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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 logging
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5 import gzip
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6 import string
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7 import os
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8 import tarfile
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9
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10 from io import BytesIO
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11 from collections import defaultdict
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12
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13 try:
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14 from Bio.SeqRecord import SeqRecord
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15 from Bio import SeqIO
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16 except ImportError:
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17 message = 'This script requires the BioPython python package\n'
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18 sys.stderr.write(message)
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19 sys.exit(1)
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20
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21 try:
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22 from plumbum import cli
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23 except ImportError:
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24 message = 'This script requires the plumbum python package\n'
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25 sys.stderr.write(message)
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26 sys.exit(1)
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27
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28 try:
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29 import ftputil
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30 except ImportError:
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31 message = 'This script requires the ftputil python package\n'
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32 sys.stderr.write(message)
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33 sys.exit(1)
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34
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35
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36 NON_ID = ''.join(c for c in map(chr, range(256)) if not c.isalnum())
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37 NON_ID = NON_ID.replace('_', '').replace('-', '')
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38 NUC_TRANS = string.maketrans('uryswkmbdhvURYSWKMBDHV', 'tnnnnnnnnnnTNNNNNNNNNN')
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39
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40 logging.basicConfig(level=logging.INFO, format='%(message)s')
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41
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42
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43 class DataDownloader(object):
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44 """ Generic class for downloading fasta records via FTP. """
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45
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46 def __init__(self, host_name, base_path, user='anonymous', password='anonymous'):
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47
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48 self.group = 'NoGroup'
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49 self.host_name = host_name
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50 self.base_path = base_path
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51
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52 self.host = ftputil.FTPHost(host_name, user, password)
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53 self.host.chdir(base_path)
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54
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55 @classmethod
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56 def _get_fasta_record(self, record, group, family, organism, identifier, sub_identifier=None, description=''):
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57
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58 record.seq._data = record.seq._data.translate(NUC_TRANS)
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59
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60 group = group.translate(None, NON_ID)
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61 family = family.translate(None, NON_ID)
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62 organism = organism.translate(None, NON_ID)
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63 identifier = identifier.translate(None, NON_ID)
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64
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65 if sub_identifier:
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66 sub_identifier = sub_identifier.translate(None, NON_ID)
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67 record.id = ';'.join([group, family, organism, identifier, sub_identifier])
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68 else:
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69 record.id = ';'.join([group, family, organism, identifier])
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70
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71 record.description = description
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72 record.name = ''
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73
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74 return record
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75
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76 def get_fasta_records(self):
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77
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78 raise NotImplementedError
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79
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80 class SilvaDownlaoder(DataDownloader):
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81 """ Downlaods rRNA transcripts from the Silva database. """
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82
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83 def __init__(self, silva_release='111'):
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84
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85 self.silva_release = silva_release
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86 self.silva_host_name = 'ftp.arb-silva.de'
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87 self.base_path = '/release_%s/Exports/' % self.silva_release
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88
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89 super(SilvaDownlaoder, self).__init__(self.silva_host_name, self.base_path)
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90
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91 self.group = 'rRNA'
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92
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93 def get_fasta_records(self):
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94
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95 remote_path = self.base_path + 'SSURef_%s_NR_tax_silva_trunc.fasta.tgz' % self.silva_release
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96 if self.host.path.isfile(remote_path):
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97
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98 with self.host.file(remote_path, 'rb') as remote_handle:
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99 remote_content = BytesIO(remote_handle.read())
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100
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101 with tarfile.open(fileobj=remote_content) as tar:
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102
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103 for subentry in tar.getnames():
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104 if subentry.endswith('.fasta'):
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105 logging.debug('Processing rRNA file %s' % subentry)
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106 subhandle = tar.extractfile(subentry)
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107
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108 for record in SeqIO.parse(subhandle, "fasta"):
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109 identifier = record.id.split('.')[0]
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110 description = '_'.join(record.description.split(' ')[1:])
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111 taxonomy = description.split(';')
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112 organism = taxonomy[-1]
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113 family = 'Unassigned'
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114
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115 for level in taxonomy:
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116 if level.endswith('eae'):
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117 family = level
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118 break
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119
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120 yield self._get_fasta_record(record, self.group, family, organism, identifier)
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121
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122 class HumanTranscriptDownloader(DataDownloader):
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123 """ Downloads human transcripts fasta records that contain the locations
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124 of their exons on the human genome within their description line.
