Even odder is that this works.Ĭat UMDTP53_all_2012_R1_US.txt | mac2unix > /tmp/UMDTP53_all_2012_R1_US.txt # dos2unix: Skipping binary file UMDTP53_all_2012_R1_US.txt Easy enough to fix with the classic utility dos2unix – in this case, called as mac2unix: We look at the file using less.Īha, the old “line endings” issue. I push on and check the number of records in the main text file. But in my experience, biologist + Mac + text files = trouble.

Don’t get me wrong I own a Macbook Air myself, I see smart people doing good work with Macs. See it anyway?Īt this point, alarm bells are ringing. What’s that weird hidden file, starting with a dot? OK, I grab the “US version” (which uses decimal points, not commas for decimal numbers) of the uncurated database:

Excel files – not perfect, but beats a PDF – and ooh, TXT files.

At first sight, it’s reasonably promising. I present what follows as “a typical day in the life of a bioinformatician”. “Take a look at the TP53 mutation database“, my colleague suggested.

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