An cute little utility

So recently I had some files that I needed to sanitize of those annoying return carriages (^M, or \r). I was originally under the impression that dos2unix would take care of this easily. For whatever reason, Ubuntu 10.04 has replaced dos2unix with fromdos, and fromdos does not do the trick. Very annoying.

So what to do? I could write my own little regular expression or Perl script to take care of this for me. I still have not mastered awk or sed (yes, go ahead and shake your heads). I did, however, find a really neat little utility that is very easy to use and does exactly what I want called tr.

Suppose I have a file dosfoo.yuck which I received from a collaborator that is full of carriage returns. To sanitize the file, I can simply run tr on the file as follows:

tr -d \r < dosfoo.yuck > foo.awesome

The -d flag stands for "delete". On the particular file I cared about when I ran this utility, the -d deleted all the the carriage returns, but now I had no more newlines in my file! Not to fear, because tr can handle this easily. Just do:

tr \r \n < dosfoo.yuck > foo.awesome

And voila! Problem solved.

Midpoint

Since my schedule tends to be fairly full, I've not posted here in a while. So here's a basic update on what's been going on.

On August 12, I became a PhD Candidate. So what does that mean? It means that I am now done with courses, preliminary examinations, and any other requirements other than my dissertation. At this point, I'm ABD, which fittingly stands for All But Done, All But Dissertation and/or All But Dead.

It's been two years since I entered Texas A&M University as a graduate student. In that amount of time, I've published four papers, with an additional two in preparation/under review. I've given a lightning talk, served on a panel, and presented numerous posters. I'm the lead author for the best algorithm for compressing phylogenetic trees, and the fastest sequential and parallel algorithms for comparing large groups of trees. This past summer, I passed four preliminary exams (one given to me by each committee member), wrote up a thesis proposal and successfully defended it.

Not bad for two years of work.

So what will happen with this blog from now on? Well, I do plan (ha ha) to keep on updating it. Most likely I'll start adding things I discover here as I play with some software.

My ubuntu-fix posts will probably be few and far between from now on -- Ubuntu 10.04 is out: it's beautiful, it's fast and it basically works. There has been no need for extra configurations like I've needed to do in the past. Gosh, I love Ubuntu. However, as I discover new things, I will definitely post them here.


That's all for now. I'll try and post something later this week.

-SM

I can't stop watching this

Ever since Kevin shared this with me, I've been watching it constantly.





I'll have an end-of-the-semester post some time soon, I promise :-) Followed by a new tech post.

For those who are wondering, yes, the paper that was referenced to in the last post got accepted :-) Now waiting to hear back on another one (sigh).


-SM

Rage.

I has it.

Waiting for paper notifications is always a pain. I do my best not to think about it, and focus my energy instead on the current algorithm I'm working on. This semester is a special case, since I should be hearing back about two papers in the next two weeks. Both are solid pieces of research and I'm incredibly proud of having been a part of both of them. At this point though, I am all too familiar with the paper reviewing process, and the endless submissions. Half the time, it's not clear to me the reviewers are actually reading the damn things... Each reviewer has so many papers to look at, and a seemingly impossible amount of time to look at it all in. Sometimes I want to scream out the same things ResearchCat is spouting above.


The tentative caption for the above picture is currently "ResearchCat on EasyChair".

And yes, I may have more ResearchCat pictures in the future... you didn't think LOLQualCats was the end, did you?


-SM