Question

I’ve used different ways for INPUT these days using python.

f=open('txt','r')
for line in f:.....


f=open ('txt','r').readlines()
for line in f:...



samtoolsin = subprocess.Popen(["/share/bin/samtools/samtools","view",bamfile],
                                      stdout=subprocess.PIPE,bufsize=1)

f = samtoolsin.stdout
for line in f:.....




f= commands.output('zcat '+ file)
for line in f:.....

For all the situations above, is f a list, or just string?
According to my experience, seems 1,2,3 are all list, but the 4th is string. But I don’t know why.thx

Answer 1

Short Answer:

• 1 and 3: file object
• 2: list
• 4: string

Long Answer (mainly links to docs):

f=open('txt','r')

• open() returns a File Object. It is iterable, but is neither a string nor a list.

---

f=open ('txt','r').readlines()

• file.readlines() returns a list

---

samtoolsin = subprocess.Popen(..., stderr=subprocess.PIPE, ...)
f = samtoolsin.stdout

• subprocess.Popen.stdout will be either a File Object (as in your case) or None.

---

f= commands.output('zcat '+ file)

• commands.getoutput() returns a string.