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1 #!/usr/bin/env python
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2 #Dan Blankenberg
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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 tempfile
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7 import shutil
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8 import optparse
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9 from ftplib import FTP
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10 import tarfile
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11 import zipfile
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12 import gzip
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13 import bz2
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14 try:
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15 # For Python 3.0 and later
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16 from urllib.request import urlopen
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17 from io import BytesIO as StringIO
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18 from io import UnsupportedOperation
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19 except ImportError:
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20 # Fall back to Python 2's urllib2
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21 from urllib2 import urlopen
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22 from StringIO import StringIO
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23 UnsupportedOperation = AttributeError
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24 from json import loads, dumps
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25
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26
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27 CHUNK_SIZE = 2**20 # 1mb
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28
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29 DATA_TABLE_NAME = 'all_gff'
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30
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31 def cleanup_before_exit( tmp_dir ):
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32 if tmp_dir and os.path.exists( tmp_dir ):
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33 shutil.rmtree( tmp_dir )
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34
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35
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36 def stop_err(msg):
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37 sys.stderr.write(msg)
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38 sys.exit(1)
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39
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40
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41 def get_dbkey_dbname_id_name( params, dbkey_description=None ):
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42 # dbkey = params['param_dict']['dbkey_source']['dbkey']
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43 #TODO: ensure sequence_id is unique and does not already appear in location file
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44 sequence_id = params['param_dict']['sequence_id']
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45 if not sequence_id:
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46 sequence_id = dbkey #uuid.uuid4() generate and use an uuid instead?
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47
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2
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48 # if params['param_dict']['dbkey_source']['dbkey_source_selector'] == 'new':
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49 # dbkey_name = params['param_dict']['dbkey_source']['dbkey_name']
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50 # if not dbkey_name:
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51 # dbkey_name = dbkey
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52 # else:
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53 # dbkey_name = None
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54 dbkey = params['param_dict']['dbkey']
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55 dbkey_name = dbkey_description
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56 sequence_name = params['param_dict']['sequence_name']
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57 if not sequence_name:
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58 sequence_name = dbkey_description
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59 if not sequence_name:
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60 sequence_name = dbkey
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61 return dbkey, dbkey_name, sequence_id, sequence_name
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62
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63
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64 def _get_files_in_ftp_path( ftp, path ):
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65 path_contents = []
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66 ftp.retrlines( 'MLSD %s' % ( path ), path_contents.append )
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67 return [ line.split( ';' )[ -1 ].lstrip() for line in path_contents ]
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68
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69
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70 def _get_stream_readers_for_tar( fh, tmp_dir ):
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71 fasta_tar = tarfile.open( fileobj=fh, mode='r:*' )
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72 return [x for x in [fasta_tar.extractfile(member) for member in fasta_tar.getmembers()] if x]
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73
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74
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75 def _get_stream_readers_for_zip( fh, tmp_dir ):
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76 """
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77 Unpacks all archived files in a zip file.
