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1. levlitichev commented on Sep 12, 2022

   

   levlitichev

   on Sep 12, 2022

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   Good catch. I think the better change would be to replace \n with os.linesep in write_version_and_dims:

   cmapPy/cmapPy/pandasGEXpress/write_gct.py

   Lines 64 to 65 in d1652c3

   	f.write(("#" + version + "\n"))
   	f.write((dims[0] + "\t" + dims[1] + "\t" + dims[2] + "\t" + dims[3] + "\n"))
2. KarlClauser commented on Sep 12, 2022

   

   KarlClauser

   on Sep 12, 2022

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   Won't that lead to \r\n line endings on Windows? We should be striving to get the entire file to be \n line endings. I seek to have a file that is identical, no matter whether it is written in linux or windows. That is how I encountered this bug.

   --Karl
3. levlitichev commented on Sep 12, 2022

   

   levlitichev

   on Sep 12, 2022

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   I understand your point, but I feel that it would be wise to follow the convention chosen by pandas to use system-specific line terminators. I confirmed (on my Mac) that the file looks the same when opened in Excel if all the terminators are either all \n or all \r\n.

   f = open("A.txt", "w")
   f.write(("A" + "\n"))
   f.write(("B" + "\n"))
   f.close()
   
   g = open("B.txt", "w")
   g.write(("A" + "\r\n"))
   g.write(("B" + "\r\n"))
   g.close()
4. KarlClauser commented on Sep 12, 2022

   

   KarlClauser

   on Sep 12, 2022

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   Hi Lev,

   I'm a Windows guy and now-a-days Windows programs can routinely handle '\n' line terminators. For reading/writing .GCT files people upstream/downstream of me use Macs. Consequently it is important to be able to read/write and get the same result. If you force windows generated files to be '\r\n' then I'm going to have fix every one I produce with cmaPy to get the desired '\n'.

   Would you please at least provide an option to specify the line terminator to be written? So long as I have a means to get '\n' then I don't care which you choose as a default.

   Thanks,

   --Karl