Mercurial > repos > davidvanzessen > mutation_analysis
changeset 5:71a12810eff3 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Tue, 23 Sep 2014 07:50:35 -0400 |
| parents | 069419cccba4 |
| children | 3c2230868300 |
| files | gene_identification.py |
| diffstat | 1 files changed, 13 insertions(+), 1 deletions(-) [+] |
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--- a/gene_identification.py Mon Sep 22 10:19:36 2014 -0400 +++ b/gene_identification.py Tue Sep 23 07:50:35 2014 -0400 @@ -112,11 +112,23 @@ lastindex = 0 start = [0] * len(seq) for i, regexp in enumerate(regularexpressions): #for every regular expression + relativeStartLocation = lastindex - (chunklength / 2) * i + if relativeStartLocation < 0 or relativeStartLocation >= len(seq): + break regex, hasVar = regexp matches = regex.finditer(seq[lastindex:]) for match in matches: #for every match with the current regex, only uses the first hit lastindex += match.start() - start[lastindex - chunklength / 2 * i] += 1 + print ID + print lastindex + print chunklength + print i + print seq[lastindex:] + print start + print len(seq) + print relativeStartLocation + print "-------------------" + start[relativeStartLocation] += 1 if hasVar: #if the regex has a variable nt in it chunkstart = chunklength / 2 * i #where in the reference does this chunk start chunkend = chunklength / 2 * i + chunklength #where in the reference does this chunk end