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78 Individual files will be concatenated (in _stream_fasta_to_file)
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79 """
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80 fasta_zip = zipfile.ZipFile( fh, 'r' )
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81 rval = []
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82 for member in fasta_zip.namelist():
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83 fasta_zip.extract( member, tmp_dir )
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84 rval.append( open( os.path.join( tmp_dir, member ), 'rb' ) )
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85 return rval
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86
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87
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88 def _get_stream_readers_for_gzip( fh, tmp_dir ):
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89 return [ gzip.GzipFile( fileobj=fh, mode='rb') ]
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90
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91
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92 def _get_stream_readers_for_bz2( fh, tmp_dir ):
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93 return [ bz2.BZ2File( fh.name, 'rb') ]
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94
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95
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96 def sort_fasta( fasta_filename, sort_method, params ):
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97 if sort_method is None:
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98 return
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99 assert sort_method in SORTING_METHODS, ValueError( "%s is not a valid sorting option." % sort_method )
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100 return SORTING_METHODS[ sort_method ]( fasta_filename, params )
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101
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102
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103 def _move_and_index_fasta_for_sorting( fasta_filename ):
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104 unsorted_filename = tempfile.NamedTemporaryFile().name
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105 shutil.move( fasta_filename, unsorted_filename )
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106 fasta_offsets = {}
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107 unsorted_fh = open( unsorted_filename )
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108 while True:
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109 offset = unsorted_fh.tell()
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110 line = unsorted_fh.readline()
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111 if not line:
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112 break
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113 if line.startswith( ">" ):
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114 line = line.split( None, 1 )[0][1:]
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115 fasta_offsets[ line ] = offset
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116 unsorted_fh.close()
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117 current_order = map( lambda x: x[1], sorted( map( lambda x: ( x[1], x[0] ), fasta_offsets.items() ) ) )
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118 return ( unsorted_filename, fasta_offsets, current_order )
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119
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120
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121 def _write_sorted_fasta( sorted_names, fasta_offsets, sorted_fasta_filename, unsorted_fasta_filename ):
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122 unsorted_fh = open( unsorted_fasta_filename )
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123 sorted_fh = open( sorted_fasta_filename, 'wb+' )
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124
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125 for name in sorted_names:
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126 offset = fasta_offsets[ name ]
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127 unsorted_fh.seek( offset )
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128 sorted_fh.write( unsorted_fh.readline() )
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129 while True:
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130 line = unsorted_fh.readline()
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131 if not line or line.startswith( ">" ):
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132 break
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133 sorted_fh.write( line )
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134 unsorted_fh.close()
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135 sorted_fh.close()
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136
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137
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138 def _sort_fasta_as_is( fasta_filename, params ):
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139 return
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140
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141 def _sort_fasta_lexicographical( fasta_filename, params ):
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142 ( unsorted_filename, fasta_offsets, current_order ) = _move_and_index_fasta_for_sorting( fasta_filename )
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143 sorted_names = sorted( fasta_offsets.keys() )
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144 if sorted_names == current_order:
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145 shutil.move( unsorted_filename, fasta_filename )
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146 else:
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147 _write_sorted_fasta( sorted_names, fasta_offsets, fasta_filename, unsorted_filename )
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148
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149
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150 def _sort_fasta_gatk( fasta_filename, params ):
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151 #This method was added by reviewer request.
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152 ( unsorted_filename, fasta_offsets, current_order ) = _move_and_index_fasta_for_sorting( fasta_filename )
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153 sorted_names = map( str, range( 1, 23 ) ) + [ 'X', 'Y' ]
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154 #detect if we have chrN, or just N
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155 has_chr = False
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156 for chrom in sorted_names:
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157 if "chr%s" % chrom in current_order:
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158 has_chr = True
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159 break
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160
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161 if has_chr:
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162 sorted_names = map( lambda x: "chr%s" % x, sorted_names)
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163 sorted_names.insert( 0, "chrM" )
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164 else:
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165 sorted_names.insert( 0, "MT" )
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166 sorted_names.extend( map( lambda x: "%s_random" % x, sorted_names ) )
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167
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168 existing_sorted_names = []
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169 for name in sorted_names:
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170 if name in current_order:
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171 existing_sorted_names.append( name )
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172 for name in current_order:
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173 #TODO: confirm that non-canonical names do not need to be sorted specially
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174 if name not in existing_sorted_names:
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175 existing_sorted_names.append( name )
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176
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177 if existing_sorted_names == current_order:
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178 shutil.move( unsorted_filename, fasta_filename )
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179 else:
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180 _write_sorted_fasta( existing_sorted_names, fasta_offsets, fasta_filename, unsorted_filename )
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181
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182
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183 def _sort_fasta_custom( fasta_filename, params ):
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184 ( unsorted_filename, fasta_offsets, current_order ) = _move_and_index_fasta_for_sorting( fasta_filename )
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185 sorted_names = []
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186 for id_repeat in params['param_dict']['sorting']['sequence_identifiers']:
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187 sorted_names.append( id_repeat[ 'identifier' ] )
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188 handle_not_listed = params['param_dict']['sorting']['handle_not_listed_selector']
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189 if handle_not_listed.startswith( 'keep' ):
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190 add_list = []
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191 for name in current_order:
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192 if name not in sorted_names:
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193 add_list.append( name )
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194 if add_list:
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195 if handle_not_listed == 'keep_append':
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196 sorted_names.extend( add_list )
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197 else:
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198 add_list.extend( sorted_names )
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199 sorted_names = add_list
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200 if sorted_names == current_order:
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201 shutil.move( unsorted_filename, fasta_filename )
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202 else:
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203 _write_sorted_fasta( sorted_names, fasta_offsets, fasta_filename, unsorted_filename )
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204
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205
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206 def _download_file(start, fh):
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207 tmp = tempfile.NamedTemporaryFile()
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208 tmp.write(start)
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209 tmp.write(fh.read())
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210 tmp.flush()
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211 tmp.seek(0)
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212 return tmp
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213
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214
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215 def get_stream_reader(fh, tmp_dir):
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216 """
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217 Check if file is compressed and return correct stream reader.
