Mercurial > repos > bebatut > convert_extract_sequence_file

annotate convert_extract_sequence_file.py @ 1:d7747e6f329f draft default tip

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planemo upload commit 0a1bbb0870f6b776175151d4bc818c5546731ca8-dirty
author bebatut
date Thu, 28 Apr 2016 08:34:50 -0400
parents b4cf778be846
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
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1 #!/usr/bin/python
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2 # -*- coding: utf-8 -*-
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3
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4 import sys
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5 import os
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6 import argparse
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7 import copy
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8 import operator
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9
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10 FASTA_FILE_LAST_POS = None
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11
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12 #################
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13 # Parse methods #
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14 #################
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15 def text_end_of_file(row):
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16 if row == '':
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17 return True
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18 else:
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19 return False
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20
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21 def get_new_line(input_file, generate_error = True):
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22 row = input_file.readline()
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23 if text_end_of_file(row):
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24 if generate_error :
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25 string = os.path.basename(__file__) + ': '
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26 string += ' unexpected end of file'
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27 raise ValueError(string)
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28 else :
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29 return None
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30 else:
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31 return row[:-1]
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32
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33 def next_fasta_record(input_file):
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34 global FASTA_FILE_LAST_POS
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35 if FASTA_FILE_LAST_POS != None:
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36 input_file.seek(FASTA_FILE_LAST_POS)
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37 else:
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38 FASTA_FILE_LAST_POS = input_file.tell()
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39
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40 id_line = get_new_line(input_file, generate_error = False)
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41 if id_line == None:
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42 return None
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43 split_line = id_line[1:].split(' ')
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44 seq_id = split_line[0]
1
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45 description = id_line[1:]
0
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46 new_line = get_new_line(input_file, generate_error = False)
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47 seq = ''
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48 while new_line != None:
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49 if new_line[0] != '>':
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50 seq += new_line
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51 FASTA_FILE_LAST_POS = input_file.tell()
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52 new_line = get_new_line(input_file, generate_error = False)
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53 else:
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54 new_line = None
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55 return SeqRecord(seq_id, seq, description)
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56
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57 def next_fastq_record(input_file):
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58 id_line = get_new_line(input_file, generate_error = False)
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59 if id_line == None:
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60 return None
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61 if id_line[0] != '@':
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62 string = os.path.basename(__file__) + ': '
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63 string += ' issue in fastq file'
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64 raise ValueError(string)
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65 split_line = id_line[1:].split(' ')
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66 seq_id = split_line[0]
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67 description = ' '.join(split_line[1:])
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68 seq = get_new_line(input_file)
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69 spacer = get_new_line(input_file)
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70 quals = get_new_line(input_file)
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71 return SeqRecord(seq_id, seq, description, quals)
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72
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73 def next_record(input_file, file_format):
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74 if file_format == 'fasta':
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75 return next_fasta_record(input_file)
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76 elif file_format == 'fastq':
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77 return next_fastq_record(input_file)
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78 else:
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79 string = os.path.basename(__file__) + ': '
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80 string += file_format + ' is not managed'
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81 raise ValueError(string)
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82
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83 def write_fasta_record(record, output_sequence_file):
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84 output_sequence_file.write('>' + record.get_id() + ' ' +
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85 record.get_description() + '\n')
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86 seq = record.get_sequence()
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87 split_seq = [seq[i:i+60] for i in xrange(0,len(seq),60)]
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88 for split in split_seq:
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89 output_sequence_file.write(split + '\n')
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90
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91 def format_qual_value(qual_score, sliding_value, authorized_range, qual_format):
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92 ascii_value = ord(qual_score)
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93 score = ascii_value-sliding_value
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94 if score < authorized_range[0] or score > authorized_range[1]:
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95 string = os.path.basename(__file__) + ': wrong score ('
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96 string += str(score) + ') with quality format ('
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97 string += qual_format
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98 raise ValueError(string)
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99 return score
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100
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101 def format_qual_string(qual_string, qual_format):
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102 if qual_format == 'sanger':
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103 return format_qual_value(qual_string, 33 ,[0,40], qual_format)
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104 elif qual_format == "solexa":
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105 return format_qual_value(qual_string, 64 ,[-5,40], qual_format)
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106 elif qual_format == "illumina_1_3":
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107 return format_qual_value(qual_string, 33 ,[0,40], qual_format)
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108 elif qual_format == "illumina_1_5":
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109 return format_qual_value(qual_string, 33 ,[3,40], qual_format)
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110 elif qual_format == "illumina_1_8":
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111 return format_qual_value(qual_string, 33 ,[0,41], qual_format)
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112 else:
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113 string = os.path.basename(__file__) + ': quality format ('
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114 string += qual_format + ') is not managed'
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115 raise ValueError(string)
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116
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117 def write_qual_record(record, output_qual_file, qual_format):
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118 output_qual_file.write('>' + record.get_id() + ' ' +
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119 record.get_description() + '\n')
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120 qual = record.get_quality()
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121 qual = [str(format_qual_string(qual_str,qual_format)) for qual_str in qual]
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122 split_seq = [qual[i:i+60] for i in xrange(0,len(qual),60)]
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123 for split in split_seq:
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124 output_qual_file.write(' '.join(split) + '\n')
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125
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126 def write_fastq_record(record, output_sequence_file):
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127 output_sequence_file.write('@' + record.get_id() + ' ' +
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128 record.get_description() + '\n')
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129 output_sequence_file.write(record.get_sequence() + '\n')
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130 output_sequence_file.write('+\n')
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131 output_sequence_file.write(record.get_quality() + '\n')
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132
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133 def write_information(record, output_file_formats, output_sequence_file,
