Mercurial > repos > iuc > extract_genomic_dna
comparison extract_genomic_dna_utils.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 |
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| 1:9af3f57e50b9 | 2:702970e4a134 |
|---|---|
| 290 return seq_path | 290 return seq_path |
| 291 except Exception, e: | 291 except Exception, e: |
| 292 stop_err('Error running faToTwoBit. ' + str(e)) | 292 stop_err('Error running faToTwoBit. ' + str(e)) |
| 293 | 293 |
| 294 | 294 |
| 295 def get_bedtools_getfasta_default_header(chrom, start, end, strand, includes_strand_col): | |
| 296 """ | |
| 297 Return a fasta header that is the default produced by the bedtools | |
| 298 getfasta tool, assuming "force strandedness". This will produce a | |
| 299 header with this format: <chrom>:<start>-<end>(strand). If the input | |
| 300 data includes a strand column and the strand is '+' or '-', then use it. | |
| 301 If the input data includes a strand column and the value of strand is | |
| 302 anything but '+' or '-', set strand to '.' in the header. If the input | |
| 303 data does not include a strand column, set strand to '.' in the header. | |
| 304 """ | |
| 305 if includes_strand_col and strand in ['+', '-']: | |
| 306 strand_val = strand | |
| 307 else: | |
| 308 strand_val = '.' | |
| 309 return '%s:%s-%s(%s)' % (chrom, start, end, strand_val) | |
| 310 | |
| 311 | |
| 312 def get_fasta_header_delimiter(delimiter): | |
| 313 # Return a specified fasta header delimiter. | |
| 314 if delimiter == 'underscore': | |
| 315 return '_' | |
| 316 if delimiter == 'semicolon': | |
| 317 return ';' | |
| 318 if delimiter == 'comma': | |
| 319 return ',' | |
| 320 if delimiter == 'tilde': | |
| 321 return '~' | |
| 322 if delimiter == 'vertical_bar': | |
| 323 return '|' | |
| 324 # Set the default to underscore. | |
| 325 return '_' | |
| 326 | |
| 327 | |
| 295 def get_lines(feature): | 328 def get_lines(feature): |
| 296 # Get feature's line(s). | 329 # Get feature's line(s). |
| 297 if isinstance(feature, GFFFeature): | 330 if isinstance(feature, GFFFeature): |
| 298 return feature.lines() | 331 return feature.lines() |
| 299 else: | 332 else: |