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1 #!/usr/bin/env python
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2 """
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3 usage: %prog $input $out_file1
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4 -1, --cols=N,N,N,N: Columns for start, end, strand in input file
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5 -d, --dbkey=N: Genome build of input file
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6 -o, --output_format=N: the data type of the output file
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7 -g, --GALAXY_DATA_INDEX_DIR=N: the directory containing alignseq.loc
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8 -I, --interpret_features: if true, complete features are interpreted when input is GFF
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9 -F, --fasta=<genomic_sequences>: genomic sequences to use for extraction
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10 -G, --gff: input and output file, when it is interval, coordinates are treated as GFF format (1-based, half-open) rather than 'traditional' 0-based, closed format.
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11 """
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12 from galaxy import eggs
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13 import pkg_resources
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14 pkg_resources.require( "bx-python" )
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15 import sys, string, os, re, tempfile, subprocess
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16 from bx.cookbook import doc_optparse
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17 from bx.intervals.io import Header, Comment
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18 import bx.seq.nib
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19 import bx.seq.twobit
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20 from galaxy.tools.util.galaxyops import *
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21 from galaxy.datatypes.util import gff_util
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22
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23 assert sys.version_info[:2] >= ( 2, 4 )
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24
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25 def stop_err( msg ):
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26 sys.stderr.write( msg )
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27 sys.exit()
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28
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29 def reverse_complement( s ):
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30 complement_dna = {"A":"T", "T":"A", "C":"G", "G":"C", "a":"t", "t":"a", "c":"g", "g":"c", "N":"N", "n":"n" }
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31 reversed_s = []
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32 for i in s:
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33 reversed_s.append( complement_dna[i] )
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34 reversed_s.reverse()
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35 return "".join( reversed_s )
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36
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37 def check_seq_file( dbkey, GALAXY_DATA_INDEX_DIR ):
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38 seq_file = "%s/alignseq.loc" % GALAXY_DATA_INDEX_DIR
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39 seq_path = ''
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40 for line in open( seq_file ):
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41 line = line.rstrip( '\r\n' )
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42 if line and not line.startswith( "#" ) and line.startswith( 'seq' ):
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43 fields = line.split( '\t' )
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44 if len( fields ) < 3:
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45 continue
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46 if fields[1] == dbkey:
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47 seq_path = fields[2].strip()
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48 break
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49 return seq_path
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50
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51 def __main__():
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52 #
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53 # Parse options, args.
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54 #
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55 options, args = doc_optparse.parse( __doc__ )
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56 try:
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57 chrom_col, start_col, end_col, strand_col = parse_cols_arg( options.cols )
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58 dbkey = options.dbkey
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59 output_format = options.output_format
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60 gff_format = options.gff
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61 interpret_features = options.interpret_features
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62 GALAXY_DATA_INDEX_DIR = options.GALAXY_DATA_INDEX_DIR
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63 fasta_file = options.fasta
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64 input_filename, output_filename = args
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65 except:
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66 doc_optparse.exception()
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67
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68 includes_strand_col = strand_col >= 0
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69 strand = None
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70 nibs = {}
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71 twobits = {}
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72
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73 #
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74 # Set path to sequence data.
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75 #
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76 if fasta_file:
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77 # Need to create 2bit file from fasta file.
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78 try:
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79 seq_path = tempfile.NamedTemporaryFile( dir="." ).name
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80 cmd = "faToTwoBit %s %s" % ( fasta_file, seq_path )
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81
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82 tmp_name = tempfile.NamedTemporaryFile( dir="." ).name
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83 tmp_stderr = open( tmp_name, 'wb' )
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84 proc = subprocess.Popen( args=cmd, shell=True, stderr=tmp_stderr.fileno() )
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85 returncode = proc.wait()
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86 tmp_stderr.close()
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87
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88 # Get stderr, allowing for case where it's very large.