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134 output_qual_file, qual_format):
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135 if "fasta" in output_file_formats:
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136 write_fasta_record(record, output_sequence_file)
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137 if "qual" in output_file_formats:
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138 write_qual_record(record, output_qual_file, qual_format)
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139 if "fastq" in output_file_formats:
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140 write_fastq_record(record, output_sequence_file)
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141
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142 def fast_test_element_in_list(element,list_to_test):
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143 to_continue = True
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144 i = 0
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145 while to_continue:
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146 if i == len(list_to_test) or list_to_test[i] >= element:
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147 to_continue = False
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148 else:
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149 i += 1
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150
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151 found = False
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152 if i < len(list_to_test):
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153 if list_to_test[i] == element:
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154 found = True
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155
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156 return found
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157
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158 #########################
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159 # Constraint definition #
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160 #########################
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161 constraints = {
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162 'equal': operator.eq,
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163 'different': operator.ne,
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164 'lower': operator.le,
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165 'strictly_lower': operator.lt,
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166 'greater': operator.ge,
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167 'strictly_greater': operator.gt,
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168 'in': operator.contains,
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169 'not_in': 'in'
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170 }
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171
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172 extractable_information = {
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173 'id': str,
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174 'length': int,
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175 'description': str
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176 }
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177
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178 ###########
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179 # Classes #
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180 ###########
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181 class SeqRecord:
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182
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183 def __init__(self, seq_id, sequence, description, quality = ""):
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184 self.id = seq_id
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185 self.sequence = sequence
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186 self.quality = quality
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187 self.description = description
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188 self.length = len(self.sequence)
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189
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190 # Getters
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191 def get_id(self):
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192 return self.id
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193
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194 def get_sequence(self):
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195 return self.sequence
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196
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197 def get_quality(self):
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198 return self.quality
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199
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200 def get_length(self):
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201 return self.length
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202
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203 def get_description(self):
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204 return self.description
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205
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206 def get(self, category):
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207 if category == 'id':
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208 return self.get_id()
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209 elif category == 'length':
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210 return self.get_length()
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211 elif category == 'description':
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212 return self.get_description()
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213 else:
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214 string = os.path.basename(__file__) + ': '
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215 string += category + ' can not be extracted from SeqRecord'
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216 raise ValueError(string)
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217
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218 # Other functions
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219 def extract_information(self,to_extract):
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220 extracted_info = []
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221 for info_to_extract in to_extract:
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222 extracted_info.append(self.get(info_to_extract))
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223 return extracted_info
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224
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225 def test_conservation(self, constraints):
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226 to_conserve = True
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227 for constrained_info in constraints:
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228 record_value = self.get(constrained_info)
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229 for constraint in constraints[constrained_info]:
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230 to_conserve &= constraint.test_constraint(record_value)
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231 return to_conserve
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232
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233 class Records:
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234
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235 def __init__(self, input_filepath, file_format, constraints):
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236 self.records = []
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237 self.conserved_records = []
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238 with open(input_filepath, 'r') as input_file:
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239 to_continue = True
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240 while to_continue:
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241 record = next_record(input_file, file_format)
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242 if record != None:
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243 self.records.append(record)
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244 to_conserve = record.test_conservation(constraints)
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245 if to_conserve:
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246 self.conserved_records.append(copy.copy(record))
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247 else:
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248 to_continue = False
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249
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250 # Getters
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251 def get_records(self):
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252 return copy.copy(self.records)
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253
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254 def get_record_nb(self):
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255 return len(self.records)
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256
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257 def get_conserved_records(self):
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258 return copy.copy(self.conserved_records)
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259
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260 def get_conserved_record_nb(self):
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261 return len(self.conserved_records)
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262
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263 # Other functions
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264 def save_conserved_records(self,args):
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265 if args.custom_extraction_type == 'True':
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266 to_extract = args.to_extract[1:-1].split(',')
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267 with open(args.output_information, 'w') as output_information_file:
1
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268 #output_information_file.write('\t'.join(to_extract) + '\n')
0
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269 for record in self.conserved_records:
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270 extracted_info = record.extract_information(to_extract)
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271 string_info = [str(info) for info in extracted_info]
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272 string = '\t'.join(string_info)
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273 output_information_file.write(string + '\n')
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274 else:
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275 qual_format = None
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276 if args.format == 'fasta':
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277 output_file_formats = ['fasta']
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278 elif args.format == 'fastq':
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279 if args.split == 'True':
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280 output_file_formats = ['fasta','qual']
