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COMBINE-lab / RapClust

Accurate, Lightweight Clustering of de novo Transcriptomes using Fragment Equivalence Classes
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issue 9 possible resolution #10

Closed k3yavi closed 8 years ago

k3yavi commented 8 years ago

Please check the modifications if looks sensible than kindly merge.

rob-p commented 8 years ago

Hi @keyavi,

These look good, except that rather than force the user to provide the aux directory, I'd read it in from the cmd_info.json file in the quant directory. Both sailfish and salmon write out such a file. If there is no entry for auxDir, it's safe to assume it takes the value aux. Otherwise, the aux directory should be given then name it has according to the cmd_info.json file. You can take a look at how I handle this in wasabi if my description here isn't clear.

k3yavi commented 8 years ago

Hi @rob-p , Yes you are right about putting aux conditionally depending on user's choice. That's why I made eqfilesuffix flag as non necessary flag and provided aux as the default path if not provided. I avoided putting things into YAML since all the tags in YAML were necessary. Hope it make sense.

rob-p commented 8 years ago

@keyavi ,

Right; I'm not suggesting putting it in the yaml, I'm suggesting reading it from the output of sailfish / salmon. If the user specifies a non-standard (i.e. non-aux) parameter, then the path they provided to sailfish / salmon will be encoded in the cmd_info.json file in salmon's / sailfish's quantification directory.

k3yavi commented 8 years ago

Please check #11

rob-p commented 8 years ago

This is superseded by PR#11.