from gusPyCode.gClasses.gSeqClasses import DNAseq
from Bio.Seq import Seq
q = Seq('kjhas')
d = DNAseq('''atgatgaagatcacgatcgccgccctcgctctgctggccgtcgccgttgctgcatacgaa
catgaggactatcattcgcatcccagctacaagttcgagtatggagtaaaggatcctcac
accggagaccacaagagccagtgggaacatcgggacggagatgtcgtcaagggagcatat
acccttcacgaggctgacggaactgagcgagtagttgagtactcgtccgacaagcacaac
ggcttccaggctcacgtcaagcgagtgggtcatgctcaccacccggaagtgtatggacac
catgaggctggacactcgtacggccatggacacggtcatggtcatggcagcagctacgcc
aacggcaacctgtaccagcaccatcactaa
''','testSeq1')
print 'repr:\n%s' % (d)
print 'str(d):\n%s' % (str(d))
print 'len(d):\n%s' % (len(d))
print 'toString:\n%s' % (d.toString())
print 'toFasta:\n%s' % (d.toFasta())
# ResFreqs and stuff
print 'Freq of "A":\n%s' % (d.getResFreq('A'))
print 'FreqTable:\n'
frqTab = d.getResFreqTable()
for res in frqTab:
print res
#slice
sd = d.slice(3,9)
print 'slice:\n%s' % (sd.toString())
outFile = '/Users/biggus/Documents/James/Data/AedesCorePromoterWork/output/TATA_Inr/Aa_Ensbl49_AaegL1.1.plus50minus100._TataInr_seqSlices_.locations.txt'
motif2 = motility.IUPAC('RGWYV')
winTo2ndMotif = (23,27) # <---- This is based from END of first motif!!!
seqList = zipped = zip(seqFile[:-1:2], seqFile[1::2])
seqDict = {}
print 'populating seqDict...'
for item in seqList:
name = item[0].replace('|Inr(..DPE)','').replace('>','')
header = item[0]
seq = item[1]
coverage = item[0].split('|')[-1].split('-')
coverage = (int(coverage[0]),int(coverage[1]))
motif1Loc = coverage[0]-6
seqDict[name] = DNAseq(seq,name,header)
seqDict[name].coverage = coverage
seqDict[name].motif1Loc = motif1Loc
def checkSlice(seqObj, motif2, winTo2ndMotif):
motif2Loc = None
mHits = motif2.find(seqObj.toString())
for each in mHits:
if each[2] == -1:
continue
elif each[0] >= winTo2ndMotif[0] and each[0]<= winTo2ndMotif[1]:
motif2Loc = each[0]
if motif2Loc:
return '%s\t%s\t%s\t%s\n' % (seqObj.name,seqObj.motif1Loc,motif2Loc+seqObj.coverage[0],motif2Loc)
