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

#include "zstr.hpp"

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

## 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 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

#!/bin/bash
####################################
USAGE: bash auto_sub.sh <QUEUE_LIM> <MAX_JOB_NUM>
###################################


USER="$(whoami)"
MAX_LIMIT=$1
MAX_JOB_NUM=$2

hiraksarkar

Useful Spacemacs commands

• SPC q q - quit
• SPC f e d - open .spacemacs file
• SPC f e R - reload .spacemacs file
• SPC w / - split window vertically
• SPC w - - split window horizontally
• SPC 1 - switch to window 1
• SPC 2 - switch to window 2
• SPC w c - delete current window

hiraksarkar

SAM and BAM filtering one-liners

@author: David Fredman, [email protected] (sans poly-A tail)
@dependencies: http://sourceforge.net/projects/bamtools/ and http://samtools.sourceforge.net/

Please extend with additional/faster/better solutions via a pull request!

BWA mapping (using piping for minimal disk I/O)

hiraksarkar

hiraksarkar