generateFakePeptidesWithMotifs

#!/usr/bin/python
import sys
import random
import numpy as np
import csv


def amplifyMotif(numPeptides, motif):
    peptides = set()
    aminoAcids = ["G","A","P","V","L","I","M","F","Y","W","S","T","C","N","Q","K","H","R","D","E"]

    for index in range(numPeptides):
        peptide = ""
        for letter in motif:
            if letter == "-":
                randomNum = random.randint(0,19)
                peptide = peptide + aminoAcids[randomNum]
            else:
                peptide = (peptide + letter)
        peptides.add(peptide)
    return peptides


def getMotifs2(index1, index2):
    motifs = []

    motif1 = ["-","A","A","A","-","-","-","-"]
    motif2 = ["A","W","T","-","-","-","-","-"]
    motif3 = ["-","-","F","I","M","-","-","-"]
    motif4 = ["-","-","C","T","C","-","-","-"]
    motif5 = ["-","E","-","-","-","-","-","A"]

    motif6 = ["I","-","-","-","-","-","-","C"]
    motif7 = ["E","-","-","-","-","-","-","E"]
    motif8 = ["-","T","V","A","-","-","-","I"]
    motif9 = ["-","E","-","E","-","-","-","-"]
    motif10 = ["-","S","H","S","-","-","-","-"]

    motif11 = ["H","-","-","-","-","-","H","-"]
    motif12 = ["-","-","-","-","E","H","-","-"]
    motif13 = ["C","A","T","-","-","-","-","-"]
    motif14 = ["-","-","-","I","I","-","-","-"]
    motif15 = ["-","-","M","R","-","-","-","G"]

    motif16 = ["-","-","-","-","-","F","E","G"]
    motif17 = ["-","G","G","-","-","-","-","E"]
    motif18 = ["-","M","-","-","-","-","T","-"]
    motif19 = ["T","-","T","-","T","-","T","-"]
    motif20 = ["-","E","-","E","-","E","-","E"]

    motif21 = ["-","-","-","-","G","S","A","-"]
    motif22 = ["-","-","-","E","H","-","-","W"]
    motif23 = ["-","R","A","T","-","-","A","-"]
    motif24 = ["M","-","-","M","-","-","-","W"]
    motif25 = ["-","-","P","-","P","G","-","-"]

    motifs.append(motif1)
    motifs.append(motif2)
    motifs.append(motif3)
    motifs.append(motif4)
    motifs.append(motif5)
    motifs.append(motif6)
    motifs.append(motif7)
    motifs.append(motif8)
    motifs.append(motif9)
    motifs.append(motif10)
    motifs.append(motif11)
    motifs.append(motif12)
    motifs.append(motif13)
    motifs.append(motif14)
    motifs.append(motif15)
    motifs.append(motif16)
    motifs.append(motif17)
    motifs.append(motif18)
    motifs.append(motif19)
    motifs.append(motif20)
    motifs.append(motif21)
    motifs.append(motif22)
    motifs.append(motif23)
    motifs.append(motif24)
    motifs.append(motif25)

    return motifs[index1:index2]




def getMotifs1(index1, index2):
    motifs = []

    motif1 = ["-","T","T","P","-","-","-","A"]
    motif2 = ["A","W","T","-","-","-","-","-"]
    motif3 = ["-","-","T","-","T","-","T","-"]
    motif4 = ["-","-","C","N","C","-","-","-"]
    motif5 = ["-","Q","-","-","-","-","-","A"]

    motif6 = ["P","-","-","-","-","-","-","W"]
    motif7 = ["M","-","-","-","-","-","-","L"]
    motif8 = ["-","V","V","L","-","-","-","I"]
    motif9 = ["-","I","-","-","-","-","-","-"]
    motif10 = ["-","S","S","S","-","-","-","-"]

    motif11 = ["Y","-","-","-","-","-","Y","-"]
    motif12 = ["-","-","-","-","Y","Y","-","-"]
    motif13 = ["H","K","H","-","-","-","-","-"]
    motif14 = ["-","-","-","L","L","-","-","-"]
    motif15 = ["-","-","D","R","-","-","-","R"]

    motif16 = ["-","-","-","-","-","F","Y","P"]
    motif17 = ["-","T","M","-","-","-","-","T"]
    motif18 = ["-","R","-","-","-","-","G","-"]
    motif19 = ["A","-","A","-","A","-","A","-"]
    motif20 = ["-","C","-","C","-","C","-","C"]

    motif21 = ["-","-","-","-","-","F","Y","P"]
    motif22 = ["-","-","K","-","H","-","-","-"]
    motif23 = ["-","V","I","V","-","-","-","-"]
    motif24 = ["-","-","-","S","P","S","-","-"]
    motif25 = ["-","T","W","-","-","-","-","W"]

