I'm beginning to recall why I didn't like C programming back in college...
Python is supposed to among the easiest languages there is, and I'm struggling.
I have a simple enough exercise to do: there's a text with 4 lines, each containing the name of a sequence, followed by a space, and then a sequence.
All I need to do is to reformat the text into a FASTA format.
But oh lord, I'm tired of writing (actually, correcting) the code for this... every time I think, 'well, that has to be the right way of doing it', I get an 'Invalid syntax' message back.
Still, I HAVE to get this right, so back to the drawing board I go.
Thursday, June 6, 2013
Wednesday, June 5, 2013
June and Ani
June has proven to be a time when Ani makes great developmental leaps:
June 7th 2011: Ani took his first steps
June 2012: Ani stopped breastfeeding completely
June 2013: Ani is completely (and I do mean COMPLETELY) potty trained. Hurray! No more diapers? I certainly hope so!
June 7th 2011: Ani took his first steps
June 2012: Ani stopped breastfeeding completely
June 2013: Ani is completely (and I do mean COMPLETELY) potty trained. Hurray! No more diapers? I certainly hope so!
Thursday, May 30, 2013
More UNIX news
Today I used grep to quickly extract chromosome-specific info from a gigantic dataset and put them into separate files.
AND I found that grep -w will get me chr1 info without giving me chr10, chr11 etc.
Computer languages.... who would have thought I could find it so much fun? Or addictive?
I am also en route to learning Perl and Python.
Soon-to-be-computer-language-polyglot signing off...
AND I found that grep -w will get me chr1 info without giving me chr10, chr11 etc.
Computer languages.... who would have thought I could find it so much fun? Or addictive?
I am also en route to learning Perl and Python.
Soon-to-be-computer-language-polyglot signing off...
Friday, May 17, 2013
Varsha Shridhar is...
... learning Unix!! OMG!
....Taking a giant leap into the dark side!
Actually, this stuff is a lot more exciting than I'd envisioned.
Might I direct similarly clueless, yet interested, folks to this page: http://korflab.ucdavis.edu/Unix_and_Perl/
Hoping to be able to write my own Perl scripts to quickly extract large amounts of relevant genomic data!
....Taking a giant leap into the dark side!
Actually, this stuff is a lot more exciting than I'd envisioned.
Might I direct similarly clueless, yet interested, folks to this page: http://korflab.ucdavis.edu/Unix_and_Perl/
Hoping to be able to write my own Perl scripts to quickly extract large amounts of relevant genomic data!
Wednesday, May 8, 2013
Ani and Durga
Durga is 8 weeks old today. She smiles, follows me with her incredibly beautiful eyes, and lets out indignant hollers if she's not carried around while awake.
Ani is 3 years old and is in preschool. He says, "Only babies go to daycare, mummy! Big boys like me go to preschool", conveniently forgetting that less than 10 days ago, he was still in daycare himself.
Ani is fascinated by Durga- for now. He gets highly tickled if she pees or poops, he says "Bless you!" when she sneezes, he thinks her flailing limbs are toys to be tinkered with, and he likes to put his nose into her mouth when she opens and closes it while hungry. He also sings to her when she cries, wipes her nose free of snot that arises from the various nasal infections that he bestows upon her, but gets upset with anyone holding her when he is hungry or sleepy.
Durga, in her turn, seems to know when Ani is happy; she is quiet then. And when she hears him bawling, she starts crying too.
Life with two kids. It is hard. But it is also getting to be quite a lot of fun.
Ani is 3 years old and is in preschool. He says, "Only babies go to daycare, mummy! Big boys like me go to preschool", conveniently forgetting that less than 10 days ago, he was still in daycare himself.
Ani is fascinated by Durga- for now. He gets highly tickled if she pees or poops, he says "Bless you!" when she sneezes, he thinks her flailing limbs are toys to be tinkered with, and he likes to put his nose into her mouth when she opens and closes it while hungry. He also sings to her when she cries, wipes her nose free of snot that arises from the various nasal infections that he bestows upon her, but gets upset with anyone holding her when he is hungry or sleepy.
Durga, in her turn, seems to know when Ani is happy; she is quiet then. And when she hears him bawling, she starts crying too.
Life with two kids. It is hard. But it is also getting to be quite a lot of fun.
