calizarr

(setq numerals
      '((ones "" "I" "II" "III" "IV" "V" "VI" "VII" "VIII" "IX")
        (tens "" "X" "XX" "XXX" "XL" "L" "LX" "LXX" "LXXX" "XC")
        (hundreds "" "C" "CC" "CCC" "CD" "D" "DC" "DCC" "DCCC" "CM")
        (thousands "" "M" "MM" "MMM")))

(defun divmod (x y)
  "Helper function to divide X by Y and return the quotient and remainder."
  (let
      ((quotient (/ x y))

calizarr

Keybase proof

I hereby claim:

• I am calizarr on github.
• I am calizarr (https://keybase.io/calizarr) on keybase.
• I have a public key ASCswhV_yMXB4800m7qPltoaNEnhkIieTFC2QEI-kdSBFQo

To claim this, I am signing this object:

calizarr

#!/bin/bash 
declare -a scaffolds
for ((i=$2; i<=$3; i++)); do
    scaffolds+=("scaffold_$i")
done

for ((i=$2; i<=$3; i+=1000)); do
    j=$((i+1000))
    if [ -f scaffolds_$j.temp ]; then
        echo "Scaffolds temp file already exists: $((i+1000))"

calizarr

# Works
for x in {bed_dir}/*.bed;do y=$(basename ${{x%.*}});sed -- 's/{original}/chr/g' $x > {outdir}/$y.sicer.bed;done;echo Converting to Bed chromosome done
# Doesn't work
for x in {bed_dir}/*.bed;do y=$(basename ${{x%.*}});sed -- 's/{original}/chr/g' $x > {outdir}/$y.sicer.bed & done;wait;echo Converting to Bed chromosome done

calizarr

def allBelow(genome,k,L,t):
   kmerCount = 0
##   print 'Beginning: '
   results = set()
   for x in range(len(genome)-k):         #looping through the genome
      kMer = genome[x:x+k]                #getting each k-mer at a time
      indices = collections.deque([])     #keeping track of the indices
      start = 0                           #for the string.find(sub) method
      if kMer not in results:             #Making sure we don't do extra work.
         while True:

calizarr

def makeMaps(filename):
    f_in = open(filename,'r')
    g, grev = {}, {}
    print "Loading from: "+str(filename)
    for line in f_in:
        nodes = [int(x) for x in line.split()]
##        print "Total nodes: "+str(nodes)
        vertex = nodes[0]
        neighbors = nodes[1:]
##        print "g[vertex]: "+str(vertex)+" has these neighbors: "+(str(neighbors))

calizarr

############################################################
############################################################
###
### 0/1 knapsack
###
############################################################
############################################################

# from earlier lecture...
class Item(object):

calizarr

def reproduce(self, popDensity, activeDrugs):
        """
        Stochastically determines whether this virus particle reproduces at a
        time step. Called by the update() method in the TreatedPatient class.

        A virus particle will only reproduce if it is resistant to ALL the drugs
        in the activeDrugs list. For example, if there are 2 drugs in the
        activeDrugs list, and the virus particle is resistant to 1 or no drugs,
        then it will NOT reproduce.

calizarr

#Reversal Distance
dataset = open('rosalind_rear_sample.txt','r')
data = dataset.read().split('\n')
dataset.close()
while len(data)>(len(data)-data.count('')):
	data.remove('')
originals = [[int(x) for x in y.split()] for y in data[::2]]
perms = [[int(x) for x in y.split()] for y in data[1::2]]
def findBreak(perm):
	num = 0

calizarr

def findDecreaseStrip(perm,start,lst):
	if start>len(perm)-1 or start+1>len(perm)-1:
		return lst
	breakpoint = abs(perm[start+1]-perm[start])
	if start+1==len(perm)-1 and perm[start]>perm[start+1] and breakpoint==1:
		lst.append(start),lst.append(start+1)
	elif perm[start]>perm[start+1] and breakpoint==1:
		lst.append(start)
		return findDecreaseStrip(perm,start+1,lst)
	else: