Code comments

[sjanssen2]

I don't know how I should leave comments for code merged into master, thus I open this list here (all regard plate_mapper.py):

• [ ] line 36: from all examples I have, you can identify the beginning of a plate by assuming first cell string startswith 'Plate#\d+'. Seems to be more save than just checking that the second cell is '1'
• [ ] loop starting at line 37: I would also test that column headers are in a strict increasing order. Currently, you cannot detect swapped columns. If you would use a variable to store how many cols the plate has, than you could test if the headers are in the appropriate order: [header] = list(range(1, colMaxNr))
• [ ] I would recommend using pandas to read tabular information and especially merge the barcode sequences.

[qiyunzhu]

Hi @sjanssen2 thanks for your very careful observation! Here are my answers to your questions: 1) This first cell does not always read "plate#\d+". It is actually a very arbitrary string for the plate name. They may write it as "fecal plate 001" or "best plate of the day". 2) The incremental order of column headers was ensured in line 40 elif int(v) != cols+1: and the raise error statement after it. The variable to store number of columns is cols. 3) @mortonjt also made this suggestion (using pandas). I will look into it. Thanks for yours!