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281 qual_format = args.quality_format
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282 else:
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283 output_file_formats = ['fastq']
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284
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285 with open(args.output_sequence,'w') as output_sequence_file:
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286 if "qual" in output_file_formats:
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287 output_qual_file = open(args.output_quality, 'w')
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288 else:
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289 output_qual_file = None
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290 for record in self.conserved_records:
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291 write_information(record, output_file_formats,
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292 output_sequence_file, output_qual_file, qual_format)
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293 if "qual" in output_file_formats:
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294 output_qual_file.close()
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295
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296 class Constraint:
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297
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298 def __init__(self, constraint_type, value, constrained_information):
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299 if not constraints.has_key(constraint_type):
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300 string = os.path.basename(__file__) + ': '
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301 string += constraint_type + ' is not a correct type of constraint'
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302 raise ValueError(string)
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303 self.raw_constraint_type = constraint_type
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304 self.type = constraints[constraint_type]
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305
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306 value_format = extractable_information[constrained_information]
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307 if self.raw_constraint_type in ['in', 'not_in']:
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308 self.values = []
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309 with open(value, 'r') as value_file:
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310 for row in value_file.readlines():
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311 value = row[:-1]
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312 self.values.append(value_format(value))
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313 else:
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314 self.values = [value_format(value)]
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315 self.values.sort()
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316
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317 def get_raw_constraint_type(self):
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318 return self.raw_constraint_type
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319
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320 def get_type(self):
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321 return self.type
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322
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323 def get_values(self):
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324 return self.values
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325
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326 def test_constraint(self, similarity_info_value):
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327 to_conserve = True
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328 if self.raw_constraint_type == 'in':
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329 to_conserve &= fast_test_element_in_list(similarity_info_value,
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330 self.values)
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331 elif self.raw_constraint_type == 'not_in':
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332 to_conserve &= (not fast_test_element_in_list(similarity_info_value,
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333 self.values))
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334 else:
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335 to_conserve &= self.type(similarity_info_value, self.values[0])
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336 return to_conserve
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337
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338 ################
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339 # Misc methods #
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340 ################
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341 def test_input_filepath(input_filepath, tool, file_format):
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342 if not os.path.exists(input_filepath):
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343 string = os.path.basename(__file__) + ': '
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344 string += input_filepath + ' does not exist'
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345 raise ValueError(string)
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346
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347 def format_constraints(constraints):
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348 formatted_constraints = {}
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349 if constraints != None:
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350 for constr in constraints:
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351 split_constraint = constr.split(': ')
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352 constrained_information = split_constraint[0]
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353 constraint = Constraint(split_constraint[1], split_constraint[2],
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354 constrained_information)
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355 formatted_constraints.setdefault(constrained_information,[]).append(
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356 constraint)
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357 return formatted_constraints
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358
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359 def convert_extract_sequence_file(args):
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360 input_filepath = args.input
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361 file_format = args.format
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362 constraints = args.constraint
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363 formatted_constraints = format_constraints(constraints)
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364
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365 records = Records(input_filepath, file_format, formatted_constraints)
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366 records.save_conserved_records(args)
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367
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368 report_filepath = args.report
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369 with open(report_filepath, 'w') as report_file:
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370
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371 report_file.write('Information to extract:\n')
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372 if args.custom_extraction_type == 'True':
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373 for info in args.to_extract[1:-1].split(','):
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374 report_file.write('\t' + info + '\n')
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375 else:
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376 report_file.write('\tsequences\n')
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377
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378 if constraints != None:
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379 report_file.write('Constraints on extraction:\n')
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380 for constrained_info in formatted_constraints:
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381 report_file.write('\tInfo to constraint: ' + constrained_info
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382 + '\n')
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383 for constraint in formatted_constraints[constrained_info]:
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384 report_file.write('\t\tType of constraint: ' +
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385 constraint.get_raw_constraint_type()
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386 + '\n')
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387 report_file.write('\t\tValues:\n')
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388 values = constraint.get_values()
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389 for value in values:
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390 report_file.write('\t\t\t' + str(value) + '\n')
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391 report_file.write('Number of similarity records: ' +
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392 str(records.get_record_nb()) + '\n')
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393 report_file.write('Number of extracted similarity records: ' +
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394 str(records.get_conserved_record_nb()) + '\n')
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395
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396 ########
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397 # Main #
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398 ########
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399 if __name__ == "__main__":
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400 parser = argparse.ArgumentParser()
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401 parser.add_argument('--input', required=True)
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402 parser.add_argument('--format', required=True)
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403 parser.add_argument('--custom_extraction_type', required=True)
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404 parser.add_argument('--to_extract')
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405 parser.add_argument('--output_information')
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406 parser.add_argument('--split')
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407 parser.add_argument('--quality_format')
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408 parser.add_argument('--output_sequence')
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409 parser.add_argument('--output_quality')
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410 parser.add_argument('--constraint', action='append')
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411 parser.add_argument('--report', required=True)
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412 args = parser.parse_args()
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413
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414 convert_extract_sequence_file(args)