Python get_from_url Examples

Example #1

File: fetch_fasta_part.py Project: metajinomics/dev

if os.path.exists(sys.argv[2]):
    print "path exists"
else :
    os.mkdir(sys.argv[2])

for id in open(sys.argv[1]):
    id = id.strip()
    line = id
    if id == "":
        continue

    words = line.strip().split('\t')
    id = words[0]
    s1 = url_template.format(words[0],words[1],words[2])

    sys.stdout.write("Fetching %s..." % id)
    sys.stdout.flush()
    gbk_out_file = os.path.join(sys.argv[2], id +words[1]+ ".fa")

    if os.path.exists(gbk_out_file):
        print "already fetched"
    else :
        seq = urllib2.urlopen(s1).read()
        if(words[3] == "minus"):
            seq = reverse_complement.get_from_url(seq)
        open(gbk_out_file, "w").write(seq)
        
    print "Done"
    time.sleep(1.0/3)

Example #2

if os.path.exists(sys.argv[2]):
    print "path exists"
else:
    os.mkdir(sys.argv[2])

for id in open(sys.argv[1]):
    id = id.strip()
    line = id
    if id == "":
        continue

    words = line.strip().split('\t')
    id = words[0]
    s1 = url_template.format(words[0], words[1], words[2])

    sys.stdout.write("Fetching %s..." % id)
    sys.stdout.flush()
    gbk_out_file = os.path.join(sys.argv[2], id + words[1] + ".fa")

    if os.path.exists(gbk_out_file):
        print "already fetched"
    else:
        seq = urllib2.urlopen(s1).read()
        if (words[3] == "minus" or words[3] == "-"):
            seq = reverse_complement.get_from_url(seq)
        open(gbk_out_file, "w").write(seq)

    print "Done"
    time.sleep(1.0 / 3)

Example #3

File: test_reverse_complement.py Project: metajinomics/dev

#!/usr/bin/python

import sys
sys.path.append('./utils')
import reverse_complement

seq = "ATGCTat"
print seq
print reverse_complement.get_rc(seq)

seq_url = ">name\nATGTatn"
print seq_url
print reverse_complement.get_from_url(seq_url)