Mercurial > repos > bgruening > find_subsequences
comparison find_subsequences.py @ 7:99f356eeba15 draft
planemo upload commit 7ff6d582464c6b7183e1acd421272167f8a2433f
| author | bgruening |
|---|---|
| date | Tue, 05 Apr 2016 15:26:05 -0400 |
| parents | 53c20f28562e |
| children |
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| 6:53c20f28562e | 7:99f356eeba15 |
|---|---|
| 32 def simple_pattern_search(sequence, pattern, outfile, strand='+'): | 32 def simple_pattern_search(sequence, pattern, outfile, strand='+'): |
| 33 """ | 33 """ |
| 34 Simple regular expression search. This is way faster than the complex search. | 34 Simple regular expression search. This is way faster than the complex search. |
| 35 """ | 35 """ |
| 36 bed_template = '%s\t%s\t%s\t%s\t%s\t%s\n' | 36 bed_template = '%s\t%s\t%s\t%s\t%s\t%s\n' |
| 37 for match in re.finditer( str(pattern), str(sequence.seq) ): | 37 for match in re.finditer( str(pattern), str(sequence.seq), re.IGNORECASE ): |
| 38 outfile.write(bed_template % (sequence.id, match.start(), match.end(), sequence.description, '', strand)) | 38 outfile.write(bed_template % (sequence.id, match.start(), match.end(), sequence.description, '', strand)) |
| 39 | 39 |
| 40 | 40 |
| 41 def complex_pattern_search(sequence, pattern, outfile, strand='+'): | 41 def complex_pattern_search(sequence, pattern, outfile, strand='+'): |
| 42 """ | 42 """ |