plate ID and empty metadata parsing

[qiyunzhu]

Upon the requests from the wet lab crew, I modified two functions: 1) "plate ID" matters, in addition to the "primer plate ID". The plate name is the first cell of a plate (upper left most). It can be any string. The "ID" is identified as the trailing numeric part of this string (if any). For example, "plate 15", "Plate15", "plate #15", "Fecal plate 15" are all valid, and their IDs are all "15". This ID will be appended to the special samples (e.g., BLANK1.A1). This is to match the tradition of the wet lab. 2) For a special sample type, if its metadata is not defined in the special sample definition file (empty list), then the original metadata as defined in the plate map will be used. Please let me know if you have any comments. Thank you!

@wasade @mortonjt @josenavas @antgonza @sjanssen2

[coveralls]

Coverage remained the same at 100.0% when pulling f4897f64ba2e090db680e1641008cc39353d28a1 on qiyunzhu:validate into 2a9065564f84b195ddb32fca2073cbead1ca1daa on biocore:master.

[mortonjt]

+1

On Wed, Feb 8, 2017 at 11:46 AM, Qiyun Zhu notifications@github.com wrote:

@qiyunzhu commented on this pull request.

In plate_mapper/plate_mapper.py https://github.com/biocore/wetlab-assistant/pull/14:

@@ -127,19 +134,22 @@ def plate_mapper(input_f, barseq_f, output_f, names_f=None, special_f=None):

[ barcode sequence, linker primer sequence, primer plate #, well ID ]

sample, property = '', [] if plate in plates:

• id = primer2plate[plate]

How about "pid" (plate ID)?

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[mortonjt]

+1

On Wed, Feb 8, 2017 at 11:45 AM, Qiyun Zhu notifications@github.com wrote:

@qiyunzhu commented on this pull request.

In plate_mapper/plate_mapper.py https://github.com/biocore/wetlab-assistant/pull/14:

@@ -127,19 +134,22 @@ def plate_mapper(input_f, barseq_f, output_f, names_f=None, special_f=None):

[ barcode sequence, linker primer sequence, primer plate #, well ID ]

sample, property = '', []

How about "metadata"?

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[coveralls]

Coverage remained the same at 100.0% when pulling 7eb6a9884b7e7d0f623de583bbcfff3595f11145 on qiyunzhu:validate into 2a9065564f84b195ddb32fca2073cbead1ca1daa on biocore:master.

[coveralls]

Coverage remained the same at 100.0% when pulling 7eb6a9884b7e7d0f623de583bbcfff3595f11145 on qiyunzhu:validate into 2a9065564f84b195ddb32fca2073cbead1ca1daa on biocore:master.

[qiyunzhu]

@wasade @mortonjt Can we merge now?

[qiyunzhu]

Regex added. @mortonjt @wasade

[coveralls]

Coverage remained the same at 100.0% when pulling 0f4304674b29d7ea7ee06b1ece66abb1fd323c63 on qiyunzhu:validate into 2a9065564f84b195ddb32fca2073cbead1ca1daa on biocore:master.

[coveralls]

Coverage remained the same at 100.0% when pulling 0f4304674b29d7ea7ee06b1ece66abb1fd323c63 on qiyunzhu:validate into 2a9065564f84b195ddb32fca2073cbead1ca1daa on biocore:master.