2023 Class
Looping through data and reading in files or writing out to files.
There are many Python functions available to do many things. Here is a link to list of many of these https://docs.python.org/3/library/functions.html.
In python if statements end with : and Indentation is required.
This indentation can be with spaces or tabs, but not a mix of each.
if TRUE:
THEN DO X
elif OTHER_THING_TRUE:
THEN DO Y
else:
THEN DO Z
Loops let you
while ( TRUE ):
Do X
for ITERATOR in LIST:
Do Y
for i in range(5):
print(i)
Most editors do this automatically but you might find it hard to detect errors looking at the code until you try to run it if there are tabs in one part and sapces in another.
This indentation can be either spaces or tabs. Emacs/Atom/Vi allow customizing your editor so that when [tab] is typed it will either insert 4 spaces or a tab. Switching between editors while editing a file can sometimes cause problems.
Solution: delete the indendentation and enter the tab (or spaces) again.
After this slide you will now understand this scene from Silicon Valley.
To test if somehting is equal use == or is.
== test numerical equality, is checks if both the variables point
to the same object. In some cases this can be different things so
avoid using is for strings and numbers.
x=10
if x == 10:
print("this == 10")
if x == "10":
print("this == '10'")
if x is 10:
print("this is a 10")
if x is "10":
print("This is '10'")
a = b = [1,2,3]
c = [1,2,3]
print( a == b) # this is true
print( a == c ) # this is true
print( a is b ) # this is true
print( a is c ) # this is false
# another example of testing for equality of string content
# and the actual object
a="fiat"
b="".join(['f','i','a','t'])
print("a is ",a)
print("b is ",b)
if a is b:
print("strings are same") # this will NOT print
if a == b:
print("these are the same string: %s %s"%(a,b)) # this will print
!= for not equal and is not for correlary test with is.
if a is not c:
print("a is not c")
if 10 != 20:
print("10 is not equal to 20")
<, <=, >, >= for less than, less than or equal to, greater than, greater than or equal to.
a=7
b=20
if b > 20:
print("b is greater than a")
not, or, and logical operators.
True and True = True
True or True = True
not True = False
False and False = False
False or False = False
not False = True
True and False = False
True or False = True
a=10
b=12
c=13
if a < b and b < c:
print("a is smaller than c")
if not a == b:
print("a is not equal to b")
else:
print("a is equal to b")
while loops iterate as long as a condition is true.
x=1
while ( x < 10 ):
print("x is ",x)
x += 1
for loops through a set of items
DNA="AACGCA"
for base in DNA:
print("base is ",base)
seq in UNIX)Simple way to setup a counter. See the range
for i in range(1,10): # forwards counting
print(i)
for i in range(10,0,-1): #backwards counting
print(i)
for i in range(2,16,2): # count by twos
print(i)
Lists are sets of values, strings, numbers. Initialize with a [
] around the values. Tuples are sets of values but they are
immutable (cannot change) and are initialized with ( ).
mylist = ['a', 'b','c']
mylist.append('z')
mylist[2]='C'
mylist.insert(0,'Start')
print(mylist)
# will print
# ['Start', 'a', 'b', 'C', 'z']
A tuple cannot be changed
mylist = ('a', 'b','c')
# this next line will throw an error
mylist.append('z')
print(mylist)
# will print (note the parens not [ ] )
# ('a', 'b', 'c')
list = [7, 10, 2, 2, 7]
for i in range(len(list)):
print("list item ",i, "=",list[i])
# print("list[%d] = %s"%(i,list[i])) # I like formatted printing too
list=(1,7,8)
for item in list:
print("item is ",item)
# prints out
# item[0] = 1
# item[1] = 7
# item[2] = 8
#can use enumerate to get the index number
for idx,item in enumerate(list):
print("item[%d] = %s"%(idx,item))
# prints out
# item [0] = 7
# item [1] = 10
Sometimes we want to exit the loop if a condition is met. continue
will jump back to the beginning of the loop and not execute any more
of the code block. break will exit the loop all together.
list = ('a', 'b', 'c', 'C','d')
for l in list:
if l == "b":
continue
if l == "C":
break
print(l)
# would print only the following
# a
# c
The open function is used to open file handles. Good reference can be found at https://en.wikibooks.org/wiki/Python_Programming/Input_and_Output
Data streams could be from cmdline (eg STDIN)
$ cat file | python myscript.py
Inside the Python code here we print every line that is sent in.
#!/usr/bin/env python3
import sys # this tells python we need to use a package called sys
i=0
for line in sys.stdin:
print("line[%d] is %s"%(i,line),
end = '')
i +=1
Can also open files for reading with open.
filehandle = open(myfile,"r")
Here is a program that will read in each line from a file and print it back out.
#!/usr/bin/env python3
i=0
file = "data1.dat"
fh = open(file,"r")
for line in fh:
print("line[%d] is %s"%(i,line),
end = ''))
i+=1
What if file wasn’t there. Try it but python will throw an error and exit. You could protect your code a bit more with this construction.
with open(myfile,"r") as fh:
for line in fh:
print(line)
The with means only run the next lines if the filehandle can be
opened. There are additional more robust error handling and catching
options.
Besides using print to the OUTPUT stream we can write to a file
#!/usr/bin/env python3
ofh = open("my_data.tab","w")
ofh.write("Species\tHabitat\tSize\n")
ofh.write("Crab\tBeach\tM\n")
ofh.write("Fish\tOcean\tS\n")
$ cat my_data.tab
Species Habitat Size
Crab Beach M
Fish Ocean S
Modules are collections of code routines. We will talk more about functions/routines in next lecture. Can use these as tools.
Remember we can pass data into a program via STDIN if we use the ‘|’ “pipes” in UNIX.
Here we just wrote a wc -l replacement.
import sys
counter = 0
for line in sys.stdin:
counter += 1
print ("There are",counter, "lines")
Can be a network connection (eg URL for web or FTP)
import urllib.request
orginfo = "https://raw.githubusercontent.com/biodataprog/GEN220_data/main/data/random_exons.csv"
info = urllib.request.urlopen(orginfo)
for line in info:
linestrip = line.decode('UTF-8').strip()
print(linestrip)
Comma delimited files can be parsed this way. The module is smart enough to handle cases where the delimiter is embedded within
quotes.
So for example test2.csv could contain these lines. You can download a copy.
Colorado State University,"Fort Collins, Colorado",CSU
University of California-Riverside,"Riverside, California",UCR
import csv
file2 = "test2.csv"
with open(file2) as csvfile:
reader = csv.reader(csvfile,delimiter=",")
for row in reader:
print("\t".join(row))
with open("outtest.csv","w") as csvfile:
writer = csv.writer(csvfile,delimiter="\t")
writer.writerow(["Name","Flavor","Color"])
writer.writerow(["Apple","Sweet","Red"])
writer.writerow(["Pretzel","Salty","Brown"])
with open("outtest2.csv","w") as csvfile:
writer = csv.writer(csvfile,delimiter="\t")
writer.writerow(["Name","Flavor","Color"])
writer.writerow(["Apple","Sweet","Red\tYellow"])
writer.writerow(["Pretzel","Salty","Brown"])
Notice how this changes when the delimiter is part of the record, csv module does this automatically.
with open("outtest2.csv","w") as csvfile:
writer = csv.writer(csvfile,delimiter=",")
writer.writerow(["Name","Flavor","Color"])
writer.writerow(["Apple","Sweet","Red,Yellow"])
writer.writerow(["Pretzel","Salty","Brown"])