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0
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1 #!/usr/bin/env python
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2 import argparse
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3 import os
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4
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9
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5 import extract_genomic_dna_utils as egdu
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0
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6 import bx.seq.nib
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7 import bx.seq.twobit
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8 from bx.intervals.io import Header, Comment
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9
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10
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11 parser = argparse.ArgumentParser()
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3
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12 parser.add_argument('--input_format', dest='input_format', help="Input dataset format")
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13 parser.add_argument('--input', dest='input', help="Input dataset")
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14 parser.add_argument('--genome', dest='genome', help="Input dataset genome build")
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15 parser.add_argument('--interpret_features', dest='interpret_features', default=None, help="Interpret features if input format is gff")
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16 parser.add_argument('--columns', dest='columns', help="Columns to use in input file")
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17 parser.add_argument('--reference_genome_source', dest='reference_genome_source', help="Source of reference genome file")
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18 parser.add_argument('--reference_genome', dest='reference_genome', help="Reference genome file")
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19 parser.add_argument('--output_format', dest='output_format', help="Output format")
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17
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20 parser.add_argument('--fasta_header_type', dest='fasta_header_type', default=None, help="Fasta header format")
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21 parser.add_argument('--fasta_header_delimiter', dest='fasta_header_delimiter', default=None, help="Fasta header field delimiter")
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3
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22 parser.add_argument('--output', dest='output', help="Output dataset")
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0
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23 args = parser.parse_args()
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24
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25 input_is_gff = args.input_format == 'gff'
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1
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26 interpret_features = input_is_gff and args.interpret_features == "yes"
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4
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27 if len(args.columns.split(',')) == 5:
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0
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28 # Bed file.
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9
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29 chrom_col, start_col, end_col, strand_col, name_col = egdu.parse_cols_arg(args.columns)
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30 else:
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31 # Gff file.
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9
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32 chrom_col, start_col, end_col, strand_col = egdu.parse_cols_arg(args.columns)
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33 name_col = False
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34
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35 if args.reference_genome_source == "history":
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9
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36 seq_path = egdu.convert_to_twobit(args.reference_genome)
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0
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37 else:
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38 seq_path = args.reference_genome
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39 seq_dir = os.path.split(seq_path)[0]
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40
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41 includes_strand_col = strand_col >= 0
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42 strand = None
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43 nibs = {}
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44 skipped_lines = 0
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45 first_invalid_line = 0
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46 invalid_lines = []
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47 warnings = []
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48 warning = ''
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49 twobitfile = None
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50 line_count = 1
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51 file_iterator = open(args.input)
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52 if interpret_features:
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9
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53 file_iterator = egdu.GFFReaderWrapper(file_iterator, fix_strand=False)
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54 out = open(args.output, 'wt')
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55
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56 for feature in file_iterator:
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57 # Ignore comments, headers.
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58 if isinstance(feature, (Header, Comment)):
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59 line_count += 1
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60 continue
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61 name = ""
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62 if interpret_features:
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63 # Processing features.
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9
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64 egdu.convert_gff_coords_to_bed(feature)
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65 chrom = feature.chrom
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66 start = feature.start
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67 end = feature.end
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68 strand = feature.strand
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69 else:
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70 # Processing lines, either interval or GFF format.
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71 line = feature.rstrip('\r\n')
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72 if line and not line.startswith("#"):
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73 fields = line.split('\t')
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74 try:
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75 chrom = fields[chrom_col]
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76 start = int(fields[start_col])
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77 end = int(fields[end_col])
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78 if name_col:
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79 name = fields[name_col]
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80 if input_is_gff:
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81 start, end = egdu.convert_gff_coords_to_bed([start, end])
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82 if includes_strand_col:
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83 strand = fields[strand_col]
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84 except:
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85 warning = "Invalid chrom, start or end column values. "
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86 warnings.append(warning)
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87 if not invalid_lines:
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88 invalid_lines = egdu.get_lines(feature)
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89 first_invalid_line = line_count
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90 skipped_lines += len(invalid_lines)
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91 continue
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92 if start > end:
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93 warning = "Invalid interval, start '%d' > end '%d'. " % (start, end)
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94 warnings.append(warning)
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95 if not invalid_lines:
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9
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96 invalid_lines = egdu.get_lines(feature)
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97 first_invalid_line = line_count
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98 skipped_lines += len(invalid_lines)
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99 continue
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100 if strand not in ['+', '-']:
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101 strand = '+'
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102 sequence = ''
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103 else:
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104 continue
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105 # Open sequence file and get sequence for feature/interval.