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218 If file has to be downloaded, do it now.
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219 """
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220 magic_dict = {
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221 b"\x1f\x8b\x08": _get_stream_readers_for_gzip,
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222 b"\x42\x5a\x68": _get_stream_readers_for_bz2,
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223 b"\x50\x4b\x03\x04": _get_stream_readers_for_zip,
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224 }
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225 start_of_file = fh.read(CHUNK_SIZE)
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226 try:
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227 fh.seek(0)
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228 except UnsupportedOperation: # This is if fh has been created by urlopen
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229 fh = _download_file(start_of_file, fh)
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230 for k,v in magic_dict.items():
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231 if start_of_file.startswith(k):
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232 return v(fh, tmp_dir)
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233 try: # Check if file is tar file
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234 if tarfile.open(fileobj=StringIO(start_of_file)):
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235 return _get_stream_readers_for_tar(fh, tmp_dir)
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236 except tarfile.ReadError:
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237 pass
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238 return fh
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239
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240
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241 def _get_ucsc_download_address(params, dbkey):
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242 """
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243 Check if we can find the correct file for the supplied dbkey on UCSC's FTP server
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244 """
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245 UCSC_FTP_SERVER = 'hgdownload.cse.ucsc.edu'
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246 UCSC_DOWNLOAD_PATH = '/goldenPath/%s/bigZips/'
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247 COMPRESSED_EXTENSIONS = ['.tar.gz', '.tgz', '.tar.bz2', '.zip', '.fa.gz', '.fa.bz2']
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248
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249 email = params['param_dict']['__user_email__']
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250 if not email:
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251 email = 'anonymous@example.com'
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252
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253 ucsc_dbkey = params['param_dict']['reference_source']['requested_dbkey'] or dbkey
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254 UCSC_CHROM_FA_FILENAMES = ['%s.chromFa' % ucsc_dbkey, 'chromFa', ucsc_dbkey]
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255
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256 ftp = FTP(UCSC_FTP_SERVER)
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257 ftp.login('anonymous', email)
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258
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259 ucsc_path = UCSC_DOWNLOAD_PATH % ucsc_dbkey
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260 path_contents = _get_files_in_ftp_path(ftp, ucsc_path)
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261 ftp.quit()
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262
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263 for ucsc_chrom_fa_filename in UCSC_CHROM_FA_FILENAMES:
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264 for ext in COMPRESSED_EXTENSIONS:
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265 if "%s%s" % (ucsc_chrom_fa_filename, ext) in path_contents:
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266 ucsc_file_name = "%s%s%s" % (ucsc_path, ucsc_chrom_fa_filename, ext)
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267 return "ftp://%s%s" % (UCSC_FTP_SERVER, ucsc_file_name)
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268
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269 raise Exception('Unable to determine filename for UCSC Genome for %s: %s' % (ucsc_dbkey, path_contents))
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270
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271 def add_fasta_to_table(data_manager_dict, fasta_readers, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, params):
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272 for data_table_name, data_table_entry in _stream_fasta_to_file( fasta_readers, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, params ):
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273 if data_table_entry:
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274 _add_data_table_entry( data_manager_dict, data_table_entry, data_table_name )
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275
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276
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277 def download_from_ucsc( data_manager_dict, params, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, tmp_dir ):
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278 url = _get_ucsc_download_address(params, dbkey)
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279 fasta_readers = get_stream_reader(urlopen(url), tmp_dir)
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280 add_fasta_to_table(data_manager_dict, fasta_readers, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, params)
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281
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282
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283 def download_from_ncbi( data_manager_dict, params, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, tmp_dir ):
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284 NCBI_DOWNLOAD_URL = 'http://togows.dbcls.jp/entry/ncbi-nucleotide/%s.fasta' #FIXME: taken from dave's genome manager...why some japan site?
