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labsyspharm / quantification

Quantification module for mcmicro
https://github.com/labsyspharm/mcmicro
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If marker_name not available it throws an error #16

Closed DenisSch closed 4 years ago

DenisSch commented 4 years ago

@JoshuaHess12 https://github.com/labsyspharm/quantification/blob/9e9475f98e656ea426b11967a6496bf77a641098/SingleCellDataExtraction.py#L171

DenisSch commented 4 years ago

@JoshuaHess12 I tried to make some changes, but it still does not work. Sniffer function fails...

JoshuaHess12 commented 4 years ago

If the problem is with single column CSVs without a header, we could instead check if the number of columns in the loaded CSV has more than one column. If it does, then we can use the “marker_name” channel. If not, we can introduce the “marker” column like the old channel name reader. This is a bit hacky and may require two different instances of reading the csv file but it would work I believe. What are your thoughts?

On Thu, Apr 9, 2020 at 11:47 PM DenisSch notifications@github.com wrote:

@JoshuaHess12 https://github.com/JoshuaHess12 I tried to make some changes, but it still does not work. Sniffer function fails...

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/labsyspharm/quantification/issues/16#issuecomment-611863901, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALCXKJCXRBBFTZWE3SCA3M3RL2JDTANCNFSM4MFDIAEQ .

JoshuaHess12 commented 4 years ago

Created a pull request for this.

On Fri, Apr 10, 2020 at 8:10 AM Joshua Hess joshmhess12@gmail.com wrote:

If the problem is with single column CSVs without a header, we could instead check if the number of columns in the loaded CSV has more than one column. If it does, then we can use the “marker_name” channel. If not, we can introduce the “marker” column like the old channel name reader. This is a bit hacky and may require two different instances of reading the csv file but it would work I believe. What are your thoughts?

On Thu, Apr 9, 2020 at 11:47 PM DenisSch notifications@github.com wrote:

@JoshuaHess12 https://github.com/JoshuaHess12 I tried to make some changes, but it still does not work. Sniffer function fails...

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/labsyspharm/quantification/issues/16#issuecomment-611863901, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALCXKJCXRBBFTZWE3SCA3M3RL2JDTANCNFSM4MFDIAEQ .

DenisSch commented 4 years ago

@JoshuaHess12 It works :) I tested on both cases local and o2.