hiraksarkar

from collections import deque
import itertools

# Make dictionary of triplets
i = 0
triplet_index = {}
inverse_triplet = {}
for x in list(itertools.product(['A','T','G','C'], repeat=3)):
    triplet_index[''.join(x)] = i
    inverse_triplet[i] = ''.join(x)

hiraksarkar

## requirement bed tools
BIN='/home/hirak/bedtools2/bin'
## Gencode 
## gencode.v29.chr_patch_hapl_scaff.annotation.gtf
GTF_FILE="gencode.v29.chr_patch_hapl_scaff.annotation.gtf"

# extract transcript boundaries 
cat $GTF_FILE | awk 'BEGIN{OFS="\t";} $3=="transcript" {print $1,$4-1,$5,$12}' | tr -d "\"" | tr -d ";" | $BIN/sortBed > gencode_transcript_intervals.bed

# merge exon boundaris 

hiraksarkar

#From stackoverflow 
def get_merged_intervals(intervals):
    sorted_by_lower_bound = sorted(intervals, key=lambda tup: tup[0])
    merged = []

    for higher in sorted_by_lower_bound:
        if not merged:
            merged.append(higher)
        else:
            lower = merged[-1]

hiraksarkar

#include <iostream>
#include <fstream>
#include <sstream>
#include <functional>
#include <sys/stat.h>
#include <memory>
#include <vector>
#include <numeric>

#include "zstr.hpp"

hiraksarkar

#!/bin/bash

MAX_LIMIT=12
#number of things queue 
#CHEKC IF it less than try submeating jobs 
while : ; do
NUM_QUEUED=`qstat -u moamin | awk '$10 == "Q" { count++ } END {print count }'`
NUM_RUNNING=`qstat -u moamin | awk '$10 == "R" { count++ } END {print count }'`
MAX_RUNNING=`qstat -u moamin | awk '$10 == "R" { print $4 }' | cut -d"_" -f3 | sort -n | tail -1`
MAX_SUBMITTED=`qstat -u moamin | awk '$10 == "Q" { print $4 }' | cut -d"_" -f3 | sort -n | tail -1`

hiraksarkar

#include "concurrentqueue.h"
#include "blockingconcurrentqueue.h"
#include <thread>
#include <atomic>
#include <vector>
#include <iostream>


using namespace moodycamel ;
using namespace std ;

hiraksarkar

1. Clone your fork:

git clone git@github.com:YOUR-USERNAME/YOUR-FORKED-REPO.git

2. Add remote from original repository in your forked repository:

cd into/cloned/fork-repo
git remote add upstream git://github.com/ORIGINAL-DEV-USERNAME/REPO-YOU-FORKED-FROM.git
git fetch upstream

hiraksarkar

PATH that worked in newton

export PATH="/home/linuxbrew/.linuxbrew/bin/:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/usr/lib/jvm/java-8-oracle/bin:/usr/lib/jvm/java-8-oracle/db/bin:/usr/lib/jvm/java-8-oracle/jre/bin:/home/linuxbrew/.linuxbrew/bin/:/home/linuxbrew/.linuxbrew/bin/"

hello

Transferring files from newton

shuf -n 1000 /bio2/home/mferdman/paired.bulk-only > oct_28/file_list\

hiraksarkar

SPC s c remove highlight

**** Files manipulations key bindings
Files manipulation commands (start with ~f~):

| Key Binding | Description                                                    |
|-------------+----------------------------------------------------------------|
| ~SPC f c~   | copy current file to a different location                      |
| ~SPC f C d~ | convert file from unix to dos encoding                         |
| ~SPC f C u~ | convert file from dos to unix encoding                         |

hiraksarkar

import glob
import pandas as pd
import tqdm
#from pyfasta import Fasta
#%matplotlib inline
import matplotlib
matplotlib.use('agg')
import matplotlib.pyplot as plt
import seaborn as sns
from collections import defaultdict