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285 requested_identifier = params['param_dict']['reference_source']['requested_identifier']
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286 url = NCBI_DOWNLOAD_URL % requested_identifier
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287 fasta_readers = get_stream_reader(urlopen(url), tmp_dir)
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288 add_fasta_to_table(data_manager_dict, fasta_readers, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, params)
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289
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290
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291 def download_from_url( data_manager_dict, params, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, tmp_dir ):
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292 urls = filter( bool, map( lambda x: x.strip(), params['param_dict']['reference_source']['user_url'].split( '\n' ) ) )
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293 fasta_readers = [ get_stream_reader(urlopen( url ), tmp_dir) for url in urls ]
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294 add_fasta_to_table(data_manager_dict, fasta_readers, target_directory, dbkey, dbkey_name, sequence_id,sequence_name, params)
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295
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296
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297 def download_from_history( data_manager_dict, params, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, tmp_dir ):
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298 #TODO: allow multiple FASTA input files
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299 input_filename = params['param_dict']['reference_source']['input_fasta']
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300 if isinstance( input_filename, list ):
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301 fasta_readers = [ get_stream_reader(open(filename, 'rb'), tmp_dir) for filename in input_filename ]
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302 else:
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303 fasta_readers = get_stream_reader(open(input_filename), tmp_dir)
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304 add_fasta_to_table(data_manager_dict, fasta_readers, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, params)
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305
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306
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307 def copy_from_directory( data_manager_dict, params, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, tmp_dir ):
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308 input_filename = params['param_dict']['reference_source']['fasta_filename']
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309 create_symlink = params['param_dict']['reference_source']['create_symlink'] == 'create_symlink'
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310 if create_symlink:
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311 data_table_entries = _create_symlink( input_filename, target_directory, dbkey, dbkey_name, sequence_id, sequence_name )
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312 else:
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313 if isinstance( input_filename, list ):
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314 fasta_readers = [ get_stream_reader(open(filename, 'rb'), tmp_dir) for filename in input_filename ]
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315 else:
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316 fasta_readers = get_stream_reader(open(input_filename), tmp_dir)
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317 data_table_entries = _stream_fasta_to_file( fasta_readers, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, params )
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318 for data_table_name, data_table_entry in data_table_entries:
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319 if data_table_entry:
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320 _add_data_table_entry( data_manager_dict, data_table_entry, data_table_name )
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321
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322
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323 def _add_data_table_entry( data_manager_dict, data_table_entry, data_table_name ):
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324 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
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325 data_manager_dict['data_tables'][data_table_name] = data_manager_dict['data_tables'].get( DATA_TABLE_NAME, [] )
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326 data_manager_dict['data_tables'][data_table_name].append( data_table_entry )
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327 return data_manager_dict
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328
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329
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330 def _stream_fasta_to_file( fasta_stream, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, params, close_stream=True ):
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331 fasta_base_filename = "%s.gff" % sequence_id
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332 fasta_filename = os.path.join( target_directory, fasta_base_filename )
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333 with open( fasta_filename, 'wb+' ) as fasta_writer:
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334
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335 if isinstance( fasta_stream, list ) and len( fasta_stream ) == 1:
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336 fasta_stream = fasta_stream[0]
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337
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338 if isinstance( fasta_stream, list ):
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339 last_char = None
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340 for fh in fasta_stream:
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341 if last_char not in [ None, '\n', '\r', b'\n', b'\r' ]:
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342 fasta_writer.write( b'\n' )
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343 while True:
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344 data = fh.read( CHUNK_SIZE )
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345 if data:
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346 fasta_writer.write( data )
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347 last_char = data[-1]
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348 else:
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349 break
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350 if close_stream:
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351 fh.close()
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352 else:
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353 while True:
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354 data = fasta_stream.read( CHUNK_SIZE )
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355 if data:
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356 fasta_writer.write( data )
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357 else:
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358 break
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359 if close_stream:
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360 fasta_stream.close()
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361