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89 tmp_stderr = open( tmp_name, 'rb' )
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90 stderr = ''
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91 buffsize = 1048576
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92 try:
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93 while True:
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94 stderr += tmp_stderr.read( buffsize )
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95 if not stderr or len( stderr ) % buffsize != 0:
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96 break
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97 except OverflowError:
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98 pass
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99 tmp_stderr.close()
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100
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101 # Error checking.
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102 if returncode != 0:
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103 raise Exception, stderr
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104 except Exception, e:
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105 stop_err( 'Error running faToTwoBit. ' + str( e ) )
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106 else:
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107 seq_path = check_seq_file( dbkey, GALAXY_DATA_INDEX_DIR )
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108 if not os.path.exists( seq_path ):
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109 # If this occurs, we need to fix the metadata validator.
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110 stop_err( "No sequences are available for '%s', request them by reporting this error." % dbkey )
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111
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112 #
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113 # Fetch sequences.
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114 #
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115
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116 # Get feature's line(s).
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117 def get_lines( feature ):
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118 if isinstance( feature, gff_util.GFFFeature ):
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119 return feature.lines()
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120 else:
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121 return [ feature.rstrip( '\r\n' ) ]
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122
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123 skipped_lines = 0
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124 first_invalid_line = 0
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125 invalid_lines = []
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126 fout = open( output_filename, "w" )
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127 warnings = []
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128 warning = ''
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129 twobitfile = None
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130 file_iterator = open( input_filename )
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131 if gff_format and interpret_features:
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132 file_iterator = gff_util.GFFReaderWrapper( file_iterator, fix_strand=False )
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133 line_count = 1
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134 for feature in file_iterator:
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135 # Ignore comments, headers.
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136 if isinstance( feature, ( Header, Comment ) ):
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137 line_count += 1
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138 continue
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139
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140 if gff_format and interpret_features:
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141 # Processing features.
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142 gff_util.convert_gff_coords_to_bed( feature )
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143 chrom = feature.chrom
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144 start = feature.start
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145 end = feature.end
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146 strand = feature.strand
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147 else:
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148 # Processing lines, either interval or GFF format.
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149 line = feature.rstrip( '\r\n' )
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150 if line and not line.startswith( "#" ):
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151 fields = line.split( '\t' )
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152 try:
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153 chrom = fields[chrom_col]
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154 start = int( fields[start_col] )
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155 end = int( fields[end_col] )
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156 if gff_format:
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157 start, end = gff_util.convert_gff_coords_to_bed( [start, end] )
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158 if includes_strand_col:
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159 strand = fields[strand_col]
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160 except:
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161 warning = "Invalid chrom, start or end column values. "
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162 warnings.append( warning )
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163 if not invalid_lines:
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164 invalid_lines = get_lines( feature )
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165 first_invalid_line = line_count
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166 skipped_lines += len( invalid_lines )
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167 continue
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168 if start > end:
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169 warning = "Invalid interval, start '%d' > end '%d'. " % ( start, end )
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170 warnings.append( warning )
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171 if not invalid_lines:
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172 invalid_lines = get_lines( feature )
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173 first_invalid_line = line_count
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174 skipped_lines += len( invalid_lines )
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175 continue
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176
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177 if strand not in ['+', '-']:
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178 strand = '+'
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179 sequence = ''
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180 else:
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181 continue
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182
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183 # Open sequence file and get sequence for feature/interval.
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184 if seq_path and os.path.exists( "%s/%s.nib" % ( seq_path, chrom ) ):
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185 # TODO: improve support for GFF-nib interaction.
