plate ID and empty metadata parsing #14

qiyunzhu · 2017-02-08T00:31:15Z

Upon the requests from the wet lab crew, I modified two functions:

"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 added two functions requested by wet lab crew #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.
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 · 2017-02-08T00:33:10Z

Coverage remained the same at 100.0% when pulling f4897f6 on qiyunzhu:validate into 2a90655 on biocore:master.

mortonjt

Minor comments about syntax.

mortonjt · 2017-02-08T19:06:33Z

plate_mapper/plate_mapper.py

@@ -110,7 +117,7 @@ def plate_mapper(input_f, barseq_f, output_f, names_f=None, special_f=None):
        for line in special_f:
            line = line.rstrip()
            l = line.split('\t')
-            if len(l) < 4:
+            if len(l) < 3:


Can you add a comment about what this number is supposed to be?

Sure! Will do. @mortonjt

mortonjt · 2017-02-08T19:07:07Z

plate_mapper/plate_mapper.py

@@ -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]


This is not recommended, since id is a reserved keyword. One option is to rename this variable to id_

How about "pid" (plate ID)?

mortonjt · 2017-02-08T19:07:50Z

plate_mapper/plate_mapper.py

@@ -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 = '', []


Too bad we didn't catch this last time. property is also a reserved keyword. This should be replace with something like property_

How about "metadata"?

mortonjt · 2017-02-08T19:08:01Z

plate_mapper/plate_mapper.py

-                    sample = '%s%s.%s' % (specs[sample]['name'], plate, well)
+                    if specs[sample]['property']:
+                        # replace property if available
+                        property = specs[sample]['property']


mortonjt · 2017-02-08T19:08:06Z

plate_mapper/plate_mapper.py

@@ -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]
            if well in plates[plate]:
                sample, property = plates[plate][well], properties[plate]


mortonjt · 2017-02-08T19:08:16Z

plate_mapper/plate_mapper.py

+                    if specs[sample]['property']:
+                        # replace property if available
+                        property = specs[sample]['property']
+                    sample = '%s%s.%s' % (specs[sample]['name'], id, well)
                else:
                    # normal sample name
                    samples.append(sample)
            elif '' in specs:
                # empty well (if defined as a special sample)
                property = specs['']['property']


mortonjt · 2017-02-08T19:47:37Z

+1

…

On Wed, Feb 8, 2017 at 11:46 AM, Qiyun Zhu ***@***.***> wrote: ***@***.**** commented on this pull request. ------------------------------ In plate_mapper/plate_mapper.py <#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)? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#14>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AD_a3fqzH01Po96MZYAby4LNEpkR-cWCks5raht6gaJpZM4L6Oit> .

mortonjt · 2017-02-08T19:47:43Z

+1

…

On Wed, Feb 8, 2017 at 11:45 AM, Qiyun Zhu ***@***.***> wrote: ***@***.**** commented on this pull request. ------------------------------ In plate_mapper/plate_mapper.py <#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"? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#14>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AD_a3TxrKZnpPVXydTf5l3eHsIU8TBjEks5rahtqgaJpZM4L6Oit> .

coveralls · 2017-02-08T19:56:34Z

Coverage remained the same at 100.0% when pulling 7eb6a98 on qiyunzhu:validate into 2a90655 on biocore:master.

coveralls · 2017-02-08T19:56:34Z

Coverage remained the same at 100.0% when pulling 7eb6a98 on qiyunzhu:validate into 2a90655 on biocore:master.

wasade

Only one minor comment

wasade · 2017-02-08T21:20:34Z

plate_mapper/plate_mapper.py

@@ -73,16 +75,21 @@ def plate_mapper(input_f, barseq_f, output_f, names_f=None, special_f=None):
                elif int(v) != cols+1:
                    raise ValueError('Error: column headers are not '
                                     'incremental integers.')
+            # get plate ID (trailing numeric part)
+            for i in reversed(l[0]):


I'm pretty sure this look can be replaced with a regex, but at the sametime, I'm not very concerned about the logic

@wasade Thanks for the comment! I love regex because I was a Perl person. Here I chose this way so that I don't have to import re. Let's leave it as is?

re comes bundled with the python standard library - so importing it shouldn't be a problem.

qiyunzhu · 2017-02-09T00:09:48Z

@wasade @mortonjt Can we merge now?

qiyunzhu · 2017-02-09T00:46:14Z

Regex added. @mortonjt @wasade

coveralls · 2017-02-09T00:46:43Z

Coverage remained the same at 100.0% when pulling 0f43046 on qiyunzhu:validate into 2a90655 on biocore:master.

coveralls · 2017-02-09T00:46:43Z

Coverage remained the same at 100.0% when pulling 0f43046 on qiyunzhu:validate into 2a90655 on biocore:master.

added plate ID parsing and empty metadata

f4897f6

mortonjt requested changes Feb 8, 2017

View reviewed changes

addressed Jamie's comments

7eb6a98

wasade reviewed Feb 8, 2017

View reviewed changes

mortonjt approved these changes Feb 9, 2017

View reviewed changes

used regex

0f43046

mortonjt merged commit e8d9424 into biocore:master Feb 9, 2017

qiyunzhu deleted the validate branch August 5, 2017 20:28

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plate ID and empty metadata parsing #14

plate ID and empty metadata parsing #14

qiyunzhu commented Feb 8, 2017 •

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qiyunzhu Feb 8, 2017 •

edited

mortonjt Feb 9, 2017

qiyunzhu commented Feb 9, 2017

qiyunzhu commented Feb 9, 2017

coveralls commented Feb 9, 2017

coveralls commented Feb 9, 2017

		@@ -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 = '', []

plate ID and empty metadata parsing #14

plate ID and empty metadata parsing #14

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qiyunzhu commented Feb 8, 2017 • edited

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mortonjt commented Feb 8, 2017 via email

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qiyunzhu commented Feb 9, 2017

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qiyunzhu commented Feb 8, 2017 •

edited

coveralls commented Feb 8, 2017 •

edited

qiyunzhu Feb 8, 2017 •

edited