    motifs.append(motif1)
    motifs.append(motif2)
    motifs.append(motif3)
    motifs.append(motif4)
    motifs.append(motif5)
    motifs.append(motif6)
    motifs.append(motif7)
    motifs.append(motif8)
    motifs.append(motif9)
    motifs.append(motif10)
    motifs.append(motif11)
    motifs.append(motif12)
    motifs.append(motif13)
    motifs.append(motif14)
    motifs.append(motif15)
    motifs.append(motif16)
    motifs.append(motif17)
    motifs.append(motif18)
    motifs.append(motif19)
    motifs.append(motif20)
    motifs.append(motif21)
    motifs.append(motif22)
    motifs.append(motif23)
    motifs.append(motif24)
    motifs.append(motif25)

    return motifs[index1:index2]

# generates output of size: (size * motifs1) [file1] + (size * motifs2) [file2]
def generateTestingBatch(size, motifs1, motifs2):
    set1Peptides = set()
    set2Peptides = set()

    for motif1 in motifs1:
        newPeptides1 = amplifyMotif(size, motif1)
        set1Peptides = set1Peptides.union(newPeptides1)

    for motif2 in motifs2:
        newPeptides2 = amplifyMotif(size, motif2)
        set2Peptides = set2Peptides.union(newPeptides2)

    # write output to file
    OutFile1 = open('large_sim_peptides1.txt', 'w')
    for peptide in set1Peptides:
        OutFile1.write(peptide + "\n")

    OutFile2 = open('large_sim_peptides2.txt', 'w')
    for peptide in set2Peptides:
        OutFile2.write(peptide + "\n")

    OutFile1.close()
    OutFile2.close()

def getRefDict():
    referenceDict = {}
    aminoAcidMatrix = "C:\\Users\\BCBrown\\Desktop\\ClementLab\\aaMatrix.csv"
    with open(aminoAcidMatrix) as csvfile:
        reader = csv.reader(csvfile, delimiter=",")
        for row in reader:
            # make new list
            aminoAcid = ""

            attributes = np.ndarray(shape = (0,), dtype = float)
            i = 0
            for value in row:
                if i == 0:
                    aminoAcid = value # save which amino acid this is for
                else:
                    attributes = np.append(attributes, float(value))
                i = i + 1
            referenceDict[aminoAcid] = attributes

    return referenceDict

def buildNewRow(qualityIndex, peptideSequence, referenceDict):
    newRow = []
    for sequenceIndex in range(len(peptideSequence)):
        peptide = peptideSequence[sequenceIndex]
        if peptide != "\n":
            try:
                newRow.append(referenceDict[peptide][qualityIndex])
            except:
                print(peptide)
                print(qualityIndex)
    return newRow


def makeMatrix(data, referenceDict):
    imageStack = []

    numQualities = len(referenceDict["A"])
    for peptide in data:
        newImage = []

        for quality in range(numQualities): # 25 of these
            newRow = buildNewRow(quality, peptide, referenceDict) # 25 new rows
            newImage.append(newRow)
        newImage = np.stack(newImage)
        imageStack.append(newImage)
    imageStack = np.stack(imageStack)
    print(imageStack.shape)
    return imageStack


def main():
    numResidues = 8
    numQualities = 25

    motifs1 = getMotifs1(0,25)
    motifs2 = getMotifs2(0,25)

    # save generated peptides to files
    generateTestingBatch(1000, motifs1, motifs2)

    # open those files
    OutFile1 = open('large_sim_peptides1.txt', 'r')
    OutFile2 = open('large_sim_peptides2.txt', 'r')

    # save those peptides in a list
    domain1Data = []
    domain2Data = []
    for line in OutFile1:
        domain1Data.append(line)
    for line in OutFile2:
        domain2Data.append(line)
    OutFile1.close()
    OutFile2.close()

    # get the reference dictionary that contains the amino acid data
    aminoAcidDict = getRefDict()

    # convert the lists into numpy arrays that are 8 x 25 images
    domain1 = makeMatrix(domain1Data, aminoAcidDict)
    domain2 = makeMatrix(domain2Data, aminoAcidDict)

    domain1 = np.expand_dims(domain1, axis=1)
    domain2 = np.expand_dims(domain2, axis=1)
    print(domain1.shape)
    print(domain1[0])
    print(domain2.shape)
    print(domain2[0])

    # save those arrays

    np.save("large_domain1", domain1)
    np.save("large_domain2", domain2)
    # tiny: 0,1
    # small: 2,7
    # large: 0,25

    # tiny 4.0:
    # small 4.0:
    # domain 4.0:


# main()