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125 """
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126
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127 def __init__(self):
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128
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129 self.ensemble_host_name = 'ftp.ensembl.org'
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130 self.gtf_path = '/pub/current_gtf/homo_sapiens'
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131 self.cdna_path = '/pub/current_fasta/homo_sapiens/cdna'
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132 self.ncrna_path = '/pub/current_fasta/homo_sapiens/ncrna'
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133
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134 super(HumanTranscriptDownloader, self).__init__(self.ensemble_host_name, self.gtf_path)
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135
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136 self.chromosomes = set()
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137 self.genes = defaultdict(set)
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138 self.regions = defaultdict(set)
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139 self.group = 'Homo_sapiens_cDNA'
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140
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141 def _cache_annotations(self):
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142 """ Obtains gtf annotations for human transcripts from ensemble and
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143 caches them in memory.
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144 """
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145
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146 self.host.chdir(self.gtf_path)
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147
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148 entries = self.host.listdir(self.host.curdir)
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149
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150 for entry in entries:
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151
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152 if self.host.path.isfile(entry):
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153 if entry.startswith('Homo_sapiens.') and entry.endswith('.gtf.gz'):
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154 logging.debug('Processing cDNA annotations %s' % entry)
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155
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156 with self.host.file(self.gtf_path + '/' + entry, 'rb') as zipped_handle:
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157 remote_content = BytesIO(zipped_handle.read())
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158
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159 with gzip.GzipFile(fileobj=remote_content) as gzipfile:
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160 for i, gtf_line in enumerate(gzipfile):
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161 if i % 100000 == 0:
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162 logging.debug('Cached %i human transcript annotations' % i)
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163
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164 self._add_annotation(gtf_line)
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165
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166 def _get_raw_transcripts(self):
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167 """ Obtains coding and noncoding human transcripts from ensemble and
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168 yields them as fasta records if they have exons that have a known location
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169 on the human genome. Fasta records contain the exon locations in their header
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170 lines.
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171 """
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172
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173 for subpath in [self.cdna_path, self.ncrna_path]:
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174
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175 self.host.chdir(subpath)
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176
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177 entries = self.host.listdir(self.host.curdir)
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178
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179 for entry in entries:
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180 if self.host.path.isfile(entry):
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181 if entry.endswith('cdna.all.fa.gz') or entry.endswith('ncrna.fa.gz'):
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182
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183 logging.debug('Processing human transcript file %s' % entry)
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184
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185 with self.host.file(subpath + '/' + entry, 'rb') as zipped_handle:
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186 remote_content = BytesIO(zipped_handle.read())
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187
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188 with gzip.GzipFile(fileobj=remote_content) as gzipfile:
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189 for i, record in enumerate(SeqIO.parse(gzipfile, "fasta")):
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190
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191 if record.id.startswith('ENST'):
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192
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193 if i % 100000 == 0:
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194 logging.debug('Retrieved %i human transcripts' % i)
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195
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196 record.description = ''
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197
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198 yield record
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199
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200 def _add_annotation(self, gtf_line):
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201 """ Parses gtf annotations and stores them in memory. """
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202
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203 if gtf_line[0] == '#':
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204 return
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205
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206 fields = gtf_line.strip().split('\t')
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207 chromosome, source, feature, start, end, score, strands, frame, attributes\
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208 = fields
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209
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210 start, end = sorted([int(start), int(end)])
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211
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212 if feature != 'exon':
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213 return
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214
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215 attributes = attributes.replace(' ', '').split(';')
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216 transcript_ids = [identifier.split('"')[1] for identifier in attributes\
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217 if identifier.startswith('transcript_id')]
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218
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219 gene_names = [identifier.split('"')[1] for identifier in attributes\
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220 if identifier.startswith('gene_name')]
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221
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222 for transcript_id in transcript_ids:
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223 self.genes[transcript_id] = self.genes[transcript_id].union(gene_names)
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224 self.regions[transcript_id].add((chromosome, start, end))
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225
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226 def get_fasta_records(self):
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227 """ Yields annotated fasta records of human transcripts. """
