Mercurial > repos > miller-lab > genome_diversity
comparison genome_diversity.py @ 12:4b6590dd7250
Uploaded
author | miller-lab |
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date | Wed, 12 Sep 2012 17:10:26 -0400 |
parents | 2c498d40ecde |
children |
comparison
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11:d4ec09e8079f | 12:4b6590dd7250 |
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1 #!/usr/bin/env python | |
2 | |
3 import sys | |
4 import cdblib | |
5 | |
6 def _openfile( filename=None, mode='r' ): | |
7 try: | |
8 fh = open( filename, mode ) | |
9 except IOError, err: | |
10 raise RuntimeError( "can't open file: %s\n" % str( err ) ) | |
11 return fh | |
12 | |
13 def get_filename_from_loc( species=None, filename=None ): | |
14 fh = _openfile( filename ) | |
15 for line in fh: | |
16 if line and not line.startswith( '#' ): | |
17 line = line.rstrip( '\r\n' ) | |
18 if line: | |
19 elems = line.split( '\t' ) | |
20 if len( elems ) >= 2 and elems[0] == species: | |
21 return elems[1] | |
22 | |
23 raise RuntimeError( "can't find '%s' in location file: %s\n" % ( species, filename ) ) | |
24 | |
25 | |
26 class SnpFile( object ): | |
27 def __init__( self, filename=None, seq_col=1, pos_col=2, ref_seq_col=7, ref_pos_col=8 ): | |
28 self.filename = filename | |
29 self.fh = _openfile( filename ) | |
30 self.seq_col = seq_col | |
31 self.pos_col = pos_col | |
32 self.ref_seq_col = ref_seq_col | |
33 self.ref_pos_col = ref_pos_col | |
34 self.elems = None | |
35 self.line = None | |
36 self.comments = [] | |
37 | |
38 def next( self ): | |
39 while self.fh: | |
40 try: | |
41 self.line = self.fh.next() | |
42 except StopIteration: | |
43 self.line = None | |
44 self.elems = None | |
45 return None | |
46 if self.line: | |
47 self.line = self.line.rstrip( '\r\n' ) | |
48 if self.line: | |
49 if self.line.startswith( '#' ): | |
50 self.comments.append( self.line ) | |
51 else: | |
52 self.elems = self.line.split( '\t' ) | |
53 return 1 | |
54 | |
55 def get_seq_pos( self ): | |
56 if self.elems: | |
57 return self.elems[ self.seq_col - 1 ], self.elems[ self.pos_col - 1 ] | |
58 else: | |
59 return None, None | |
60 | |
61 def get_ref_seq_pos( self ): | |
62 if self.elems: | |
63 return self.elems[ self.ref_seq_seq - 1 ], self.elems[ self.ref_pos_col - 1 ] | |
64 else: | |
65 return None, None | |
66 | |
67 | |
68 class IndexedFile( object ): | |
69 | |
70 def __init__( self, data_file=None, index_file=None ): | |
71 self.data_file = data_file | |
72 self.index_file = index_file | |
73 self.data_fh = _openfile( data_file ) | |
74 self.index_fh = _openfile( index_file ) | |
75 self._reader = cdblib.Reader( self.index_fh.read(), hash ) | |
76 | |
77 def get_indexed_line( self, key=None ): | |
78 line = None | |
79 if key in self._reader: | |
80 offset = self._reader.getint( key ) | |
81 self.data_fh.seek( offset ) | |
82 try: | |
83 line = self.data_fh.next() | |
84 except StopIteration: | |
85 raise RuntimeError( 'index file out of sync for %s' % key ) | |
86 return line | |
87 | |
88 class PrimersFile( IndexedFile ): | |
89 def get_primer_header( self, sequence=None, position=None ): | |
90 key = "%s %s" % ( str( sequence ), str( position ) ) | |
91 header = self.get_indexed_line( key ) | |
92 if header: | |
93 if header.startswith( '>' ): | |
94 elems = header.split() | |
95 if len( elems ) < 3: | |
96 raise RuntimeError( 'short primers header for %s' % key ) | |
97 if sequence != elems[1] or str( position ) != elems[2]: | |
98 raise RuntimeError( 'primers index for %s finds %s %s' % ( key, elems[1], elems[2] ) ) | |
99 else: | |
100 raise RuntimeError( 'primers index out of sync for %s' % key ) | |
101 return header | |
102 | |
103 def get_entry( self, sequence=None, position=None ): | |
104 entry = self.get_primer_header( sequence, position ) | |
105 if entry: | |
106 while self.data_fh: | |
107 try: | |
108 line = self.data_fh.next() | |
109 except StopIteration: | |
110 break | |
111 if line.startswith( '>' ): | |
112 break | |
113 entry += line | |
114 return entry | |
115 | |
116 def get_enzymes( self, sequence=None, position=None ): | |
117 entry = self.get_primer_header( sequence, position ) | |
118 enzyme_list = [] | |
119 if entry: | |
120 try: | |
121 line = self.data_fh.next() | |
122 except StopIteration: | |
123 raise RuntimeError( 'primers entry for %s %s is truncated' % ( str( sequence ), str( position ) ) ) | |
124 if line.startswith( '>' ): | |
125 raise RuntimeError( 'primers entry for %s %s is truncated' % ( str( sequence ), str( position ) ) ) | |
126 line.rstrip( '\r\n' ) | |
