rJava in R Studio

This is just a note to myself rather than other.

I got a mail from my Boss asking if I could convert a table of markers/locus on the genome to an idiogram. That should be easy!, I thought.

As always I use bottom-up approach.

1. I found an R package plotting idiograms (karyoploteR).

2. To install it, I needed R 3.4. I had been running R.3.3 but latest version of R-studio. So I downloaded and updated R(not R studio) and restarted R. That helped me install KaryoploteR.

3. I converted the markers to chromosomal positions (in bp) and combined to make an excel file.

4. Now, I was not able to open ‘xlsx’ package in my R-studio. To finish the job I just used ‘readxl’ but many of my packages were using ‘xlsx’ package, so I had to get it working.

5. Although I solved by following the error messages, rather than answers
I had something like this problem. Link

#25 solved it.


Happy Ashoka Vijaya Dashmi

It is Dhamma Chakkra Parivartan Divas. This day in 1956, Babasaheb, along with millions of men, women and children, takes vows to reject the religion and rituals that enforced the caste system and embraced Buddhism- the religion of Sila, Samadhi and Prajna. This is probably one of his last and final acts efforts to annihilate caste system. Twenty years before, in “Annihilation of Caste”, he admits caste is a notion of mind, a belief system, that cannot be undone with a mere change of practices such as discouraging untouchability (by promoting a ritual of dining together) or inter-caste marriages. [Theoretically, inter-caste marriages do have the potential obliterate caste eventually, but remember that mate-choice is not solely be driven by the purpose of obliterating caste. Given the huge inequalities built up between castes, the inter-caste marriages are too few and far between to create a ripple in the sea of this labyrinth of graded-inequal caste society. More importantly what will be a principle or motivation to for a casteless society either through inter-caste marriage or other means?] The only principle that can push for that he concludes, is the principle of liberty, equality, and fraternity. Hindu Sastras ordain against that. With the Hindu faith, the notion of caste-system is mixed like milk and water. He draws up suggestions to restructure Hinduism so as to inculcate the principle of liberty, equality, and fraternity. He is convinced that Hindus would not come anywhere near it and declares he is leaving Hinduism.

So Dhamma Chakkra Parivartan Divas is the day to recite the vows to leave that notion of mind and the belief system, the faith that sustains it and embrace a principled and rational Dhamma. That is why the 22 vows that Babasaheb Dr. B. R. Ambedkar takes start with rejecting Hindu rituals and go on to accepting Budhhism. Also, that is why it is not surprising that Dhamma Chakkra Parivartan Divas fell on the Hindu festival day Vijaya Dashmi and it is celebrated Ashoka Vijaya Dashmi as a tribute to the beginning of Emperor Ashoka’s life as a Buddhist.

That is why one cannot celebrate Dussehra and Dhamma Chakkra Parivartan Divas the same time. That is why one cannot be a Hindu and a Budhhist the same time. It is the day one should be celebrating rejection of the practices that bound a million of people to the inhuman condition. Have things changed today? Is the priest doing puja not Brahmin? Are the community and the priest doing puja reject all aspects of Sastra that support caste and inequality? Do you see a proportionate representation of Indian population in that puja community? If not, why? Do you not see, hear or read about in caste-based atrocities anymore?

It is even difficult for someone who grows up participating in religious festivals in the fringes. Growing up untouchable, there are Durga Pujas at every important location, but he watches from a distance. Now, you can tell him did anyone told you not to go near it? You can ask him did you even try to go near it? And he would be dumbstruck. No, he knew like that baby elephant who knows he can’t fly not to go near it. The notion of mind becomes an insurmountable wall that he can’t scale. But sometimes the human instincts take over and the borders are drawn, infiltrator is put down and shown his place. Like many before him, he does not forget it. In a one-out-of-thousand case, a miracle happens. A caterpillar turns into a butterfly in the eyes of the same kind of people. He is still scarred by his previous humiliating incidences, but now he can pass off as if nothing ever happened. He probably can cross those boundaries without having to ask anyone.