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228
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229 logging.debug('Caching annotations')
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230 self._cache_annotations()
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231
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232 logging.debug('Downloading and annotating transcripts')
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233 for record in self._get_raw_transcripts():
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234 transcript_id = record.id
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235
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236 if transcript_id in self.regions:
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237
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238 mapping_locations = self.regions[transcript_id]
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239
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240 description = '|'.join([';'.join(map(str, location))\
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241 for location in mapping_locations])
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242
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243 # Obtain gene name for transcript
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244 gene_names = self.genes[transcript_id]
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245 if gene_names:
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246 gene_name = list(gene_names)[0]
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247 else:
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248 gene_name = transcript_id
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249
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250 yield self._get_fasta_record(record, self.group , 'Hominidae', 'Homo_sapiens', gene_name, sub_identifier=transcript_id, description=description)
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251
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252 class RefSeqDownloader(DataDownloader):
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253 """ Generic downloader that known how to interpret and parse genbank records """
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254
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255 def __init__(self, group):
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256
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257 self.refseq_host_name = 'ftp.ncbi.nih.gov'
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258 self.base_path = '/genomes/' + group
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259
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260 super(RefSeqDownloader, self).__init__(self.refseq_host_name, self.base_path)
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261
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262 self.group = group
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263
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264
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265 @classmethod
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266 def _get_project_from_genbank(self, gb_record):
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267 """ Parses genbank project identifier from genbank record. """
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268
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269 project = ''
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270 for dbxref in gb_record.dbxrefs:
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271 for entry in dbxref.split(' '):
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272 if entry.startswith('BioProject'):
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273 project = entry.split(':')[1]
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274 return project
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275
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276 if not project:
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277 for dbxref in gb_record.dbxrefs:
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278 for entry in dbxref.split(' '):
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279 if entry.startswith('Project'):
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280 project = entry.split(':')[1]
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281 return project
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282
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283 return project
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284
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285 @classmethod
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286 def _get_annotations_from_genbank(self, gb_record):
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287 """ Parses taxonomic annotation from genbank record. """
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288
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289 accession = gb_record.annotations['accessions'][0]
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290 organism = gb_record.annotations['organism'].replace(' ', '_')
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291 organism = '_'.join(organism.split('_')[:2])
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292 taxonomy = ("; ").join(gb_record.annotations['taxonomy'])
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293 gi = gb_record.annotations['gi']
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294
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295 family = 'Unassigned'
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296 if len(gb_record.annotations['taxonomy']) > 0:
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297 for level in gb_record.annotations['taxonomy']:
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298 if level.endswith('dae') or level.endswith('aceae'):
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299 family = level
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300 break
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301
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302 if family == 'Unassigned':
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303 logging.debug('Unassigned family found based on %s' % taxonomy)
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304
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305 return organism, accession, gi, taxonomy, family
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306
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307 @classmethod
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308 def _get_record_from_genbank(self, gb_record):
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309 """ Parses sequence from genbank record. """
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310
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311 return SeqRecord(gb_record.seq)
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312
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313 @classmethod
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314 def _parse_genbank_records(self, file_handle):
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315
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316 for gb_record in SeqIO.parse(file_handle, 'genbank'):
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317
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318 project = self._get_project_from_genbank(gb_record)
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319 organism, accession, gi, taxonomy, family =\
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320 self._get_annotations_from_genbank(gb_record)
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321 record = self._get_record_from_genbank(gb_record)
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322
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323 if len(record) > 0:
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324 yield record, project, taxonomy, family, organism, gi
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325
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326 def _get_nc(self, entry_path):
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327
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328 if self.host.path.isfile(entry_path):
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329 logging.debug('Processing refseq entry %s' % entry_path)
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330 with self.host.file(entry_path) as remote_handle:
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331
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332