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186 if chrom in nibs:
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187 nib = nibs[chrom]
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188 else:
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189 nibs[chrom] = nib = bx.seq.nib.NibFile( file( "%s/%s.nib" % ( seq_path, chrom ) ) )
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190 try:
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191 sequence = nib.get( start, end-start )
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192 except Exception, e:
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193 warning = "Unable to fetch the sequence from '%d' to '%d' for build '%s'. " %( start, end-start, dbkey )
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194 warnings.append( warning )
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195 if not invalid_lines:
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196 invalid_lines = get_lines( feature )
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197 first_invalid_line = line_count
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198 skipped_lines += len( invalid_lines )
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199 continue
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200 elif seq_path and os.path.isfile( seq_path ):
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201 if not(twobitfile):
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202 twobitfile = bx.seq.twobit.TwoBitFile( file( seq_path ) )
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203 try:
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204 if options.gff and interpret_features:
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205 # Create sequence from intervals within a feature.
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206 sequence = ''
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207 for interval in feature.intervals:
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208 sequence += twobitfile[interval.chrom][interval.start:interval.end]
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209 else:
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210 sequence = twobitfile[chrom][start:end]
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211 except:
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212 warning = "Unable to fetch the sequence from '%d' to '%d' for chrom '%s'. " %( start, end-start, chrom )
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213 warnings.append( warning )
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214 if not invalid_lines:
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215 invalid_lines = get_lines( feature )
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216 first_invalid_line = line_count
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217 skipped_lines += len( invalid_lines )
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218 continue
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219 else:
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220 warning = "Chromosome by name '%s' was not found for build '%s'. " % ( chrom, dbkey )
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221 warnings.append( warning )
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222 if not invalid_lines:
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223 invalid_lines = get_lines( feature )
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224 first_invalid_line = line_count
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225 skipped_lines += len( invalid_lines )
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226 continue
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227 if sequence == '':
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228 warning = "Chrom: '%s', start: '%s', end: '%s' is either invalid or not present in build '%s'. " \
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229 % ( chrom, start, end, dbkey )
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230 warnings.append( warning )
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231 if not invalid_lines:
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232 invalid_lines = get_lines( feature )
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233 first_invalid_line = line_count
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234 skipped_lines += len( invalid_lines )
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235 continue
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236 if includes_strand_col and strand == "-":
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237 sequence = reverse_complement( sequence )
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238
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239 if output_format == "fasta" :
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240 l = len( sequence )
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241 c = 0
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242 if gff_format:
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243 start, end = gff_util.convert_bed_coords_to_gff( [ start, end ] )
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244 fields = [dbkey, str( chrom ), str( start ), str( end ), strand]
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245 meta_data = "_".join( fields )
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246 fout.write( ">%s\n" % meta_data )
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247 while c < l:
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248 b = min( c + 50, l )
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249 fout.write( "%s\n" % str( sequence[c:b] ) )
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250 c = b
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251 else: # output_format == "interval"
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252 if gff_format and interpret_features:
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253 # TODO: need better GFF Reader to capture all information needed
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254 # to produce this line.
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255 meta_data = "\t".join(
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256 [feature.chrom, "galaxy_extract_genomic_dna", "interval", \
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257 str( feature.start ), str( feature.end ), feature.score, feature.strand,
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258 ".", gff_util.gff_attributes_to_str( feature.attributes, "GTF" ) ] )
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259 else:
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260 meta_data = "\t".join( fields )
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261 if gff_format:
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262 format_str = "%s seq \"%s\";\n"
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263 else:
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264 format_str = "%s\t%s\n"
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265 fout.write( format_str % ( meta_data, str( sequence ) ) )
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266
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267 # Update line count.
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268 if isinstance( feature, gff_util.GFFFeature ):
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269 line_count += len( feature.intervals )
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270 else:
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271 line_count += 1
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272
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273 fout.close()
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274
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275 if warnings:
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276 warn_msg = "%d warnings, 1st is: " % len( warnings )
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277 warn_msg += warnings[0]
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278 print warn_msg
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279 if skipped_lines:
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280 # Error message includes up to the first 10 skipped lines.
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281 print 'Skipped %d invalid lines, 1st is #%d, "%s"' % ( skipped_lines, first_invalid_line, '\n'.join( invalid_lines[:10] ) )
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282
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283 if __name__ == "__main__": __main__()
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