d = {"blue":10, "green":20}
d # may be printed in different order
d = {}
d["blue"]=10 # it's weird that we use [] here and not {}
d["green"]=20
d
# access the value of a key, or simply check if a key exists
"blue" in d
d.get("blue")
d["blue"]
"red" in d
d["red"] # oops
d.get("red")
d.get("red") == None
d.get("red", 5)
# remove things
del d["green"] # deletes element (binding)
d
a = d.pop("blue") # deletes, but returns value
d

dna = "TCAATAGGTGGTCGTTGTTT"
k2mer = {} # variable names cannot start with a digit
bases = ["A","C","G","T"]
for nuc1 in bases:
  for nuc2 in bases:
    mycount = dna.count(nuc1+nuc2)
    if mycount:
      k2mer[nuc1+nuc2] = mycount

trimer_count = {} # variable names cannot start with a digit
bases = ["A","C","G","T"]
for i in range(0,(len(dna)-2)):
  trimer = dna[i:(i+3)]
  if trimer in trimer_count:
    trimer_count[trimer] += 1
  else:
    trimer_count[trimer] = 1

trimer_count
trimer_count["TTT"]
trimer_count["GCC"] # key error
trimer_count.get("GCC", 0) # default to 0 if key not found

for trinucleotide in trimer_count:
  print("count for " + trinucleotide + ":", trimer_count[trinucleotide])

for k,v in trimer_count.items(): # k,v for key,value. (k,v) is a tuple
  print("count for " + k + ":", v)

for tn in sorted(trimer_count.keys()): # k,v for key,value
  print("count for " + tn + ":", trimer_count[tn])

for tn in trimer_count:
  if trimer_count[tn] == 2:
    print(tn, "appears twice")

s1 = {"blue","green"}
for color in s1:
  print(color)
s1.add("green") # was already there: no change
s1
s1.add("orange")
s1
"red" in s1
"blue" in s1
s1.remove("green")
a = s1.pop()
s
s2 = s1.union({"green","blue"})
s3 = {"green","purple"}
s2.intersection(s3)
s2.difference(s3) # s2 \ s3

set(trimer_count.keys())

[xxx for y in z]
[xxx for y in z if uuu]

[k for k in trimer_count] # list of keys, here list of trimers present in the sequence
[k for k,v in trimer_count.items() if v>1] # trimers appearing 2+ times

paramvalues = [10 ** i for i in range(-3,2)] # from "range" object
[v**2 for v in paramvalues]
[v**2 for v in paramvalues if v >= 0.1] # from list, with condition

d = {'xtolrel':0.01, 'xtolabs':0.001, 'Nfail':50} # d for dictionary
d # note possibly different order
[d[k]*2 for k in d] # k for key
[d[k]*2 for k in d if k.startswith("xtol")] # with condition
[[k, v*2] for k,v in d.items()] # k for key, v for value. returns a list

# extract a subset of values
x = [18, 1, 54, 0, 2, 72]
wanted = [True, True, False, False, True, False]
[x[i] for i in range(len(x)) if wanted[i]]

dict( [[k, v*2] for k,v in d.items()] ) # wasteful
{ k:v*2 for k,v in d.items() } # same result
{ k for k,v in d.items() } # set: like a dict but keys only, no values
{ k for k in d } # same as above
set(d.keys())    # same result
{ k for k in d if re.search(r'tol',k)}

paramvalues = [a * (10 ** i) for i in range(-3,2) for a in [1,2]]

import subprocess

subprocess.call("date -u", shell=True) # return exist status: 0 if good

subprocess.check_output("date")
res = subprocess.check_output(["date", "+%B"])
res
type(res)
res.decode("utf-8")
res = subprocess.check_output("ps -u ane | grep python", shell=True)
res
print(res.decode("utf-8"))

print(subprocess.run("/bin/date")) # does not capture output
res = subprocess.run("/bin/date +%B", shell=True, stdout=subprocess.PIPE)
res = subprocess.run(["/bin/date", "+%B"],        stdout=subprocess.PIPE)
print("return code: ", res.returncode,
      "\nstdout: ", res.stdout,
      "\nstderr:", res.stderr)
res = subprocess.run(["ls", "wrong/path"], stdout=subprocess.PIPE) # stderr to screen
res = subprocess.run(["ls", "wrong/path"], capture_output=True)) # stderr captured too

ord("\0") # null character
ord("\n")
ord("\r")
ord("é")  # unicode character number 233
ord("🙂") # 128578
len(bytes("🙂", encoding='utf-8')) # 4 bytes
a = bytes("é", encoding='utf-8')
len(a) # coded with 2 bytes using UTF8 encoding
a      # b'\xc3\xa9'
a[0]   # 195 = 12*16 + 3 > 128: not ASCII
a[1]   # 169 = 10*16 + 9
bin(a[0]) # 0b11000011
bin(a[1]) # 0b10101001
# so UFT-8 code for é is: 1100001110101001