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comparison xml.py @ 0:e1c29f302301 draft

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author devteam
date Fri, 17 Aug 2012 09:10:31 -0400
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-1:000000000000 0:e1c29f302301
1 """
2 BlastXml class
3 """
4
5 from galaxy.datatypes.data import get_file_peek
6 from galaxy.datatypes.data import Text
7 from galaxy.datatypes.xml import GenericXml
8
9 class BlastXml( GenericXml ):
10 """NCBI Blast XML Output data"""
11 file_ext = "blastxml"
12
13 def set_peek( self, dataset, is_multi_byte=False ):
14 """Set the peek and blurb text"""
15 if not dataset.dataset.purged:
16 dataset.peek = get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
17 dataset.blurb = 'NCBI Blast XML data'
18 else:
19 dataset.peek = 'file does not exist'
20 dataset.blurb = 'file purged from disk'
21 def sniff( self, filename ):
22 """
23 Determines whether the file is blastxml
24
25 >>> fname = get_test_fname( 'megablast_xml_parser_test1.blastxml' )
26 >>> BlastXml().sniff( fname )
27 True
28 >>> fname = get_test_fname( 'tblastn_four_human_vs_rhodopsin.xml' )
29 >>> BlastXml().sniff( fname )
30 True
31 >>> fname = get_test_fname( 'interval.interval' )
32 >>> BlastXml().sniff( fname )
33 False
34 """
35 #TODO - Use a context manager on Python 2.5+ to close handle
36 handle = open(filename)
37 line = handle.readline()
38 if line.strip() != '<?xml version="1.0"?>':
39 handle.close()
40 return False
41 line = handle.readline()
42 if line.strip() not in ['<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">',
43 '<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "NCBI_BlastOutput.dtd">']:
44 handle.close()
45 return False
46 line = handle.readline()
47 if line.strip() != '<BlastOutput>':
48 handle.close()
49 return False
50 handle.close()
51 return True
52
53 def merge(split_files, output_file):
54 """Merging multiple XML files is non-trivial and must be done in subclasses."""
55 if len(split_files) == 1:
56 #For one file only, use base class method (move/copy)
57 return Text.merge(split_files, output_file)
58 out = open(output_file, "w")
59 h = None
60 for f in split_files:
61 h = open(f)
62 body = False
63 header = h.readline()
64 if not header:
65 out.close()
66 h.close()
67 raise ValueError("BLAST XML file %s was empty" % f)
68 if header.strip() != '<?xml version="1.0"?>':
69 out.write(header) #for diagnosis
70 out.close()
71 h.close()
72 raise ValueError("%s is not an XML file!" % f)
73 line = h.readline()
74 header += line
75 if line.strip() not in ['<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">',
76 '<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "NCBI_BlastOutput.dtd">']:
77 out.write(header) #for diagnosis
78 out.close()
79 h.close()
80 raise ValueError("%s is not a BLAST XML file!" % f)
81 while True:
82 line = h.readline()
83 if not line:
84 out.write(header) #for diagnosis
85 out.close()
86 h.close()
87 raise ValueError("BLAST XML file %s ended prematurely" % f)
88 header += line
89 if "<Iteration>" in line:
90 break
91 if len(header) > 10000:
92 #Something has gone wrong, don't load too much into memory!
93 #Write what we have to the merged file for diagnostics
94 out.write(header)
95 out.close()
96 h.close()
97 raise ValueError("BLAST XML file %s has too long a header!" % f)
98 if "<BlastOutput>" not in header:
99 out.close()
100 h.close()
101 raise ValueError("%s is not a BLAST XML file:\n%s\n..." % (f, header))
102 if f == split_files[0]:
103 out.write(header)
104 old_header = header
105 elif old_header[:300] != header[:300]:
106 #Enough to check <BlastOutput_program> and <BlastOutput_version> match
107 out.close()
108 h.close()
109 raise ValueError("BLAST XML headers don't match for %s and %s - have:\n%s\n...\n\nAnd:\n%s\n...\n" \
110 % (split_files[0], f, old_header[:300], header[:300]))
111 else:
112 out.write(" <Iteration>\n")
113 for line in h:
114 if "</BlastOutput_iterations>" in line:
115 break
116 #TODO - Increment <Iteration_iter-num> and if required automatic query names
117 #like <Iteration_query-ID>Query_3</Iteration_query-ID> to be increasing?
118 out.write(line)
119 h.close()
120 out.write(" </BlastOutput_iterations>\n")
121 out.write("</BlastOutput>\n")
122 out.close()
123 merge = staticmethod(merge)
124