Need a better way to work

I’m working on annotating my results at the moment and that means that I have to take each region and input it into a website, search the website for the information that I want and then hand copy it down to my spreadsheet. This is unacceptable, I am a computer scientist. There has to be a better way.

What I have is:

1) a .csv file that contains the regions that I am interested in.

2) a file that contains data about these regions (but single mutations can have 4-6 entries on each variant)

3) a website that I can manually look up to find this data.

If only I had a wheelbarrow, that would be something.

What I need to do is get the data for the areas that I want and then write a new program to take that data, process it and spit out the tables that I want. But first I must ask myself what do I want from these tables?

What I want is:

1) Chromosome and population of sample

2) start and end of region

3) nearest gene and if there is no overlap I need to know the distance to the nearest gene

4) The number of non-synonymous mutations (those that change the expressed protein)

5) The number of non-coding functional mutations in the region

6) if the hit region overlaps a gene (or more)

7) gene function information

This seems like a bigger task than it is, I should be able to do this fairly easy but I am having a mental block on getting started. It is usually about this time that I start asking for advice on how you get past the wall of starting terror.


New Year, New Goals

Happy New Year! I have been very lax in my writing recently, but 2013 was a very hard year for me with many troubles in my personal life. However, things are starting to level off and get better so here is a list of what I am doing for the new year:

1) Dryathalon – – I am giving up drinking for January and as part of it I am trying to raise money for Cancer Research UK. A few years ago we lost my mother in law to her battle with cancer, my wife won her battle with cancer, and my step-mother is currently battling cancer. This disease has had a massive and negative affect on my life in the past few years and I want to do something to help find a cure. Being a researcher, I feel that supporting more research is the best way forward, so if you have a couple of pounds/dollars/euro/etc spare would you mind throwing them at my fund raiser?

2) Losing weight – I was doing very well at taking some inches off my waist before my life blew up last year. So in addition to cutting alcohol out of my life, I am also going on a low carb diet that worked out pretty well for me last time. This time last year I went vegan for a couple of months and that was pretty good, but since I cook for my family it becomes a battle between myself and my children as to what we eat. In this case I can just not eat the pasta/rice/potato that I prepare for them and I can enjoy the rest of the meal. I am currently at a 42.5″ waist and my goal is to get down to 38″. I think this is a very achievable goal.

3) Finish my transfer report – I have been working on this paper for months now, and I need to get it done. I think I am finally finished getting results for my paper now that I have two chromosomes for five populations. I need to do the analysis and write the damn thing up. My department has been very understanding letting me have the time I need to finish it given everything else that has been going on, but I am feeling the pinch to get back to work and get things done. I have some promising results and some interesting things to report, now just to do it.

4) The 500 words a day challenge – – This post is actually doing double duty of getting my to do list on the web and being my first post for the 500 word a day challenge. I need to spend more time writing and getting things done, so this is my way of helping to force myself to get it done.

5) Finish my short story – I started work on a short story last year, a dystopian story about a gay man that became a brain in a box in an ultra religious society. I am quite happy with the concept, now I need to execute it.

So that is my 500 words done. See you tomorrow.

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