Mercurial > repos > iuc > extract_genomic_dna
comparison extract_genomic_dna.py @ 2:702970e4a134 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
| author | iuc |
|---|---|
| date | Wed, 09 Mar 2016 05:07:21 -0500 |
| parents | 8dd8e89c0603 |
| children | b71579ad576c |
comparison
equal
deleted
inserted
replaced
| 1:9af3f57e50b9 | 2:702970e4a134 |
|---|---|
| 15 parser.add_argument('--interpret_features', dest='interpret_features', default=None, help="Interpret features if input format is gff") | 15 parser.add_argument('--interpret_features', dest='interpret_features', default=None, help="Interpret features if input format is gff") |
| 16 parser.add_argument('--columns', dest='columns', help="Columns to use in input file") | 16 parser.add_argument('--columns', dest='columns', help="Columns to use in input file") |
| 17 parser.add_argument('--reference_genome_source', dest='reference_genome_source', help="Source of reference genome file") | 17 parser.add_argument('--reference_genome_source', dest='reference_genome_source', help="Source of reference genome file") |
| 18 parser.add_argument('--reference_genome', dest='reference_genome', help="Reference genome file") | 18 parser.add_argument('--reference_genome', dest='reference_genome', help="Reference genome file") |
| 19 parser.add_argument('--output_format', dest='output_format', help="Output format") | 19 parser.add_argument('--output_format', dest='output_format', help="Output format") |
| 20 parser.add_argument('--fasta_header_type', dest='fasta_header_type', default=None, help="Fasta header format") | |
| 21 parser.add_argument('--fasta_header_delimiter', dest='fasta_header_delimiter', default=None, help="Fasta header field delimiter") | |
| 20 parser.add_argument('--output', dest='output', help="Output dataset") | 22 parser.add_argument('--output', dest='output', help="Output dataset") |
| 21 args = parser.parse_args() | 23 args = parser.parse_args() |
| 22 | 24 |
| 23 input_is_gff = args.input_format == 'gff' | 25 input_is_gff = args.input_format == 'gff' |
| 24 interpret_features = input_is_gff and args.interpret_features == "yes" | 26 interpret_features = input_is_gff and args.interpret_features == "yes" |
| 156 if args.output_format == "fasta": | 158 if args.output_format == "fasta": |
| 157 l = len(sequence) | 159 l = len(sequence) |
| 158 c = 0 | 160 c = 0 |
| 159 if input_is_gff: | 161 if input_is_gff: |
| 160 start, end = egdu.convert_bed_coords_to_gff([start, end]) | 162 start, end = egdu.convert_bed_coords_to_gff([start, end]) |
| 161 fields = [args.genome, str(chrom), str(start), str(end), strand] | 163 if args.fasta_header_type == "bedtools_getfasta_default": |
| 162 meta_data = "_".join(fields) | 164 out.write(">%s\n" % egdu.get_bedtools_getfasta_default_header(str(chrom), |
| 163 if name.strip(): | 165 str(start), |
| 164 out.write(">%s %s\n" % (meta_data, name)) | 166 str(end), |
| 165 else: | 167 strand, |
| 166 out.write(">%s\n" % meta_data) | 168 includes_strand_col)) |
| 169 else: | |
| 170 # args.fasta_header_type == "char_delimited": | |
| 171 fields = [args.genome, str(chrom), str(start), str(end), strand] | |
| 172 field_delimiter = egdu.get_fasta_header_delimiter(args.fasta_header_delimiter) | |
| 173 meta_data = field_delimiter.join(fields) | |
| 174 if name.strip(): | |
| 175 out.write(">%s %s\n" % (meta_data, name)) | |
| 176 else: | |
| 177 out.write(">%s\n" % meta_data) | |
| 167 while c < l: | 178 while c < l: |
| 168 b = min(c + 50, l) | 179 b = min(c + 50, l) |
| 169 out.write("%s\n" % str(sequence[c:b])) | 180 out.write("%s\n" % str(sequence[c:b])) |
| 170 c = b | 181 c = b |
| 171 else: | 182 else: |
| 179 feature.score, | 190 feature.score, |
| 180 feature.strand, | 191 feature.strand, |
| 181 ".", | 192 ".", |
| 182 egdu.gff_attributes_to_str(feature.attributes, "GTF")]) | 193 egdu.gff_attributes_to_str(feature.attributes, "GTF")]) |
| 183 else: | 194 else: |
| 184 # Where is fields being set here? | 195 # Here fields was set up around line 73. |
| 185 meta_data = "\t".join(fields) | 196 meta_data = "\t".join(fields) |
| 186 if input_is_gff: | 197 if input_is_gff: |
| 187 format_str = "%s seq \"%s\";\n" | 198 format_str = "%s seq \"%s\";\n" |
| 188 else: | 199 else: |
| 189 format_str = "%s\t%s\n" | 200 format_str = "%s\t%s\n" |