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333 for record, project, taxonomy, family, organism, gi\
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334 in self._parse_genbank_records(remote_handle):
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335
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336 cleaned = self._get_fasta_record(record, self.group , family, organism, gi)
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337
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338 yield cleaned
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339
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340 def _get_nz(self, entry_path):
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341
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342 scaffold_path = entry_path.replace('.gbk', '.scaffold.gbk.tgz')
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343 if self.host.path.isfile(scaffold_path):
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344 logging.debug('Processing refseq entry %s' % scaffold_path)
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345 with self.host.file(scaffold_path, 'rb') as remote_handle:
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346 remote_content = BytesIO(remote_handle.read())
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347 with tarfile.open(fileobj=remote_content) as tar:
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348 for subentry in tar.getnames():
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349 if subentry.endswith('.gbk'):
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350 logging.debug('Processing subaccession %s' % subentry)
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351 subhandle = tar.extractfile(subentry)
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352 for record, project, taxonomy, family, organism, gi in self._parse_genbank_records(subhandle):
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353 yield self._get_fasta_record(record, self.group , family, organism, gi)
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354
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355
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356 def get_fasta_records(self):
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357
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358 species_dirs = self.host.listdir(self.host.curdir)
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359
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360 for species_dir in species_dirs:
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361
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362 species_path = self.base_path + '/' + species_dir
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363
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364 if self.host.path.isdir(species_path):
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365
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366 self.host.chdir(species_path)
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367
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368 logging.debug('Processing species directory %s' % species_path)
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369
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370 if self.host.path.isdir(species_path):
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371
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372 self.host.chdir(species_path)
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373
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374 entries = self.host.listdir(self.host.curdir)
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375
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376 for entry in entries:
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377
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378 if self.host.path.isfile(self.host.curdir + '/' + entry):
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379
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380 if entry.endswith('.gbk') or entry.endswith('.gbk.gz'):
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381
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382 logging.debug('Processing entry %s' % entry)
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383
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384 entry_path = species_path + '/' + entry
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385
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386 if entry.startswith('NC_'):
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387 for record in self._get_nc(entry_path):
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388 yield record
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389
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390 elif entry.startswith('NZ_'):
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391 for record in self._get_nz(entry_path):
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392 yield record
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393
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394 class HumanGenomeDownloader(DataDownloader):
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395
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396 def __init__(self):
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397
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398 self.ensemble_host_name = 'ftp.ensembl.org'
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399 self.base_path = '/pub/current_fasta/homo_sapiens/dna'
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400
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401 super(HumanGenomeDownloader, self).__init__(self.ensemble_host_name, self.base_path)
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402
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403 self.group = 'Homo_sapiens'
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404
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405 def get_fasta_records(self):
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406
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407 entries = self.host.listdir(self.host.curdir)
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408 for entry in entries:
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409
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410 if self.host.path.isfile(entry):
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411
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412 # You may want to change your filtering criteria here if you would like to include patches and haplotypes
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413 if entry.endswith('fa.gz') and 'dna_sm.primary_assembly' in entry:
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414
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415 logging.debug('Processing human entry %s' % entry)
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416
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417 with self.host.file(self.host.getcwd() + '/' + entry, 'rb') as zipped_handle:
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418 remote_content = BytesIO(zipped_handle.read())
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419
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420 with gzip.GzipFile(fileobj=remote_content) as gzipfile:
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421
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422 for record in SeqIO.parse(gzipfile, "fasta"):
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423
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424 identifier = record.id
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425 organism = 'Homo_sapiens'
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426 family = 'Hominidae'
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427
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428 yield self._get_fasta_record(record, self.group, family, organism, identifier)
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429
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430 class UniVecDownloader(DataDownloader):
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431
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432 def __init__(self):
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433
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434 self.univec_host_name = 'ftp.ncbi.nih.gov'
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435 self.base_path = '/pub/UniVec'
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436
