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biocore / wetlab-assistant

BSD 3-Clause "New" or "Revised" License
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added special sample processing function #13

Closed qiyunzhu closed 7 years ago

qiyunzhu commented 7 years ago

Hi all, here is a new function.

In many cases special types of sample names, such as "blank1.A1", "posctl2.B2", etc., are entered in the plate map and the subsequent mapping file. Apparently, those are not real biological samples, but they will be stored in Qiita for reference. Currently, these names are manually typed by the wet lab crew, and their corresponding metadata (person, data, tool...) are manually added by Gail. This process can be simpler. That's the purpose of this PR.

This optional function requires a "special sample definition" file in the disk. It defines each special sample type, its abbr (typically a single key stroke) and its metadata. The user (wet lab) will only have to type the abbr (e.g., "+" for positive control") in the plate map, and the script will translate it into "PosCtl3.C3" based on its definition and position (here primer plate #3, well C3).

For more details please see the updated manual.html and the sample files: /tests/data/xxxx_w_special.txt

Thank you very much if you can review and share your opinion :) @antgonza @josenavas @wasade @sjanssen2 @mortonjt

coveralls commented 7 years ago

Coverage Status

Coverage remained the same at 100.0% when pulling de7023a7be15b2e54f5ab651c4605177a8c0132d on qiyunzhu:validate into c67190b130f352be0e49474a749638f3bb4c8d70 on biocore:master.

coveralls commented 7 years ago

Coverage Status

Coverage remained the same at 100.0% when pulling de7023a7be15b2e54f5ab651c4605177a8c0132d on qiyunzhu:validate into c67190b130f352be0e49474a749638f3bb4c8d70 on biocore:master.

coveralls commented 7 years ago

Coverage Status

Coverage remained the same at 100.0% when pulling 96f195ed5836ad3176d6c4852af1c25be961a615 on qiyunzhu:validate into c67190b130f352be0e49474a749638f3bb4c8d70 on biocore:master.

coveralls commented 7 years ago

Coverage Status

Coverage remained the same at 100.0% when pulling 96f195ed5836ad3176d6c4852af1c25be961a615 on qiyunzhu:validate into c67190b130f352be0e49474a749638f3bb4c8d70 on biocore:master.

qiyunzhu commented 7 years ago

Hello @wasade Thanks for reviewing my code! Sorry for the late response. Here they are. Happy weekend!