When he is invited to cross one of those boundaries, he is forced by the same human instincts that made him cross those boundaries before, to remember those incidences and ask, “are those lines still there?”.

“By walking across the line, am I saying those millions who can’t, ‘be one of the thousands like me and maybe someday the line won’t restrict you’.”

“Can I actually assure that? What about the nine hundred ninety-nine”

These are places he is not allowed to ask that question. Someone somewhere decides for him. He has to cross the line knowing that he is an infiltrator. Limited desecration is allowed. Caste has become immune to contamination. Earlier, caste was an anxious a tiny drop of precious water in an undulating lily leave. Touch and it is gone. See it and it is gone. But never lost, as an ode to its eternal character. Caste thrives. Like a Satan, it grows powerful the more people it touches by allowing to cross that line and making sure they never question that notion-of-mind that is deeply interwoven with the Sastras.

He is now an accomplice.

Patels in Gujrat

Patels in Gujrat should be given reservation!

Yes, I said it! They should be given reservation, under PH category. To demand either give us reservation or scape reservation policy is a sign of complete idiocy. For the same reason, coming in expensive cars to reservation rallys to demand for reservation your ownself, is an icing of idiocy on top of complete idiocy.

Should this idiocy reservation be applicable for the leader(s) only or the entire patel community?

Did the leader come to the rally alone? NO? Then stop vying for the PH category and stop being an idiot.

I stand with you, Gaza

In the only canteen in a university you-never-heard-of, the the glass-door refrigerator is almost empty. There is a box of Cadburry chocolates. For a week now, the refrigerator is empty. One day few bottles of Schweppes gingerales appeared and disappeared again. The canteen is crowded, everyone asks for “cold drinks”. The walls are still adorned with smiling bollywood stars with a data-card or a coca-cola in hand. The counter is busy. Behind the counter sits, occasionally, a bearded person in a skull cap.

And I think, how many of the students ask why coca-cola disappeared from the fridge? How many may know there might be an internationalist living among them, serving them not food-for-thought but the real food ( absolutely necessary for any thought)? The university-you-never-heard-of is in a place and culture where there is nothing-unknown, nothing-unanswerable. Every subject/topic is met with the same lack of interest a plate of plain boiled rice is met with after a delicious and hearty meal. Nowhere in the campus, where alignment and movement of cosmic bodies are a matter of daily concern, does the international alignment with apartheid, movement of projectiles into the bodies of children, women, innocent hard-working men and fighters or soldiers does figure in discussions.

Reading everyday about the ongoing pogrom, I can’t tell for sure, why I am reading these at all. Can it at all be that, instead of being concerned I am morbidly interested in conflicts, massacres, oppression. Afterall, I see it where others don’t. What happens to the people who are gathering up around the tree to see a young girl hanging? Do they go home completely shaken, their faith in humanity destroyed or they go home satiated of their curiosity of the event? Silently watching, reading, knowing the tireless injustice perpetrated must be making us at least partially the audience for who it is made. The world is a stage, I remember.

I have not asked at the canteen, if they are simply showing solidarity with the businessmen in Mumbai who joined BDS campaign. He might be the lone person in this place-you-never-been to have heard of BDS against Israel. As people die, and with them hope of peace, freedom and justice, we must remember to be shaken with such brutalities.

Normalising Narendra Modi

Nehru, Gandhi and the Neheru-Gandhis(N,G & N-Gs) are probably the most criticised leaders in India in the circle of the hindu nationalists. I am forced to use the word “hindu” nationalists” here in absence of a non-offensive and/or self-described word to mean someone who supports the ideals of the BJP, RSS and their sister organisations. Evidently, Narendra Modi has described himself as a hindu nationalist, but that seem to have been in more rue than glee. Notwithstanding the widely differing visions, works of the N, G and N-Gs, the HNs can hardly agree with them on anything. Pick any book of slightly right-wing ideals, and you are most like to have Nehru’s patriotism in suspect, his vision discredited. This makes sense though, since the politics of the HNs positions itself as an alternative to the N,G & N-Gs. However, the N,G & N-G do have a stellar stand in Indian politics, in terms of the sheer number of terms they have headed the govt. of this country but also the way they have shaped the country’s economic progress and global recognition. I admit both of these are interdependent and highly controversial, but both illustrate BJP’s quintessential conundrum – it is the fame of these N, G & NGs which Hindu nationalists defame they need to match.

