11/26/2023 0 Comments Grep unique values from a fileNow she types this: wc -l *.txt | sort -n | head -n 3 240 NENE02018B.txt As a quick sanity check, starting from her home directory, Nelle types: cd north-pacific-gyre/ Nelle has run her samples through the assay machines and created 1520 files in the north-pacific-gyre/ directory. Not only would she miss her paper deadline, the chances of her typing all of those commands right are practically zero. At 30 seconds each, that will take more than two weeks. The bad news is that if she has to run goostat and goodiff by hand, she’ll have to enter filenames and click “OK” 45,150 times (300 runs of goostat, plus 300x299/2 runs of goodiff). Since her lab has eight assay machines that she can use in parallel, this step will “only” take about two weeks. The good news is that it only takes two minutes to set each one up. It takes about half an hour for the assay machine to process each sample. Her supervisor would really like her to do this by the end of the month so that her paper can appear in an upcoming special issue of Aquatic Goo Letters. The machine’s output for a single sample is a file with one line for each protein.Ĭalculate statistics for each of the proteins separately using a program her supervisor wrote called goostat.Ĭompare the statistics for each protein with corresponding statistics for each other protein using a program one of the other graduate students wrote called goodiff. Run each sample through an assay machine that will measure the relative abundance of 300 different proteins. She has 300 samples in all, and now needs to: Nelle Nemo, a marine biologist, has just returned from a six-month survey of the North Pacific Gyre 2, where she has been sampling gelatinous marine life in the Great Pacific Garbage Patch 3. We can now use it locally without affecting the content of the molecules directory. We are going to transfer (move) file length.txt which is inside the molecules directoy and bring it into the current directory or. Since data-shell contains molecules it is the “parent” and therefore can be represented symbolically with dot-dot. We then move back into the data-shell directory. The command sends the results to the screen display (standard ouptut), but we know how to “capture” this information and send the results to a file instead thanks to redirection with > into a new file we call lengths.txt. But since we are only interested in the number of lines we’ll use wc -l as we have seen before. We will now use the word count commannd wc we learned previously to count the number of lines. On the other hand the symbol ? represents one character and more than one ? can be used to specify excatly how many characters should match.Įxercise: Try the following commands: ls ?thane.pdb The wild card can replace an number of characters. We could also call all the files that end with. Therefore p* would represent all files that start with p no matter what comes after: ls molecules/p* molecules/pentane.pdb In that case we would use of a new symbol: * called the wild card which is meant to match zero or more characters in a command. What if we wanted only files that start with the letter p and we did not want to specify what the rest of the file name was. ls -C molecules cubane.pdb methane.pdb octane.pdb propane.pdbĪll files end with the. pdb) files, a plain text format that specifies the type and position of each atom in the molecule, derived by X-ray crystallography or NMR. We start by looking into the molecules directory containing six Protein Data Bank (. The key is that any program that reads lines of text from standard input and writes lines of text to standard output can be combined with every other program that behaves this way as well. Almost all of the standard Unix tools can work this way: unless told to do otherwise, they read from standard input, do something with what they’ve read, and write to standard output. Little programs transform a stream of input into a stream of output. This programming model is called “pipes and filters”. Instead of creating enormous programs that try to do many different things, Unix programmers focus on creating lots of simple tools that each do one job well, and that work well with each other. Two main ingredients make Unix (Linux/MacOS) powerful (quoting from the tutorial): We will practise the commands and concepts we learned and look at the shell’s most powerful feature: the ease with which it lets us combine existing programs in new ways. This section reflects content from software carpentry tutorial page
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