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annotate utils/getreads.py @ 18:e4d75f9efb90 draft

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planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
author nick
date Thu, 02 Feb 2017 18:44:31 -0500
parents af383638de66
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
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1 """A simple parser for FASTA, FASTQ, SAM, etc. Create generators that just return the read name and
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2 sequence.
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3 All format parsers follow this API:
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4 with open('sequence.fasta') as fasta:
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5 for read in getreads.getparser(fasta, filetype='fasta'):
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6 print "There is a sequence with this FASTA identifier: "+read.id
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7 print "Its sequence is "+read.seq
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8 The properties of Read are:
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9 name: The entire FASTA header line, SAM column 1, etc.
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10 id: The first whitespace-delimited part of the name.
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11 seq: The sequence.
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12 qual: The quality scores (unless the format is FASTA).
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13 """
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14
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15
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16 def getparser(filehandle, filetype='fasta'):
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17 if filetype == 'fasta':
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18 return FastaReader(filehandle)
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19 elif filetype == 'fastq':
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20 return FastqReader(filehandle)
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21 elif filetype == 'sam':
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22 return SamReader(filehandle)
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23 elif filetype == 'tsv':
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24 return TsvReader(filehandle)
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25 else:
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26 raise ValueError('Illegal argument: filetype=\''+filetype+'\'')
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29 class FormatError(Exception):
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30 def __init__(self, message=None):
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31 if message:
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32 Exception.__init__(self, message)
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33
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34
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35 class Read(object):
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36 def __init__(self, name='', seq='', id_='', qual=''):
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37 self.name = name
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38 self.seq = seq
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39 self.id = id_
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40 self.qual = qual
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41
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42
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43 class Reader(object):
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44 """Base class for all other parsers."""
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45 def __init__(self, filehandle):
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46 self.filehandle = filehandle
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47 def __iter__(self):
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48 return self.parser()
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49
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50
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51 class TsvReader(Reader):
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52 """A parser for a simple tab-delimited format.
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53 Column 1: name
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54 Column 2: sequence
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55 Column 3: quality scores (optional)"""
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56 def parser(self):
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57 for line in self.filehandle:
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58 fields = line.rstrip('\r\n').split('\t')
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59 if len(fields) < 2:
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60 continue
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61 read = Read()
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62 read.name = fields[0]
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63 if read.name:
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64 read.id = read.name.split()[0]
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65 read.seq = fields[1]
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66 if len(fields) >= 3:
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67 read.qual = fields[2]
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68 yield read
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69
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70
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71 class SamReader(Reader):
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72 """A simple SAM parser.
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73 Assumptions:
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74 Lines starting with "@" with 3 fields are headers. All others are alignments.
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75 All alignment lines have 11 or more fields. Other lines will be skipped.
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76 """
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77 def parser(self):
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78 for line in self.filehandle:
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79 fields = line.split('\t')
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80 if len(fields) < 11:
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81 continue
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82 # Skip headers.
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83 if fields[0].startswith('@') and len(fields[0]) == 3:
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84 continue
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85 read = Read()
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86 read.name = fields[0]
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87 if read.name:
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88 read.id = read.name.split()[0]
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89 read.seq = fields[9]
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90 read.qual = fields[10].rstrip('\r\n')
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91 yield read
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92
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93
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94 class FastaReader(Reader):
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95 """A simple FASTA parser that reads one sequence at a time into memory."""
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96 def parser(self):
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97 read = Read()
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98 while True:
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99 line_raw = self.filehandle.readline()
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100 if not line_raw:
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101 if read.seq:
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102 yield read
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103 raise StopIteration
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104 line = line_raw.strip()
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105 # Allow empty lines.
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106 if not line:
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107 continue
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108 if line.startswith('>'):
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109 if read.seq:
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110 yield read
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111 read = Read()
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112 read.name = line[1:] # remove ">"
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113 if read.name:
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114 read.id = read.name.split()[0]
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115 continue
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116 else:
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117 read.seq += line
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118
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119
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120 class FastqReader(Reader):
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121 """A simple FASTQ parser. Can handle multi-line sequences, though."""
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122 def parser(self):
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123 read = Read()
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124 state = 'header'
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125 while True:
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126 line_raw = self.filehandle.readline()
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127 if not line_raw:
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128 if read.seq:
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129 yield read
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130 raise StopIteration
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131 line = line_raw.strip()
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132 # Allow empty lines.
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133 if not line:
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134 continue
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135 if state == 'header':
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136 if not line.startswith('@'):
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137 raise FormatError('line state = "header" but line does not start with "@"')
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138 if read.seq:
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139 yield read
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140 read = Read()
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141 read.name = line[1:] # remove '@'
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142 if read.name:
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143 read.id = read.name.split()[0]
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144 state = 'sequence'
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145 elif state == 'sequence':
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146 if line.startswith('+'):
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147 state = 'plus'
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148 else:
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149 read.seq += line
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150 elif state == 'plus' or state == 'quality':
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151 state = 'quality'
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152 togo = len(read.seq) - len(read.qual)
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153 read.qual += line[:togo]
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154 # The end of the quality lines is when we have a quality string as long as the sequence.
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155 if len(read.qual) >= len(read.seq):
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156 state = 'header'