Friday, March 29, 2013
At Long Last....A Couple of Great Books
Have been using much of maternity leave devouring the online books available at CLP. For the past few months, I haven't been able to read anything too upsetting- my mind goes into overdrive and I get visions of those horrible things that I've just read about happening to my kids and I spend the next week broody and depressed.
This happened after reading the first half of J.K.Rowling's "A Casual Vacancy". That book upset me no end. Sure, the writing is beautiful and there are some sentences that are masterful in their understated irony. But the story itself? Drugged mothers, abusive fathers, rape, looting, despair,drugs. I hated the story. I kept wondering if Ani and Durga would end up like some of the kids in the book, if we would ever have a cordial relationship and how in the world I was to become a good parent.
Anyway, that's why I stopped reading the book halfway. Couldn't take the sheer nastiness anymore.
The safest feel-good books are romances, but God, spare me those implausible plots and the saccharine dialogues. I still read romances, of course, but it's getting harder to find truly good books. My safe options- Eloisa James, Lisa Kleypas and Loretta Chase- are not bringing out books fast enough for me.
Since time is on my side, I have been scouring the pages of CLP's "eBooks Available Now" looking for something decent. What do I mean by "something decent"? The book should have good writing and a plot that engrosses me. It shouldn't be vulgar. And it should have something in it, some deeper meaning or nuance that I can ponder on long after I read the book. The gold standard here is something like "Atonement"- a book that sweeps one away, a book that is filled with compassion, horror and humanity that it is instantly recognizable and yet quite unforgettable.
Here are my picks so far:
a) The Descendents by Kaui Hart Hemmings. Exquisite. Poignant. I am curious about how they made the movie, because so much of the story lies in what is not expressed.
b) More down to earth, but quite entertaining: A Duty to the Dead by Charles Todd. Mystery novels set in the time of WWI with the protagonist as a nurse serving with the Brits (who else? Why can't somebody write a novel with a German or French protagonist in the times of WWI or WWII? Oh wait, I suppose you could say that 'Allo 'Allo is a work with French protagonists... though it was actually created by the British. As for the Germans, I can think of one.... a novel by Chris Bohjalian... though not in this genre)
*****Update****
On much more reflection, I don't think The Descendents is worthy of my gushing praise above. It's too black-and-white.
Charles Todd's Bess Crawford books are far nicer to read than the Ian Rutledge series. But where's the romance? There needs to be at least a hint of it, for me to continue the series!
This happened after reading the first half of J.K.Rowling's "A Casual Vacancy". That book upset me no end. Sure, the writing is beautiful and there are some sentences that are masterful in their understated irony. But the story itself? Drugged mothers, abusive fathers, rape, looting, despair,drugs. I hated the story. I kept wondering if Ani and Durga would end up like some of the kids in the book, if we would ever have a cordial relationship and how in the world I was to become a good parent.
Anyway, that's why I stopped reading the book halfway. Couldn't take the sheer nastiness anymore.
The safest feel-good books are romances, but God, spare me those implausible plots and the saccharine dialogues. I still read romances, of course, but it's getting harder to find truly good books. My safe options- Eloisa James, Lisa Kleypas and Loretta Chase- are not bringing out books fast enough for me.
Since time is on my side, I have been scouring the pages of CLP's "eBooks Available Now" looking for something decent. What do I mean by "something decent"? The book should have good writing and a plot that engrosses me. It shouldn't be vulgar. And it should have something in it, some deeper meaning or nuance that I can ponder on long after I read the book. The gold standard here is something like "Atonement"- a book that sweeps one away, a book that is filled with compassion, horror and humanity that it is instantly recognizable and yet quite unforgettable.
Here are my picks so far:
a) The Descendents by Kaui Hart Hemmings. Exquisite. Poignant. I am curious about how they made the movie, because so much of the story lies in what is not expressed.
b) More down to earth, but quite entertaining: A Duty to the Dead by Charles Todd. Mystery novels set in the time of WWI with the protagonist as a nurse serving with the Brits (who else? Why can't somebody write a novel with a German or French protagonist in the times of WWI or WWII? Oh wait, I suppose you could say that 'Allo 'Allo is a work with French protagonists... though it was actually created by the British. As for the Germans, I can think of one.... a novel by Chris Bohjalian... though not in this genre)
*****Update****
On much more reflection, I don't think The Descendents is worthy of my gushing praise above. It's too black-and-white.
Charles Todd's Bess Crawford books are far nicer to read than the Ian Rutledge series. But where's the romance? There needs to be at least a hint of it, for me to continue the series!
