Tuesday, June 30, 2009

Eppendork's terrible, horrible, no good, very bad six months

I confess I have a problem. It is all to do with my love of praise and dislike of disappointing people and feeling like a failure. I have spent the last six months spending more of my time feeling like I am dog paddling in the pool of wanton science dreams. Yep you heard floating/dog paddling and not swimming and I am getting tired. I desperately want to get my shit together and I am hoping my research proposal will meet with supervisor A and supervisor B's approval so that i can get my shit together. My manic depressive relatonship with supervisor A is not helping my balance - he is a really high achieving and extremely well respected in our field (which makes lit reviews fun when he's on half the papers you are talking about), he has high expectations of all his staff and students and gets all disappointed (verbalises this both in front of other people and has been known to lose his temper at people in front of people even at visiting students - which reduces you and whoever else is around to feeling super duper crap). He does give you praise and its honest not manipulative praise - when i get it im like omg the world is brighter, better more fabulous place and then in the next breath he will go 'I'm disappointed' or I dont have time for this go away and do it again (tbh some of the time its me thats cocked up - but more often he changes his mind about what he wants after I spend ages on it and I have to do it again. Or he just doesnt listen and you have to push the point and make him hear you or he will walk all over you with his assumptions.  I made a choice I chose this project this supervisor go me!

Having said that i love this field, I love the kind of work I am and have been doing. I am not stupid. I will resolve it. I just need a really big wine right now. Tommorrow is a new day - I have a project proposal to work on and hopefully they will buy it and not throw me out on my ear.


Monday, June 22, 2009

Be scared, be very scared and dont fall asleep!

Electronic Positronic Person Engineered for Nocturnal Destruction, Observation and Rational Killing

Get Your Cyborg Name

Heehehe - eat my cyborg dust science!

That is all.


Monday, June 15, 2009

Everybody say Yey-ah! Yey-ah!

I got the script to work :-p which is good and maybe i will share with you maybe I wont in the future - probably will! But then in future planning will remember about the primary key needing to be the same as the key you want to join the tables with :-p but i think that is relatively easily solved I think a new_list.remove will work - let us all cross our fingers and tune in next time for when we hear Eppendork say Yey-yah! uhuh! Yey-yah!


Tuesday, June 9, 2009

Calling all Pythonistas!

Okay so I have a question:

I have a pile of sequences (200+) in fasta format in a text file eg 




I need to make it into columns like this:

geneA asdfsdfasdfsdfsdfsdfasdfsfasdfsdfafsdfsdfasdfasdfsdfasdfs
geneB asdfsdfasdfsdfsdfsdfasdfsfasdfsdfafsdfsdfasdfasdfsdfasdfs
geneC asdfsdfasdfsdfsdfsdfasdfsfasdfsdfafsdfsdfasdfasdfsdfasdfs

all in one line.  I want to have the text file set up like this because i want to use python to stuff the text file into an SQL table - only I dont know how to do it - I can concatenate the sequence bit of it in excel for one of the sequences but that doesnt work for the 200+ other sequences I have.  Everything I have found on fasta and or concatenation involves simple exercises or pulling down individual fasta sequences from genbank which didnt help me a lot.

So what I want to know is how do i get the sequence name in one column and all sequences in the other so that I can make an output file that I can open using a python script then stuff into an SQL table.  Any ideas?


Friday, June 5, 2009

It's a good day today

I feel slightly like I have a manic-depressive relationship with my supervisor.  One its good and he's happy and all is right with my world (sometimes I feel really good).  Then the next day he will just be tearing strips off me and handing my arse to me on a plate and I feel like what the hell was I thinking doing a Phd.   Kinda like this:

SELECT * FROM "Eppendork"
WHERE "EmotionalState" LIKE  'F%'
ORDER BY "Dayoftheweek" 
AND "Houroftheday"

Which roughly would give you the hours and days of the week where I felt F**d or Fabulous. Yes this week has been good for SQL and me making a start on learning Python.  I got excited today by:

n = int(raw_input('What's my favourite number?: '))
if x >4:
print 'No that is not my favourite number!'
elif x<4:
print 'No that is not my favourite number!'
print 'Yes that is my favourite number! Woot!'

I know baby steps - its the small things.