127 if line: | |
128 enzymes = line.split( ',' ) | |
129 for enzyme in enzymes: | |
130 enzyme = enzyme.strip() | |
131 if enzyme: | |
132 enzyme_list.append( enzyme ) | |
133 return enzyme_list | |
134 | |
135 class SnpcallsFile( IndexedFile ): | |
136 def get_snp_seq( self, sequence=None, position=None ): | |
137 key = "%s %s" % ( str( sequence ), str( position ) ) | |
138 line = self.get_indexed_line( key ) | |
139 if line: | |
140 elems = line.split( '\t' ) | |
141 if len (elems) < 3: | |
142 raise RuntimeError( 'short snpcalls line for %s' % key ) | |
143 if sequence != elems[0] or str( position ) != elems[1]: | |
144 raise RuntimeError( 'snpcalls index for %s finds %s %s' % ( key, elems[0], elems[1] ) ) | |
145 return elems[2] | |
146 else: | |
147 return None | |
148 | |
149 def get_flanking_dna( self, sequence=None, position=None, format='fasta' ): | |
150 if format != 'fasta' and format != 'primer3': | |
151 raise RuntimeError( 'invalid format for flanking dna: %s' % str( format ) ) | |
152 seq = self.get_snp_seq( sequence, position ) | |
153 if seq: | |
154 p = seq.find('[') | |
155 if p == -1: | |
156 raise RuntimeError( 'snpcalls entry for %s %s missing left bracket: %s' % ( str( sequence ), str( position ), seq ) ) | |
157 q = seq.find(']', p + 1) | |
158 if q == -1: | |
159 raise RuntimeError( 'snpcalls entry for %s %s missing right bracket: %s' % ( str( sequence ), str( position ), seq ) ) | |
160 q += 1 | |
161 | |
162 if format == 'fasta': | |
163 flanking_seq = '> ' | |
164 else: | |
165 flanking_seq = 'SEQUENCE_ID=' | |
166 | |
167 flanking_seq += "%s %s %s %s\n" % ( str( sequence ), str( position ), seq[p+1], seq[p+3] ) | |
168 | |
169 if format == 'primer3': | |
170 flanking_seq += 'SEQUENCE_TEMPLATE=' | |
171 | |
172 flanking_seq += "%sn%s\n" % ( seq[0:p], seq[q:] ) | |
173 | |
174 if format == 'primer3': | |
175 flanking_seq += "SEQUENCE_TARGET=%d,11\n=\n" % ( p - 5 ) | |
176 | |
177 return flanking_seq | |
178 else: | |
179 return None | |
180 | |
181 | |
182 | |
183 class LocationFile( object ): | |
184 def __init__(self, filename): | |
185 self.build_map(filename) | |
186 | |
187 def build_map(self, filename): | |
188 self.map = {} | |
189 self.open_file(filename) | |
190 for line in self.read_lines(): | |
191 elems = line.split('\t', 1) | |
192 if len(elems) == 2: | |
193 self.map[ elems[0].strip() ] = elems[1].strip() | |
194 self.close_file() | |
195 | |
196 def read_lines(self): | |
197 for line in self.fh: | |
198 if not line.startswith('#'): | |
199 line = line.rstrip('\r\n') | |
200 yield line | |
201 | |
202 def open_file(self, filename): | |
203 self.filename = filename | |
204 try: | |
205 self.fh = open(filename, 'r') | |
206 except IOError, err: | |
207 print >> sys.stderr, "Error opening location file '%s': %s" % (filename, str(err)) | |
208 sys.exit(1) | |
209 | |
210 def close_file(self): | |
211 self.fh.close() | |
212 | |
213 def loc_file( self, key ): | |
214 if key in self.map: | |
215 return self.map[key] | |
216 else: | |
217 print >> sys.stderr, "'%s' does not appear in location file '%s'" % (key, self.filename) | |
218 sys.exit(1) | |
219 | |
220 class ChrLens( object ): | |
221 def __init__( self, chrlen_filename ): | |
222 self.chrlen_filename = chrlen_filename | |
223 self.build_map() | |
224 | |
225 def build_map(self): | |
226 self.map = {} | |
227 self.open_file(self.chrlen_filename) | |
228 for line in self.read_lines(): | |
229 elems = line.split('\t', 1) | |
230 if len(elems) == 2: | |
231 chrom = elems[0].strip() | |
232 chrom_len_text = elems[1].strip() | |
233 try: | |
234 chrom_len = int( chrom_len_text ) | |
235 except ValueError: | |
236 print >> sys.stderr, "Bad length '%s' for chromosome '%s' in '%s'" % (chrom_len_text, chrom, self.chrlen_filename) | |
237 self.map[ chrom ] = chrom_len | |
238 self.close_file() | |
239 | |
240 def read_lines(self): | |
241 for line in self.fh: | |
242 if not line.startswith('#'): | |
243 line = line.rstrip('\r\n') | |
244 yield line | |
245 | |
246 def open_file(self, filename): | |
247 self.filename = filename | |
248 try: | |
249 self.fh = open(filename, 'r') | |
250 except IOError, err: | |
251 print >> sys.stderr, "Error opening chromosome length file '%s': %s" % (filename, str(err)) | |
252 sys.exit(1) | |
253 | |
254 def close_file(self): | |
255 self.fh.close() | |
256 | |
257 def length( self, key ): | |
258 if key in self.map: | |
259 return self.map[key] | |
260 else: | |
261 return None | |
262 | |
263 def __iter__( self ): | |
264 for chrom in self.map: | |
265 yield chrom | |
266 |