Wednesday, January 2, 2013
The Name Game
What's in a name, after all?
Everything, I think. Or at the very least, a lot. A name can be, and is, more than just a label. A name embodies traits and meanings and can serve as a beacon to its holder.
And that's why choosing a name for one's child can be so fraught with stress. It needs to be perfect!
The process of choosing a name is just as important as the name itself. In my parents' and grandparents' generations, the process of choosing a baby's name was very different than it is in mine. In their generations, the name was likely to be chosen and bestowed, not by the parents, but by the family elder, or a priest or a scholar, in a process completely entwined with family politics and dynamics.
In my household (if not generation), Ram and I are democratic and exclusive in equal parts. We are adamant that the choice should be ours, while being receptive to the ideas of close family members. And we follow a democratic process between ourselves: we discuss possible sources of names and shortlist some, go through the sources, pick a list of names and discuss those. This process has worked really well so far.
However, I'm finding that choosing a name for a daughter is harder than choosing a name for a son.
When I was pregnant with Ani, Ram and I had a sure-shot method of finding a name. We got hold of a copy of the Vishnu Sahasranamam (a convenient repository of 1000 names of Vishnu), parked ourselves down on the floor and chanted out the text. And sure enough, within a few pages, we found the name that we both liked, which not only sounded good, but was rich in the meaning that we wanted our son's name to have: Aniruddha means unstoppable, someone who recognizes no barriers. This, we felt, was a good trait for a son to have. It would inspire him to great heights and help him overcome difficulties on his way. Plus, it was also the name of a grandson of Krishna, a God who is much loved by both Ram and me.
Now, there are tons of girls' names that sound incredibly pretty. The names that leap to my mind are variations of 'happy' (Shambhavi, for example) or 'playful' (Lalitha, a favorite of mine), or 'beautiful' (too many to list).
But what do I want my daughter to be? Sure, she should be happy and playful and no doubt, she will be beautiful. But I want her to be so much more! I would like my daughter to be strong, resilient, fierce, truthful, and optimistic. I also want her to be ethical, just, and loyal. So she needs a name that reminds her of all this. She needs a name that will lift her out of darkness and show her the light.
So the hunt for the perfect name is still on.
Everything, I think. Or at the very least, a lot. A name can be, and is, more than just a label. A name embodies traits and meanings and can serve as a beacon to its holder.
And that's why choosing a name for one's child can be so fraught with stress. It needs to be perfect!
The process of choosing a name is just as important as the name itself. In my parents' and grandparents' generations, the process of choosing a baby's name was very different than it is in mine. In their generations, the name was likely to be chosen and bestowed, not by the parents, but by the family elder, or a priest or a scholar, in a process completely entwined with family politics and dynamics.
In my household (if not generation), Ram and I are democratic and exclusive in equal parts. We are adamant that the choice should be ours, while being receptive to the ideas of close family members. And we follow a democratic process between ourselves: we discuss possible sources of names and shortlist some, go through the sources, pick a list of names and discuss those. This process has worked really well so far.
However, I'm finding that choosing a name for a daughter is harder than choosing a name for a son.
When I was pregnant with Ani, Ram and I had a sure-shot method of finding a name. We got hold of a copy of the Vishnu Sahasranamam (a convenient repository of 1000 names of Vishnu), parked ourselves down on the floor and chanted out the text. And sure enough, within a few pages, we found the name that we both liked, which not only sounded good, but was rich in the meaning that we wanted our son's name to have: Aniruddha means unstoppable, someone who recognizes no barriers. This, we felt, was a good trait for a son to have. It would inspire him to great heights and help him overcome difficulties on his way. Plus, it was also the name of a grandson of Krishna, a God who is much loved by both Ram and me.
Now, there are tons of girls' names that sound incredibly pretty. The names that leap to my mind are variations of 'happy' (Shambhavi, for example) or 'playful' (Lalitha, a favorite of mine), or 'beautiful' (too many to list).
But what do I want my daughter to be? Sure, she should be happy and playful and no doubt, she will be beautiful. But I want her to be so much more! I would like my daughter to be strong, resilient, fierce, truthful, and optimistic. I also want her to be ethical, just, and loyal. So she needs a name that reminds her of all this. She needs a name that will lift her out of darkness and show her the light.
So the hunt for the perfect name is still on.
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