annotate tools/mytools/seq2meme.py @ 0:9071e359b9a3

Uploaded

# -*- coding: iso-8859-1 -*-
import random,sys,math

#import pylab

def readMotifFile(filename):
 
    try:
        f=open(filename)
    except IOError:
        print "could not open",filename,"Are you sure this file exists?"
        sys.exit(1)
    
    seqs=[]
    maxL = 0
    for line in f:
        if '>' in line or 'N' in line:
            next
        else:
            seq = line.strip().upper()
            if maxL < len(seq):
                maxL = len(seq)
            seqs.append(seq)
    f.close()

    print len(seqs),'sequences loaded'
    print 'max seq length:',maxL
    for i in range(len(seqs)):
        if len(seqs[i]) < maxL:
            del seqs[i]
    print len(seqs),'sequences with length = ',maxL
    return seqs


def createWeightMatrix(seqs,psuedocont):

    motifWidth = len(seqs[0])
    weightMatrix = []
    for i in range(motifWidth):
        weightMatrix.append({'A':psuedocont,'C':psuedocont,'G':psuedocont,'T':psuedocont})

    #Use a for loop to iterate through all the sequences. For each sequence, begin at the start site in starts, and look at motifWidth bases. Count how many times each base appears in each position of the motif
    #YOUR CODE HERE
    for seq in seqs:
        for pos in range(motifWidth):
            weightMatrix[pos][seq[pos]] = weightMatrix[pos][seq[pos]] + 1.0
    
    #Normalize your weight matrix (so that it contains probabilities rather than counts)
    #Remember the added psuedocounts when you normalize!
    for pos in range(motifWidth):
        totalCount = sum(weightMatrix[pos].values())
        for letter in weightMatrix[pos].keys():
            weightMatrix[pos][letter] = weightMatrix[pos][letter]/totalCount
    
    #Return your weight matrix
    return weightMatrix

def printMemeFormat(weightMatrix,motifName,filename,nSite,background):
    f = open(filename,'w')
    f.write('MEME version 4.4\n\n')
    
    f.write('ALPHABET= ACGT\n\n')

    f.write('strands: + -\n\n')

    f.write('Background letter frequencies (from:\n')
    f.write(background+'\n\n')

    f.write('MOTIF '+motifName+'\n\n') 

    f.write('letter-probability matrix: alength= 4 '+'w= '+str(len(weightMatrix))+' nsites= '+str(nSite)+' E= 0\n')
    for position in range(len(weightMatrix)):
        probsThisPosition=weightMatrix[position]
        f.write('  '+"%.6f" %(probsThisPosition['A'])+'\t  '+"%.6f" %(probsThisPosition['C'])+'\t  '+"%.6f" %(probsThisPosition['G'])+'\t  '+"%.6f" %(probsThisPosition['T'])+'\t\n')
    f.write('\n\n')
    f.close()
    
#get a two decimal-place string representation of a float f
def twoDecimal(f):
    return "%.6f" %(f)

def run():

    #Get file name from command line
    if len(sys.argv) < 3:
        print "python seq2meme.py motif_fasta outputfile motifName psuedocont background"
        sys.exit(1)
    else:
        motifFile=sys.argv[1] #
        outFile=sys.argv[2]
        motifName=sys.argv[3]
        psuedocont = float(sys.argv[4])
        background=' '.join(sys.argv[5].strip().split(','))
                
    motifs=readMotifFile(motifFile)

    #Create weight matrix
    motifWeightMatrix=createWeightMatrix(motifs,psuedocont)
    printMemeFormat(motifWeightMatrix,motifName,outFile,len(motifs),background)
run()