STAT115, 2014 BETA, Galaxy, Cistrome Python regular expression
STAT115, 2014 BETA, Galaxy, Cistrome Python regular expression. Lin Liu Yang Li. Integrative Analysis. Differential gene expression Transcription factor binding sites What’s next? One option is “target analysis”: trying to sort out which genes are regulated by a certain protein. BETA.
STAT115, 2014 BETA, Galaxy, Cistrome Python regular expression
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STAT115, 2014 BETA, Galaxy, Cistrome Python regular expression Lin Liu Yang Li
Integrative Analysis Differential gene expression Transcription factor binding sites What’s next? One option is “target analysis”: trying to sort out which genes are regulated by a certain protein
BETA Three main functions: Predicting TF functions: active or repressive Predicting the target gene of a TF Searching for motif around targeted genes, and predicting potential cooperative factors
BETA $ module load centos6/BETA_1.0.5 $ BETA basic –p 3656_peaks.bed –e AR_diff_expr.xls–k LIM –g hg19 --da 500 –n basic
Python: Regular expression import re sequence = ‘AGGCTAGGTCGAT’ re.findall(‘A.G’, sequence) line = "Cats are smarter than dogs" matchObj = re.match( r'(.*) are (.*?) .*', line, re.M|re.I) if matchObj: print "matchObj.group() : ", matchObj.group() print "matchObj.group(1) : ", matchObj.group(1) print "matchObj.group(2) : ", matchObj.group(2) else: print "No match!!"
