now we need to gather the evaluateFounders.tbl results. We do this using prepareForPostProcessEvaluateFounders.sh.
## caprisa_002 v3:
./prepareForPostProcessEvaluateFounders.sh /fh/fast/edlefsen_p/bakeoff/gold_standard/caprisa_002/v3/ /fh/fast/edlefsen_p/bakeoff_analysis_results/raw_edited_20160216/v3_edited_20160216/1m
./prepareForPostProcessEvaluateFounders.sh /fh/fast/edlefsen_p/bakeoff/gold_standard/caprisa_002/v3/ /fh/fast/edlefsen_p/bakeoff_analysis_results/raw_edited_20160216/v3_edited_20160216/6m
./prepareForPostProcessEvaluateFounders.sh /fh/fast/edlefsen_p/bakeoff/gold_standard/caprisa_002/v3/ /fh/fast/edlefsen_p/bakeoff_analysis_results/raw_edited_20160216/v3_edited_20160216/1m6m
infer:
./prepareForPostProcessEvaluateFounders.sh /fh/fast/edlefsen_p/bakeoff/gold_standard/caprisa_002/v3/ /fh/fast/edlefsen_p/bakeoff_analysis_results/raw_edited_20160216/v3_edited_20160216/1m/infer
./prepareForPostProcessEvaluateFounders.sh /fh/fast/edlefsen_p/bakeoff/gold_standard/caprisa_002/v3/ /fh/fast/edlefsen_p/bakeoff_analysis_results/raw_edited_20160216/v3_edited_20160216/6m/infer
./prepareForPostProcessEvaluateFounders.sh /fh/fast/edlefsen_p/bakeoff/gold_standard/caprisa_002/v3/ /fh/fast/edlefsen_p/bakeoff_analysis_results/raw_edited_20160216/v3_edited_20160216/1m6m/infer
#####################################################
## Completes analysis of isMultiple for all three: nflg and both v3s:
#./evaluateIsMultiple.bash /fh/fast/edlefsen_p/bakeoff_analysis_results/raw_edited_20160216
./evaluateTimings.sh
#./postProcessEvaluateFounders.sh