It began with Atal Bihari Bajpayee. Around the time he trumped the then Iron man (IM-I) L. K. Advani for this un-vetted secularism, an anecdote circulated. That Nehru once remarked, “he has prime ministerial timber” after listening to Bajpayee in the parliament,  was something that caught the string of the unthinking middle class. I am not sure, if Nehru waxed poetry in his speeches, or found the especially slow-flow of words particularly prime ministerial, we even don’t know if the younger AB Bajpayee also spoke in slow-mow, but it was Nehru’s tacit and a rather prescient approval of AB Bajpayee to adorn “his(?)”  throne which placed him in public imagination. You could find out, it wouldn’t be a Hindu nationalist to circulate that anecdote.

Ram Chandra Guha does not claim to be a Hindu nationalist. It was he who would start the same normalization of another Iron man (IM-II), Modi. In his unashamed ogling published in “The Hindu” he says, “There is something of Indira Gandhi in Narendra Modi”. Perhaps that was not enough. Not perfect enough for an “Iron Man” to be compared to a female leader (although an Iron lady herself). So we get Tavleen Singh, famed for her gossip column in Indian express who says, “Modi is the first major political leader since Jawaharlal Nehru who has articulated a clear economic vision.” It would be interesting to dissect this heap of praise, but to do that to a line of a journalist who has deep respect and warmth for Advani despite her disliking of his politics and rath yatra, because he called her after reading her book and because she had travelled with him in 1977 would be a waste of time. (By the way, people were killed in massive numbers because of that yatra and politics.)

But notice here the insinuation of political legitimacy and competency of the BJP leaders by banking on the public memory of the long-serving former Prime ministers of India. It is a hollow assurance these columnists tender to the people of India based on completely hypothetical correlation. The nature of political expediency is such that a party that opposed political dynasty in democracy needs to prove its royal blood. 

However absolute Narendra Modi’s accomplishments in Gujrat’s economy be, it is a wonder how people who claim to be liberal and apololitical otherwise, notwithstanding the contradiction in terms, completely ignore Gujrat riot. With interactions of various actors in this extended Hindu Nationalist family, over past 10 years suggest me four ways they could rationalize Gujarat riot of 2002.

  1. Not True: They simply refuse to accept that Gujarat riot happened. In the next few years after the riot, this was a major stand of the expatiate Gujaratis, and a lot of them continue to hold major English dailies responsible for spreading the “misinformation” about Gujarat 2002. They position themselves as alternative news-source, claiming themselves more authentic than the rest since they hail from Gujarat, and eloquently brand every other voice “pseudo-secularists”, communists or congress conspirators. It is important to remember that, much of the vernacular media during the period did not report the large-scale loss of lives and properties of the muslims nor it did report the of the magnitude of the carnage. This probably had created a cognitive dissonance in the mind of this group of people, for which they could be initially forgiven. But after 13 years of the pogrom, it is simple blind faith, ignorance and prejudice.
  2. True, but not Modi: Some acknowledge the Gujarat riot, even the disproportionate loss to the Muslims. These people however squarely exonerate Modi of being responsible for it.  If Modi was the Chief Minister during the riot of 2002, he is also the Chief Minister during the next 10 years of peaceful growth, they argue. L.K.Advani is among the leading voices in this argument. However, this argument is very informative in itself because what it proves is that if a govt. is interested it could administer relative peace for as along as it wants. If CM Modi did it for 10 years in Gujarat now, CM Mayawati could do it in one of the most volatile states regarding communal riots. And if govt. does want not peace, Gujrat 2002 results. Fractions of this group of people like to see the riot as a consequence of Godhra train burning. Lets put the facts aside, and ask if the disproportionate loss of lives, properties, honor and home of only a particular community far from the site of burning can happen spontaneously?
  3. Can we move on?: Gujarat riot-2002 is not fiction; Narendra Modi is in the center of it. As facts emerged, documentaries, sting operations, court, CBI investigations vacillate between almost trying Modi and his ministers/officers and giving clean chits, it is increasingly difficult for some people deny all of it. Instead they ask can we move on now, focus instead on growth and development, clean governance for a change? Yes, we should, but there is a probable killer among us, in fact not among but above us, hoping to rule us tomorrow. How comfortable you would be to know that your boss had got few people killed for whatever reason? Or that, your spouse is a killer? How much of a development-freak you would be to move on, if your neighbours, members of your community, yourself were victims?
  4. We did it!!: There is a fourth category of Modi supporters. They acknowledge the massacre, the rapes, the loots with all its enormity, celebrate it and are grateful to Modi for it.

