1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
|
"""Testing online code for fetching sequences, and parsing them
Uses Bio.SeqIO to parse files downloaded with Bio.GenBank, Bio.WWW.NCBI,
Bio.ExPASy etc.
Goals:
Make sure that all retrieval is working as expected.
May catch some format changes early too.
"""
import requires_internet
#We want to test these:
from Bio import GenBank
from Bio import ExPASy
#In order to check any sequences returned
from Bio import SeqIO
from StringIO import StringIO
from Bio.SeqUtils.CheckSum import seguid
def checksum_summary(record) :
if len(record.seq) < 25 :
short = record.seq.tostring()
else :
short = record.seq.tostring()[:19] \
+ "..." + record.seq.tostring()[-3:]
return "%s [%s] len %i" \
% (short, seguid(record.seq), len(record.seq))
#####################################################################
print "Checking Bio.ExPASy.get_sprot_raw()"
id_list = ["O23729"]
for identifier in id_list :
print "- Fetching %s" % identifier
handle = ExPASy.get_sprot_raw(identifier)
records = list(SeqIO.parse(handle, "swiss"))
assert len(records)==1
record = records[0]
print " Got " + checksum_summary(record)
assert record.id == identifier
del id_list, handle, identifier, records, record
#####################################################################
print "Checking Bio.GenBank.download_many()"
id_list = ['6273290', '6273289']
handle = GenBank.download_many(id_list)
for identifier, record in zip(id_list, SeqIO.parse(handle, "genbank")) :
print "- Fetched GI %s as genbank" % identifier
print " Got " + checksum_summary(record)
assert record.annotations["gi"] == identifier
handle.close()
del id_list, handle, identifier, record
#####################################################################
print "Checking Bio.GenBank.NCBIDictionary()"
for database, format, entry in [("genome","fasta","X52960"),
("genome","genbank","X52960"),
("nucleotide", "fasta", "6273291"),
("nucleotide", "genbank", "6273291"),
("protein", "fasta", "16130152"),
("protein", "genbank", "16130152")] :
print "- Fetching %s from %s as %s" % (entry, database, format)
ncbi_dict = GenBank.NCBIDictionary(database, format)
data = ncbi_dict[entry]
assert isinstance(data, str)
handle = StringIO(data) #turn into a handle
records = list(SeqIO.parse(handle, format))
handle.close()
assert len(records) == 1
print " Got " + checksum_summary(records[0])
del database, format, entry, handle, data, records
#####################################################################
|
