Reading a Fasta file from Url address - url

Question

I'm using Python 3.4.
I wrote some code to read Fasta file from internet site, but it didn't work.
http://www.uniprot.org/uniprot/B5ZC00.fasta
(I can download and read it as text file, but I'm planning to read multiple Fasta files from given site.)
(1) The first attempt
# read FASTA file
def read_fasta(filename_as_string):
"""
open text file with FASTA format
read it and convert it into string list
convert the list to dictionary
>>> read_fasta('sample.txt')
{'Rosalind_0000':'GTAT....ATGA', ... }
"""
f = open(filename_as_string,'r')
content = [line.strip() for line in f]
f.close()
new_content = []
for line in content:
if '>Rosalind' in line:
new_content.append(line.strip('>'))
new_content.append('')
else:
new_content[-1] += line
dict = {}
for i in range(len(new_content)-1):
if i % 2 == 0:
dict[new_content[i]] = new_content[i+1]
return dict
This code can read any Fasta file in my desktop computer, but it failed to read the same Fasta file from internet site.
>>> from urllib.request import urlopen
>>> html = urlopen("http://www.uniprot.org/uniprot/B5ZC00.fasta")
>>> print (read_fasta(html))
TypeError: invalid file: <http.client.HTTPResponse object at 0x02A62EF0>
(2) The second attempt
>>> from urllib.request import urlopen
>>> html = urlopen("http://www.uniprot.org/uniprot/B5ZC00.fasta")
>>> lines = [x.strip() for x in html.readlines()]
>>> print (lines)
[b'>sp|B5ZC00|SYG_UREU1 Glycine--tRNA ligase OS=Ureaplasma urealyticum serovar 10 (strain ATCC 33699 / Western) GN=glyQS PE=3 SV=1', b'MKNKFKTQEELVNHLKTVGFVFANSEIYNGLANAWDYGPLGVLLKNNLKNLWWKEFVTKQ', b'KDVVGLDSAIILNPLVWKASGHLDNFSDPLIDCKNCKARYRADKLIESFDENIHIAENSS', b'NEEFAKVLNDYEISCPTCKQFNWTEIRHFNLMFKTYQGVIEDAKNVVYLRPETAQGIFVN', b'FKNVQRSMRLHLPFGIAQIGKSFRNEITPGNFIFRTREFEQMEIEFFLKEESAYDIFDKY', b'LNQIENWLVSACGLSLNNLRKHEHPKEELSHYSKKTIDFEYNFLHGFSELYGIAYRTNYD', b'LSVHMNLSKKDLTYFDEQTKEKYVPHVIEPSVGVERLLYAILTEATFIEKLENDDERILM', b'DLKYDLAPYKIAVMPLVNKLKDKAEEIYGKILDLNISATFDNSGSIGKRYRRQDAIGTIY', b'CLTIDFDSLDDQQDPSFTIRERNSMAQKRIKLSELPLYLNQKAHEDFQRQCQK']
I thought that I could modify my code to read online Fasta file as a string list, but soon I realized that it was not easy.
>>> print (type(lines[0]))
<class 'bytes'>
I can't remove the dirty 'b' character in the head of each element of list.
>>> print (lines[0])
b'>sp|B5ZC00|SYG_UREU1 Glycine--tRNA ligase ...
>>> print (lines[0][1:])
b'sp|B5ZC00|SYG_UREU1 Glycine--tRNA ligase ...
(3) Questions
How can I remove the dirty 'b' character?
Is there any better way to read Fasta file from given Url?
With some help, I think I can modify and complete my code.
Thanks.

Answer 1

I'm late, but I answer if useful
in python 2
import urllib2
url = "http://www.uniprot.org/uniprot/B5ZC00.fasta"
response = urllib2.urlopen(url)
fasta = response.read()
print fasta
in python 3
from urllib.request import urlopen
url = "http://www.uniprot.org/uniprot/B5ZC00.fasta"
response = urlopen(url)
fasta = response.read().decode("utf-8", "ignore")
print(fasta)
you get:
>sp|B5ZC00|SYG_UREU1 Glycine--tRNA ligase OS=Ureaplasma urealyticum serovar 10 (strain ATCC 33699 / Western) GN=glyQS PE=3 SV=1
MKNKFKTQEELVNHLKTVGFVFANSEIYNGLANAWDYGPLGVLLKNNLKNLWWKEFVTKQ
KDVVGLDSAIILNPLVWKASGHLDNFSDPLIDCKNCKARYRADKLIESFDENIHIAENSS
NEEFAKVLNDYEISCPTCKQFNWTEIRHFNLMFKTYQGVIEDAKNVVYLRPETAQGIFVN
FKNVQRSMRLHLPFGIAQIGKSFRNEITPGNFIFRTREFEQMEIEFFLKEESAYDIFDKY
LNQIENWLVSACGLSLNNLRKHEHPKEELSHYSKKTIDFEYNFLHGFSELYGIAYRTNYD
LSVHMNLSKKDLTYFDEQTKEKYVPHVIEPSVGVERLLYAILTEATFIEKLENDDERILM
DLKYDLAPYKIAVMPLVNKLKDKAEEIYGKILDLNISATFDNSGSIGKRYRRQDAIGTIY
CLTIDFDSLDDQQDPSFTIRERNSMAQKRIKLSELPLYLNQKAHEDFQRQCQK
BONUS
It is better using biopython (example for python 2)
from Bio import SeqIO
import urllib2
url = "http://www.uniprot.org/uniprot/B5ZC00.fasta"
response = urllib2.urlopen(url)
fasta_iterator = SeqIO.parse(response, "fasta")
for seq in fasta_iterator:
print seq.format("fasta")

Answer 2

If you're only interested in the primary amino acid sequence (wanting to ignore the header), try the following:
link = str(sys.argv[1]) #fasta file URL provided as command line argument
FASTA = urllib.urlopen(link).readlines()[1:] # as list without header (">...")
FASTA = "".join(FASTA).replace("\n","") # as a string free of new line markers
print FASTA

Answer 3

A little late to the party, but trying Jose's Biopython answer no longer works in Python 3. Here's an alternative:
from Bio import SeqIO
import requests
from io import StringIO
link = "http://www.uniprot.org/uniprot/B5ZC00.fasta"
data = requests.get(link).text
fasta_iterator = SeqIO.parse(StringIO(data), "fasta")
# Pretty print the fasta info
for seq in fasta_iterator:
print(seq.format("fasta"))