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comparison reference_bins.py @ 0:7db7ecc78ad6 draft

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author damion
date Mon, 02 Mar 2015 20:46:00 -0500
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-1:000000000000 0:7db7ecc78ad6
1 import os.path
2 import common
3
4 class ReferenceBins:
5
6 def __init__(self, db_spec_path = None):
7 """
8 @param db_spec_path string path to fasta databases specification file. This file has format:
9 #value id type active name path
10 16S_euzby 16S 1 Euzby /usr/local/galaxy/shared/ngs_data/
11 ...
12 """
13 self.reference_bins = []
14
15 if db_spec_path == None: # Default to the command-line lookup table in code's folder:
16 db_spec_path = os.path.join(os.path.dirname(__file__), 'fasta_reference_dbs.tab')
17 self.fieldSpec = common.FieldSpec(db_spec_path)
18
19 def __main__(self): pass
20
21 # Could double check to see if it exists?
22 def build_bins(self, bins, columns):
23
24 if bins == None:
25 self.reference_bins = []
26 return False
27
28 for myfield in bins.strip().strip(';').split(';'):
29 field_spec = myfield.strip().split(':')
30 field_name = field_spec[0].strip()
31
32 if field_name != '':
33 if not field_name.replace('_','').isalnum():
34 common.stop_err("Invalid bin name: " + field_name + ':' + myfield)
35
36 if len(field_spec) < 2: field_spec.append('column') # default grouping = column
37 if len(field_spec) < 3: field_spec.append('') # default filtering = none
38 if len(field_spec) < 4: field_spec.append('') # default no description
39
40 grouping = field_spec[1].strip()
41 if not grouping in ['table', 'column', 'hidden']:
42 common.stop_err("Invalid bin layout: " + grouping)
43
44 bin_filter = field_spec[2].strip()
45 if not bin_filter in ['', 'include', 'exclude']:
46 common.stop_err("Invalid bin sort: " + bin_filter)
47
48 newbin = self.buildBin(field_name, bin_filter)
49 self.reference_bins.append(newbin)
50
51 field = { # any time we have a bin we want sort descending
52 'field': field_name,
53 'group': grouping,
54 'sort': 'desc',
55 'label': newbin.name,
56 'type': 'bin'
57 }
58 columns.append(field)
59 if (field_spec[3] == 'true'): # description field requested
60 field = {
61 'field': field_name + '_desc',
62 'group': 'column',
63 'sort': '', # Allow other sorts????
64 'label': newbin.name + ' Description',
65 'type': 'text'
66 }
67 columns.append(field)
68
69
70 def buildBin(self, bin_folder_name, bin_filter):
71 """
72 Create a lookup table consisting of a dictionary entry for each accession id held in dictionary's file.
73 @param bin_folder_name string name of requested db, e.g 16S_ncbi
74 @param bin_filter string '' or 'include' or 'exclude'
75
76 """
77 bin = ReferenceBin(self.fieldSpec, bin_folder_name, bin_filter)
78
79 try:
80 with open(bin.file_path) as file_in:
81 for line in file_in: # Should always contains succession id
82 #FUTURE: Preprocess so accession ID ready to go.
83 keyValue = line.rstrip().split("\t",1)
84 # keep only first term minus integer portion of id
85 accGeneralId = keyValue[0].split('.')[0]
86 if len(keyValue) >1: description = keyValue[1]
87 else: description = ''
88 bin.lookup[accGeneralId] = description
89
90 file_in.close()
91
92 except IOError:
93 stop_err("Reference bin could not be found or opened: " + self.path + bin_folder_name + '/accession_ids.tab')
94
95 return bin
96
97 def setStatus(self, record):
98
99 if len(self.reference_bins) == 0: return #no bins
100
101 # Use of "extended slices" http://docs.python.org/2.3/whatsnew/section-slices.html
102 # Example sallseqid is 'gi|194753780|ref|XR_046072.1|;gi|195119578|ref|XR_047594.1|;gi|195154052|ref|XR_047967.1|'
103 # Example accs is ['XR_046072.1', 'XR_047594.1', 'XR_047967.1']
104 # Original code was "[1::2][1::2]" (select every 2nd item, then every 2nd item of that)
105 accs = record.sallseqid.split('|')
106
107 if common.re_default_ncbi_id.match(record.sseqid):
108 accs = accs[3::4] #Select every 4th item starting offset 4
109
110 elif common.re_default_ref_id.match(record.sseqid):
111 accs = accs[1::2]
112
113
114 # Check each accession # against each bin.
115 for ptr, bin in enumerate(self.reference_bins):
116 setattr(record, bin.field, '') #Using '','1' not FALSE/TRUE because of tab delim output
117 setattr(record, bin.field + '_desc', '')
118 for acc in accs:
119 accGeneralId = acc.split('.')[0]
120 if accGeneralId in bin.lookup:
121 if bin.exclude: return False
122 setattr(record, bin.field, str(ptr+1))
123 # Include any bin notes for this item
124 setattr(record, bin.field + '_desc', bin.lookup[accGeneralId])
125 break # This result has been binned to this bin so break.
126
127
128
129
130 def __str__(self):
131 return "name: %s dict: %s" % (self.name, str(self.lookup))
132
133 class ReferenceBin:
134 def __init__(self, fieldSpec, bin_folder_name, bin_filter):
135 self.lookup = {}
136 self.folder = bin_folder_name
137 self.name = fieldSpec.getAttribute(bin_folder_name, 'name')
138 self.field = bin_folder_name
139 self.path = fieldSpec.getAttribute(bin_folder_name, 'path')
140 self.exclude = bin_filter
141 #absolute path to reference bins folder: /usr/local/galaxy/shared/ngs_data/
142 self.file_path = os.path.join(self.path + self.folder + '/accession_ids.tab')
143
144 if __name__ == '__main__':
145
146 binManager = ReferenceBins()
147 binManager.__main__()
148