MedWorm provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest medical blog items that have been tagged with 'bash'. Sat, 03 Sep 2011 03:00:03 +0100 http://www.medworm.com/index.php?rid=4693447&cid=t_162830_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2011%2F04%2F08%2Ffixing-aberrant-files-using-r-and-the-shell%2F Once in a while, you embark on what looks like a simple computational procedure only to encounter frustration very early on. “I can’t even read my file into R!” you cry. Step back, take a deep breath and take note of what the software is trying to tell you. Most times, you’ve just missed something very straightforward. Here’s an example. Recently, I was trying to retrieve some data describing characteristics of microbial genomes from the NCBI FTP site. The file, lproks_0.txt (direct link), looked like a regular tab-delimited file with a couple of header lines: head lproks_0.txt ## Microbial Organism Information Page ## Columns: "RefSeq project ID" "Project ID" "Taxonomy ID" "Organism Name" "Super Kingdom" &qu... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=4693447 Fri, 08 Apr 2011 04:41:37 +0100 4693447 http://www.medworm.com/index.php?rid=4168128&cid=t_162830_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F11%2F16%2Fdropbox-tip-continued-convert-a-file-tree-to-html%2F A couple of posts ago, I outlined a small bash script to generate an index.html file, containing links to other files in a directory. This was for generating links to files in a Dropbox public directory. I had completely forgotten about the very useful UNIX/Linux command named tree. If not installed, it should be in your distribution repository (e.g. sudo apt-get install tree for Ubuntu/Debian). Then simply: cd Dropbox/Public/mydirectory tree -H . > index.html Next, navigate to index.html at the Dropbox website and you should see something like the tree on the right. It’s a little ugly and obviously, not as convenient as something like Github, but can be a good quick and dirty fix if you need to share a hierarchy of directories and files. Filed under: computing, linux, ... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=4168128 Tue, 16 Nov 2010 02:29:37 +0100 4168128 http://www.medworm.com/index.php?rid=4152099&cid=t_162830_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F11%2F09%2Fa-quick-bash-tip-add-an-index-html-file-to-a-dropbox-public-folder%2F You know that Dropbox is terrific, of course. No? Go and check it out now. One issue: files in your Public folder have a public URL, that you can send to other people. Unfortunately, directories do not. So how do you share a public directory full of files? Answer: create an index.html file and share that. Let’s say that your files end in “.txt” and reside in ~/Dropbox/Public/entrez. Do this: cd ~/Dropbox/Public/entrez echo "<ol>" > index.html for i in `ls *.txt`; do echo "<li><a href='$i'>$i</a></li>" >> index.html; done echo "</ol>" >> index.html Now you can share the link to the index.html, which when clicked will display a list of links to all the other files in the directory. Filed unde... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=4152099 Tue, 09 Nov 2010 00:26:01 +0100 4152099 http://www.medworm.com/index.php?rid=2083948&cid=t_162830_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2009%2F01%2F07%2Ftext-to-fasta-and-other-delights-of-the-shell%2F One thing I’ve learned in my current job is that some familiarity with Linux tools for processing text files: awk, sed, grep, head/tail, cut/paste and so on, often provides a speedier solution than writing a script in (insert scripting language of choice here). I know this stuff is trivial to shell gurus, but I still get a little buzz out of it. A couple of real-life examples. Delimited text to fasta Your collaborator has developed “peptides on a chip” and sends you a text file describing said chip where column 1 = spot number, column 2 = peptide sequence: 1 ELDQGSLATSF 2 VDLAATPTDVR 3 TTNEEYLDLSQ 4 SSLDVYDGRFL 5 ALVHSYMTGRR Your analysis requires that the peptide sequences be in fasta format. Easy, using awk: awk '{print ">peptide" $1 "\n&qu... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=2083948 Wed, 07 Jan 2009 03:02:42 +0100 2083948 http://www.medworm.com/index.php?rid=2523543&cid=t_162830_132_f&fid=35021&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FYourBonesGotALittleMachine%2F%7E3%2FXttIOC7bqfg%2F Sometimes it’s nice to quickly check how many sequences are in a FASTA format sequence file. It barely warrants it’s own blog post, but here we go anyhow: my one-liner shell script for counting the number of sequences in a FASTA “flat-file database”, based on the presence of the “>” header symbol. #!/bin/sh # ~/bin/countseqs # Counts the number of sequences in a FASTA format file grep ">" $1 | wc -l Dead easy huh ? I put this in ~/bin/countseqs, make it executable (chmod +x ~/bin/countseqs) and use it in lots of situations, as a quick sanity check. (oh, btw, this is not public domain and u can’t use it for commercial gain without paying me a license fee. academic users can fax me something for a free license. k thx bye). Couldn&#821... Your bones got a little machine. blogs http://www.medworm.com/rss/comments.php?id=2523543 Mon, 01 Sep 2008 05:49:38 +0100 2523543 http://www.medworm.com/index.php?rid=1434543&cid=t_162830_133_f&fid=35129&url=http%3A%2F%2Fwhitterer-autism.blogspot.com%2F2008%2F05%2F6-words-meme.html "Angela" over at "Memoirs of a Chaotic Mommy" has tagged me for this 'Your life in 6 words" meme. Hers is much more pleasant than mine.However, as if that wasn't enough, she also added an extremely helpful note about derivation and pronunciation, as follows:-'What is a meme?!A meme has been explained to me in two ways:1. Meme--pronounced 'mem', a memory2. Meme--rhymes with 'theme', a theme where I am tagged to answer questions about 'me' or myself...'Now isn't that illuminating? If that has been a test I'd have scored zero, or naught as I would prefer to refer to it.So my life in six words would be this:-'Rambunctious, rowdy, revelry raising unruly renegades.'So now I need to tag six people?Six it is. Watch out next six commenters, you'll be in the hot seat.So first up is "Joker" from "Mus... Whitterer on Autism blogs http://www.medworm.com/rss/comments.php?id=1434543 Sun, 11 May 2008 23:51:08 +0100 1434543 http://www.medworm.com/index.php?rid=1129355&cid=t_162830_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2008%2F01%2F04%2Flinux-tip-sort-a-tab-delimited-file%2F The Linux command “sort” is both powerful and confusing. The manpage tells us that the “-t” switch can be used to set the field delimiter. If you’ve tried various combinations of “-t” and “\t” to tell sort that your file is tab-delimited without success, try this (bash shell): TAB=`echo -e "\t"` sort -t"$TAB" myfile with “-kN” as appropriate, where N is the column on which to sort. Long-winded discussion with much incorrect syntax in this forum; or get straight to the point in this mail archive. (Source: What You're Doing Is Rather Desperate) What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1129355 Fri, 04 Jan 2008 05:50:20 +0100 1129355