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362 #sort_fasta( fasta_filename, params['param_dict']['sorting']['sort_selector'], params )
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363
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364
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2
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365 return [ ( DATA_TABLE_NAME, dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_filename ) ) ]
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0
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366
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367
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368 def compute_fasta_length( fasta_file, out_file, keep_first_word=False ):
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369
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370 infile = fasta_file
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371 out = open( out_file, 'w')
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372
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373 fasta_title = ''
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374 seq_len = 0
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375
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376 first_entry = True
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377
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378 for line in open( infile ):
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379 line = line.strip()
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380 if not line or line.startswith( '#' ):
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381 continue
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382 if line[0] == '>':
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383 if first_entry == False:
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384 if keep_first_word:
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385 fasta_title = fasta_title.split()[0]
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386 out.write( "%s\t%d\n" % ( fasta_title[ 1: ], seq_len ) )
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387 else:
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388 first_entry = False
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389 fasta_title = line
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390 seq_len = 0
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391 else:
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392 seq_len += len(line)
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393
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394 # last fasta-entry
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395 if keep_first_word:
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396 fasta_title = fasta_title.split()[0]
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397 out.write( "%s\t%d\n" % ( fasta_title[ 1: ], seq_len ) )
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398 out.close()
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399
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400
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401 def _create_symlink( input_filename, target_directory, dbkey, dbkey_name, sequence_id, sequence_name ):
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402 fasta_base_filename = "%s.fa" % sequence_id
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403 fasta_filename = os.path.join( target_directory, fasta_base_filename )
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404 os.symlink( input_filename, fasta_filename )
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2
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405 return [ ( DATA_TABLE_NAME, dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_filename ) ) ]
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0
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406
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407
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408 REFERENCE_SOURCE_TO_DOWNLOAD = dict( ucsc=download_from_ucsc, ncbi=download_from_ncbi, url=download_from_url, history=download_from_history, directory=copy_from_directory )
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409
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410 SORTING_METHODS = dict( as_is=_sort_fasta_as_is, lexicographical=_sort_fasta_lexicographical, gatk=_sort_fasta_gatk, custom=_sort_fasta_custom )
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411
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412
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413 def main():
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414 #Parse Command Line
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415 parser = optparse.OptionParser()
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416 parser.add_option( '-d', '--dbkey_description', dest='dbkey_description', action='store', type="string", default=None, help='dbkey_description' )
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417 parser.add_option( '-t', '--type', dest='file_type', action='store', type='string', default=None, help='file_type')
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418 (options, args) = parser.parse_args()
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419
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420 filename = args[0]
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421 global DATA_TABLE_NAME
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422 if options.file_type == 'representative':
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|
423 DATA_TABLE_NAME= 'representative_gff'
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|
424 params = loads( open( filename ).read() )
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425 target_directory = params[ 'output_data' ][0]['extra_files_path']
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|
426 os.mkdir( target_directory )
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|
427 data_manager_dict = {}
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428
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429 dbkey, dbkey_name, sequence_id, sequence_name = get_dbkey_dbname_id_name( params, dbkey_description=options.dbkey_description )
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430
|
|
431 if dbkey in [ None, '', '?' ]:
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432 raise Exception( '"%s" is not a valid dbkey. You must specify a valid dbkey.' % ( dbkey ) )
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|
433
|
|
434 # Create a tmp_dir, in case a zip file needs to be uncompressed
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|
435 tmp_dir = tempfile.mkdtemp()
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|
436 #Fetch the FASTA
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|
437 try:
|
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438 REFERENCE_SOURCE_TO_DOWNLOAD[ params['param_dict']['reference_source']['reference_source_selector'] ]( data_manager_dict, params, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, tmp_dir )
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439 finally:
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440 cleanup_before_exit(tmp_dir)
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441 #save info to json file
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|
442 open( filename, 'wb' ).write( dumps( data_manager_dict ).encode() )
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443
|
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444 if __name__ == "__main__":
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|
445 main()
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