Most of us are not blind to deny any violence did occur, nor bigoted enough to celebrate such things. Even if we were, we cannot be publicly so. But it is the idea that we should move on, whoever be responsible, so empathetically argued by the extended family, does not, result in a new socio-economic reality. The fact about development is almost like the cliché, “all that glitters are not gold”. Multilane roads, flyovers, sky-scrappers and Memorials (lets keep Maya in loop too) are easier to build than a more equitable, pluralistic society. Infrastructural investment in a short time can give you a “vikash purush” (development man) but it takes years of societal investment to have vikashita janata (developed citizenry). Modi had 20 years to do that, still Gujrat carries some worst human development indices. But again, Jyoti Basu also had 27 years.

In a zerosum game of electoral politics, a thousand different reasons to support Modi do lead to coronation of an alleged mass murderer as Prime ministerial candidate of a major national party. The effect of which would be far-reaching.

Enforcing Impunity

The recent judgement of Laxmanpur Bathe Massacre, where the High court bench chaired by Sinha and Lal acquitted all the 26 accused, 16 of who were previously given death sentence, casts serious doubts on the role of judiciary (along with the involved investigating agencies) in delivering justice when it comes to Dalit atrocity. A massacre of 58 Dalits by a gang of men (Ranvir Sena) going unpunished after 16 long years is a travesty of justice which a democratic country should be ASHAMED of.

There is an important dimension to Dalit-atrocities that often a deeper involvement into the issue brings forth. The impunity an ordinary caste-hindu enjoys in doing anything illegal, uncivil against a Dalit. The same caste-hindu might never pick a quarrel with another caste-hindu but feels free to transgress a Dalit’s right whenever she feels uncomfortable. In small societies, such as villages there are social stigma (negative reinforcement) against bad behavior/criminality, but only if it is against the caste-hindus. Bad behavior/criminality against the Dalits are justified by tradition and religion. This “perceived impunity” that even a pre-teen caste-hindu is so conceived is not biological, THERE IS NO INNATE CASTEIST FACULTY, but inherited prejudice duly enriched myths, mythologies and religious scriptures and emboldened by the deeds of her fellow caste-hindus.

In the villages, where most of these Dalit-atrocities occur, there is NOTHING which breaks the “perceived impunity”.There are three important agencies which break the news to the stone-age caste-hindu villagers that, that is in fact no impunity.

First, is the school where probably the next best thing children can learn after alphabets and arithmetics is the principles of mutual-respect and co-existence.  In fact, these things children should learn along with or even before they learns the prescribed school education. The school years should enhance the rationale of these principles, which will let the pupils question their ‘inherited prejudice’ at least.

Second are the law-enforcement agencies, the police, the court, and many other govt. agencies. Ideally the guidebook for them is the constitution and the penal codes, which grant none of the ‘perceived impunity’. Any case of establishing and protecting the rights of a marginalized group would serve as an example for the hapless caste-hindu pree-teen who was otherwise going to turn out to be carrier of the disease- casteism.  A collusion of caste-hindu brotherhood and irrational religiosity help enforce the “perceived impunity”.  The court verdict like the Patna HC on Laxmanpur bathe, in the pretext of ‘lack of reliable evidence’ makes the perceived impunity real. It is not the final verdict yet, there is a Supreme Court, of course, but it does tell a crucial fact. The apex court thinks, the killers can not be punished.