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106 if os.path.exists("%s/%s.nib" % (seq_dir, chrom)):
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107 if chrom in nibs:
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108 nib = nibs[chrom]
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109 else:
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110 nibs[chrom] = nib = bx.seq.nib.NibFile(open("%s/%s.nib" % (seq_path, chrom)))
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111 try:
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112 sequence = nib.get(start, end - start)
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113 except Exception, e:
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114 warning = "Unable to fetch the sequence from '%d' to '%d' for build '%s'. " % (start, end - start, args.genome)
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115 warnings.append(warning)
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116 if not invalid_lines:
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117 invalid_lines = egdu.get_lines(feature)
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118 first_invalid_line = line_count
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119 skipped_lines += len(invalid_lines)
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120 continue
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5
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121 elif os.path.isfile(seq_path):
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122 if not(twobitfile):
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123 twobitfile = bx.seq.twobit.TwoBitFile(open(seq_path))
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124 try:
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125 if interpret_features:
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126 # Create sequence from intervals within a feature.
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127 sequence = ''
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128 for interval in feature.intervals:
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129 sequence += twobitfile[interval.chrom][interval.start:interval.end]
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130 else:
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131 sequence = twobitfile[chrom][start:end]
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132 except:
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133 warning = "Unable to fetch the sequence from '%d' to '%d' for chrom '%s'. " % (start, end - start, chrom)
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134 warnings.append(warning)
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135 if not invalid_lines:
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136 invalid_lines = egdu.get_lines(feature)
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137 first_invalid_line = line_count
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138 skipped_lines += len(invalid_lines)
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139 continue
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140 else:
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141 warning = "Chromosome by name '%s' was not found for build '%s'. " % (chrom, args.genome)
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142 warnings.append(warning)
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143 if not invalid_lines:
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144 invalid_lines = egdu.get_lines(feature)
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145 first_invalid_line = line_count
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146 skipped_lines += len(invalid_lines)
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147 continue
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148 if sequence == '':
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149 warning = "Chrom: '%s', start: '%d', end: '%d' is either invalid or not present in build '%s'. " % (chrom, start, end, args.genome)
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150 warnings.append(warning)
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151 if not invalid_lines:
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152 invalid_lines = egdu.get_lines(feature)
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153 first_invalid_line = line_count
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154 skipped_lines += len(invalid_lines)
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155 continue
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156 if includes_strand_col and strand == "-":
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157 sequence = egdu.reverse_complement(sequence)
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158 if args.output_format == "fasta":
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159 l = len(sequence)
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160 c = 0
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161 if input_is_gff:
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162 start, end = egdu.convert_bed_coords_to_gff([start, end])
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17
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163 if args.fasta_header_type == "bedtools_getfasta_default":
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164 out.write(">%s\n" % egdu.get_bedtools_getfasta_default_header(str(chrom),
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165 str(start),
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166 str(end),
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167 strand,
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168 includes_strand_col))
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169 else:
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17
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170 # args.fasta_header_type == "char_delimited":
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171 fields = [args.genome, str(chrom), str(start), str(end), strand]
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172 field_delimiter = egdu.get_fasta_header_delimiter(args.fasta_header_delimiter)
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173 meta_data = field_delimiter.join(fields)
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174 if name.strip():
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175 out.write(">%s %s\n" % (meta_data, name))
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176 else:
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177 out.write(">%s\n" % meta_data)
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178 while c < l:
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179 b = min(c + 50, l)
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180 out.write("%s\n" % str(sequence[c:b]))
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181 c = b
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182 else:
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183 # output_format == "interval".
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184 if interpret_features:
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185 meta_data = "\t".join([feature.chrom,
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186 "galaxy_extract_genomic_dna",
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187 "interval",
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188 str(feature.start),
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189 str(feature.end),
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190 feature.score,
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191 feature.strand,
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192 ".",
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193 egdu.gff_attributes_to_str(feature.attributes, "GTF")])
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194 else:
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17
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195 # Here fields was set up around line 73.
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196 meta_data = "\t".join(fields)
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197 if input_is_gff:
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198 format_str = "%s seq \"%s\";\n"
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199 else:
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200 format_str = "%s\t%s\n"
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201 out.write(format_str % (meta_data, str(sequence)))
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202 # Update line count.
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203 if isinstance(feature, egdu.GFFFeature):
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204 line_count += len(feature.intervals)
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205 else:
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206 line_count += 1
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207 out.close()
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208
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209 if warnings:
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210 warn_msg = "%d warnings, 1st is: " % len(warnings)
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211 warn_msg += warnings[0]
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212 print warn_msg
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213 if skipped_lines:
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214 # Error message includes up to the first 10 skipped lines.
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215 print 'Skipped %d invalid lines, 1st is #%d, "%s"' % (skipped_lines, first_invalid_line, '\n'.join(invalid_lines[:10]))
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216
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217 if args.reference_genome_source == "history":
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218 os.remove(seq_path)
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