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