With a Casteist Judiciary like that, the third, and probably the last way out of this abyss of ignorance (as you might have guessed the “percieved impunity is just plain ignorance or inability to accept the truth), for the poor caste-hindu is Newspapers.  Remember, how Indian express took up the cause of the two slain IAS officers, by covering the issue in front page, day after day? How The Hindu serialized publication of wiki-leaks? These newspapers very well consider themselves opinion makers, and they are to certain extent, in addition to their role as reporter of facts. None of these papers wrote up an editorial condemning the derelict judiciary or criticizing the court verdict. These National Toilet Papers (again to use VTR’s word) have criticized court rulings before, in all too subtle ways to extricate themselves from the law’s tentacles. More importantly, when Dalit parliamentarians forced the MHRD to admit changes in school textbook, because some cartoons were defamatory to Dr. Ambedkar, these were the paper who surfaced more than 89 editorials and open-editorials, a list of those are with me. None of them would say it, at least, it was wrong on the part of the court to justify Dalit killings, and letting the accused free, even when surviors are unequivocal on their identification and even without a directive to the police/CBI to bring the culprit to justice.

The impunity for caste based violence (forget discrimination!) is sanctified by Hindu religion, employed primarily to subjugate Dalits, to deny them them their dignity and individuality, is guranteed by the court and actively encouraged by education and media.

Update: “The Hindu”, our responsible newspaper deems it necessary to publish an editorial on “Persecution of Jwala”. Apparently, the female start badminton play not being allowed to play in Denmark by Badminton Association of India is quite more serious issue than massacres like Laxmanpur bathe.

Between Temples and Toilets

This is the 21st century, and India still does not know how to clean up its own shit.

Unwittingly Narendra Modi parroted Jairam Ramesh. He would have to do that a lot more, because the more you are required to speak the more you’d be required to repeat, sometimes your own self, sometimes others. Pitting public sanitation ahead of (not against) temples results from an embarrassing fact, that almost half of the villages in India defecate in open spaces. That sounds like a horrible thing, only if we didn’t believe that a minimum of 53% people (i.e in delhi) live in slums without toilets. Think about mumbai, percentage population of slum dwellers can be easily 70-80%. In such case, toilets sounds pretty progressive, a development issue.

Where it does not sound progressive is, what kind of toilets?

Gujrat, along with Uttar Pradesh (where Mayawati ruled), are incidentally few states where a particular type of toilets are probably worst kind of “non-violent” human cruelty. The dry latrines are simply enclosed places where the ‘caste-hindu’ shit. Next day, someone needs to clean it up, put it in a basket and take it to the open space. This toilets are a thousand times worse than open-defecation. Navsarjan Trust, a foundation started by veteran activist Martin Macwan, has been fighting it out since 1992, when “manual Scavenging” as the work is known, was banned in Gujrat. Till 2013, Gujrat govt. refused to carry out the survey even, forget about punishment of the employer, rehabilitation of the worker in this inhumane trade. Not surprisingly because, for Modi as was for his compatriot Mohandas Gandhi, cleaning toilets is the spiritual duty of the dalits. The biggest defaulter of humanity is the central government run railway. It uses a form of toilets which are open-defecation in reality, like the dry latrines. Because Mr. Modi and Mr. Ramesh, the definition of “open defecation” is not based on whether you are in the open space while you defecate, but whether your feces is left in the open.

In a radical new theory, supported by emperical data, Dean Spear of Princeton university has argued that shunted growth of Indian children are because of open-defecation. In his theory, “Faeces contain germs that, when released into the environment, make their way onto children’s fingers and feet, into their food and water, and wherever flies take them. Exposure to these germs not only gives children diarrhoea, but over the long term, also can cause changes in the tissues of their intestines that prevent the absorption and use of nutrients in food, even when the child does not seem sick”.

Can you guess what about the Dalits?

Between the making of secular and pro-development masks, the dalits are left in the lurch.