import os.path
sig_dir = "D://project//gff//out//"
w_dir = "D://project//gff//cgc_table5//"
# fw= open(w_dir,"w")

cgc_number = 0
yuzhi = 4
for parent,dirnames,filenames in os.walk(sig_dir):
    for filename in filenames:
        gen = filename
        f = open(os.path.join(parent,filename))
        h = f.readlines()
        f.close()
        h_len = len(h)
        prev_reseq = h[0].split("   ")[0]
        list=[]
        #wirte cluster
        fw = open(w_dir+gen,"w")
        for i in range(h_len):
            if h[i]=='\n':
                continue
            line = h[i].split(" ")
            if prev_reseq != line[0]:
                #write the cluster
                cluster=[]
                cazy = 0
                tc = 0
                tf = 0
                list_len = len(list)
                cgc_no = 1
                #wirte the cluster
                for k in range(list_len):
                    cluster.append(list[k])
                    #print cluster[-1]
                    if list[k][-1] <= yuzhi :
                        if list[k][1]=="TC-DB":
                            tc = tc+1
                        elif list[k][1]=="TF":
                            tf = tf+1
                        elif list[k][1]=="CAZyme":
                            cazy = cazy +1
                    else :
                        if (cazy > 0 and tc > 0 and tf >0):
                        # if (cazy>0 and tc >0) or (cazy>0 and tf>0):
                            cnt = 0
                            for j in range(cluster[-1][0]+1-cluster[0][0]):
                                if h[cluster[0][0] + j].split()[-1] == "null":
                                    for p in range(4):
                                        fw.write("null" + " ")
                                else:
                                    for p in range(4):
                                        fw.write(str(cluster[cnt][p]) + "   ")
                                    cnt = cnt + 1
                                fw.write(prev_reseq+"-"+"CGC"+str(cgc_no)+" "+h[cluster[0][0]+j])
                            fw.write("+++\n")
                            cazy = 0
                            tc = 0
                            tf = 0
                            cgc_no = cgc_no +1
                            cgc_number = cgc_number+1
                        cluster=[] #delete the cluster
                #write the left cluster
                if len(cluster)>0:
                    if (cazy > 0 and tc > 0 and tf > 0):
                    # if (cazy > 0 and tc > 0) or (cazy > 0 and tf > 0):
                        cnt = 0
                        for j in range(cluster[-1][0] + 1 - cluster[0][0]):
                            if h[cluster[0][0] + j].split()[-1] == "null":
                                for p in range(4):
                                    fw.write("null" + " ")
                            else:
                                for p in range(4):
                                    fw.write(str(cluster[cnt][p]) + "   ")
                                cnt = cnt + 1
                            fw.write(prev_reseq + "-" + "CGC" + str(cgc_no) + " " + h[cluster[0][0] + j])
                        fw.write("+++\n")
                        cazy = 0
                        tc = 0
                        tf = 0
                        cgc_no = cgc_no + 1
                        cgc_number = cgc_number + 1
                    cluster = []  # delete the cluster
                # process the new refseq
                list = []
            if line[6] != "null":
                sig = line[6].split('|')[0]
                if len(list) == 0:
                    dis_prev = 0
                else:
                    dis_prev = i - list[-1][0]
                    list[-1][3] = dis_prev
                dis_next = 0
                list.append([i, sig, dis_prev, dis_next])
                prev_reseq = line[0]
        # write left cluster
        if len(list)>0:
            cluster = []
            cazy = 0
            tc = 0
            tf = 0
            list_len = len(list)
            cgc_no=1
            # wirte the cluster
            for k in range(list_len):
                cluster.append(list[k])
                if list[k][-1] <= yuzhi :
                    if list[k][1] == "TC-DB":
                        tc = tc + 1
                    elif list[k][1] == "TF":
                        tf = tf + 1
                    elif list[k][1] == "CAZyme":
                        cazy = cazy + 1
                else:
                    if (cazy > 0 and tc > 0 and tf > 0):
                    # if (cazy > 0 and tc > 0) or (cazy > 0 and tf > 0):
                        cnt = 0
                        for j in range(cluster[-1][0] + 1 - cluster[0][0]):
                            if h[cluster[0][0] + j].split()[-1] == "null":
                                for p in range(4):
                                    fw.write("null" + " ")
                            else:
                                for p in range(4):
                                    fw.write(str(cluster[cnt][p]) + "   ")
                                cnt = cnt + 1
                            fw.write(prev_reseq + "-" + "CGC" + str(cgc_no) + " " + h[cluster[0][0] + j])
                        fw.write("+++\n")
                        cazy = 0
                        tc = 0
                        tf = 0
                        cgc_no = cgc_no + 1
                        cgc_number = cgc_number + 1

                    cluster = []  # delete the cluster
            # write the left cluster
            if len(cluster) > 0:
                if (cazy > 0 and tc > 0 and tf > 0):
                # if (cazy > 0 and tc > 0) or (cazy > 0 and tf > 0):
                    cnt = 0
                    for j in range(cluster[-1][0] + 1 - cluster[0][0]):
                        if h[cluster[0][0] + j].split()[-1] == "null":
                            for p in range(4):
                                fw.write("null" + " ")
                        else:
                            for p in range(4):
                                fw.write(str(cluster[cnt][p]) + "   ")
                            cnt = cnt + 1
                        fw.write(prev_reseq + "-" + "CGC" + str(cgc_no) + " " + h[cluster[0][0] + j])
                    cazy = 0
                    tc = 0
                    tf = 0
                    cgc_no = cgc_no + 1
                    cgc_number = cgc_number + 1
                cluster = []  # delete the cluster
            # process the new refseq
            list = []
print cgc_number