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437 super(UniVecDownloader, self).__init__(self.univec_host_name, self.base_path)
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438
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439 self.group = 'UniVec'
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440
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441 def get_fasta_records(self):
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442
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443 logging.debug('Processing Univec entries')
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444
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445 with self.host.file(self.host.getcwd() + '/' + 'UniVec') as remote_handle:
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446 for record in SeqIO.parse(remote_handle, "fasta"):
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447 organism = '_'.join(record.description.split(' ')[1:])
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448 family = 'Unassigned'
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449 identifier = '000000000'
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450
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451 yield self._get_fasta_record(record, self.group, family, organism, identifier)
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452
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453 class CLI(cli.Application):
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454 """"""
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455 PROGNAME = "metamap"
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456 VERSION = "1.0.0"
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457 DESCRIPTION = """"""
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458
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459 def main(self, *args):
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460
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461 if args:
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462 print("Unknown command %r" % (args[0]))
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463 print self.USAGE
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464 return 1
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465
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466 if not self.nested_command:
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467 print("No command given")
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468 print self.USAGE
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469 return 1
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470
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471 @CLI.subcommand("fasta")
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472 class References(cli.Application):
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473 """ Obtains NCBI RefSeq and Ensembl reference genomes and transcripts"""
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474
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475 valid_references = ['Fungi', 'Fungi_DRAFT', 'Bacteria',
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476 'Bacteria_DRAFT', 'Homo_sapiens',
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477 'Viruses', 'UniVec', 'Plasmids',
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478 'Protozoa', 'rRNA', 'Homo_sapiens_cDNA']
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479
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480 references = cli.SwitchAttr(['-r', '--reference'],
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481 cli.Set(*valid_references, case_sensitive=True),
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482 list=True, default=valid_references,
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483 mandatory=False,
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484 help="Sets the kind of references to obtain")
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485
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486 fasta_path = cli.SwitchAttr(['-o', '--output_file'], str, mandatory=True,
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487 help="Sets the fasta output file")
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488
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489 zipped = cli.Flag(["-z", "--zipped"], help="Write gzipped output")
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490 debug = cli.Flag(["-d", "--debug"], help="Enable debug messages")
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491
|
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492
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493 def main(self):
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494 """ Downloads genome fasta files from reference databases"""
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495
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496 if self.debug:
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497 logging.getLogger().setLevel(logging.DEBUG)
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498
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499 if os.path.dirname(self.fasta_path) and not os.path.exists(os.path.dirname(self.fasta_path)):
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500 logging.debug('Making directories for output file %s' % self.fasta_path)
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|
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501 os.makedirs(os.path.dirname(self.fasta_path))
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502
|
|
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503 if self.zipped:
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504 logging.debug('Making zipped output file %s' % self.fasta_path)
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|
|
505 output_file = gzip.open(self.fasta_path, 'wb')
|
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506
|
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507 else:
|
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|
508 logging.debug('Making regular output file %s' % self.fasta_path)
|
|
|
509 output_file = open(self.fasta_path, 'w', buffering=100 * 1024 * 1024)
|
|
|
510
|
|
|
511
|
|
|
512 for reference in self.references:
|
|
|
513
|
|
|
514 if reference == 'UniVec':
|
|
|
515 downloader = UniVecDownloader()
|
|
|
516 elif reference == 'Homo_sapiens':
|
|
|
517 downloader = HumanGenomeDownloader()
|
|
|
518 elif reference == 'rRNA':
|
|
|
519 downloader = SilvaDownlaoder()
|
|
|
520 elif reference == 'Homo_sapiens_cDNA':
|
|
|
521 downloader = HumanTranscriptDownloader()
|
|
|
522 else:
|
|
|
523 downloader = RefSeqDownloader(group=reference)
|
|
|
524
|
|
|
525 for record in downloader.get_fasta_records():
|
|
|
526 SeqIO.write([record], output_file, "fasta")
|
|
|
527
|
|
|
528 output_file.close()
|
|
|
529
|
|
|
530 @CLI.subcommand("blast")
|
|
|
531 class Blast(cli.Application):
|
|
|
532 """ Obtains blast databases """
|
|
|
533
|
|
|
534 valid_references = ['nt', 'nr']
|
|
|
535
|
|
|
536 references = cli.SwitchAttr(['-r', '--reference_database'],
|
|
|
537 cli.Set(*valid_references, case_sensitive=True),
|
|
|
538 list=True, default=valid_references,
|
|
|
539 mandatory=False,
|
|
|
540 help="Sets the kind of database to obtain")
|
|
|
541
|
|
|
542 database_path = cli.SwitchAttr(['-o', '--output_path'], str, mandatory=True,
|
|
|
543 help="Sets the fasta output file")
|
|
|
544
|
|
|
545 debug = cli.Flag(["-d", "--debug"], help="Enable debug messages")
|
|
|
546
|
|
|
547 def main(self):
|
|
|
548 """ Downloads blast database files """
|
|
|
549
|
|
|
550 if self.debug:
|
|
|
551 logging.getLogger().setLevel(logging.DEBUG)
|
|
|
552
|
|
|
553 if not os.path.exists(self.database_path):
|
|
|
554 logging.debug('Making output directory %s' % self.database_path)
|
|
|
555 os.makedirs(self.database_path)
|
|
|
556
|
|
|
557 host_name = 'ftp.ncbi.nih.gov'
|
|
|
558 host = ftputil.FTPHost(host_name, 'anonymous', 'anonymous')
|
|
|
559
|
|
|
560 for reference in self.references:
|
|
|
561
|
|
|
562 path = '/blast/db'
|
|
|
563 host.chdir(path)
|
|
|
564
|
|
|
565 entries = host.listdir(host.curdir)
|
|
|
566
|
|
|
567 for entry in entries:
|
|
|
568
|
|
|
569 if host.path.isfile(entry):
|
|
|
570
|
|
|
571 if entry.startswith(reference) and entry.endswith('.tar.gz'):
|
|
|
572 logging.debug('Downloading %s' % entry)
|
|
|
573 local_path = os.path.join(self.database_path, entry)
|
|
|
574 host.download(entry, local_path, 'b')
|
|
|
575 logging.debug('Unpacking %s' % entry)
|
|
|
576 tfile = tarfile.open(local_path, 'r:gz')
|
|
|
577 tfile.extractall(self.database_path)
|
|
|
578 os.remove(local_path)
|
|
|
579
|
|
|
580 if __name__ == "__main__":
|
|
|
581 CLI.run()
|
|
|
582
|
