python：把CAZyme注释文件统计并合并统计

众所周知，run_dbcan是CAZyme注释的最经典软件

linnabrown/run_dbcan: Run_dbcan V4, using genomes/metagenomes/proteomes of any assembled organisms (prokaryotes, fungi, plants, animals, viruses) to search for CAZymes. (github.com)

而run_dbcan的结果通常储存在overview.txt文件之中：

 这里选择的是HMMER方式跑的，所以只有第三列有注释的结果

为了统计overview.txt文件的各个家族情况，写下一个简单的代码：

inputTXT = args.inputTXT 
output = args.output
f = open("%s" %(inputTXT), "r")
db= {}
for line in f.readlines():
    line = line.split("\t")[2]
    if "HMMER" not in line:
        line = line.split("+")
        for i in line:
            i = i.split("(")[0]
            if i in db:
                db[i] += 1
            if i not in db:
                db[i] = 1

f2 = open("%s" %(output),"a")
print("\t"+inputTXT,file=f2)
for ID, seq in db.items():
    ID_3 = ID.strip()
    
    print(ID_3,end="\t",file=f2)
    print(seq,file=f2)

f.close()
f2.close()

统计结果为

 但是，当我们有好几个overview文件之后，因为每个文件的第一列的类型不一样，不能随便的进行文件组合，不好分析，所以想写一个脚本组合之后方便分析。

ls_xijie_result = []
ls_domain_result = {}
ls_db_result = []
for txt in os.listdir(os.getcwd()):
    if "_xijie.txt" in txt:
        ls_xijie_result.append(txt)
for file in ls_xijie_result:
    f = open("%s" % (file),"r")
    for line in f.readlines():
        if ".txt" not in line:
            line = line.split("\t")[0].strip("\n")
            ls_domain_result[line] = 0
    f.close()
file_count=0
for file in ls_xijie_result:
    f2 = open("%s" % (file), "r")
    file_count += 1
    db=str(file)
    db=ls_domain_result.copy()
    for line in f2.readlines():
        if ".txt" in line:
            line = line.split("\t")[1].strip("\n")
            file_name=line
        if ".txt" not in line:
            domain = line.split("\t")[0].strip("\n")
            count = line.split("\t")[1].strip("\n")
            if domain in db.keys():
                db[domain]=count
    ls_db_result.append(db)
    f2.close()

header=[]
for key in ls_domain_result.keys():
    header.append(key)

with open('merge_overview_2.csv', 'a', encoding='utf-8', newline='') as f3:
    dictWriter = csv.DictWriter(f3,header)
    dictWriter.writeheader()
    dictWriter.writerows(ls_db_result)
f3_rows=[]
f3 = open('merge_overview_2.csv',"r")
for line in f3.readlines():
    f3_rows.append(line)
f3.close()
f4 = open('merge_overview_3.csv',"a")
print("",end=",",file=f4)
print(f3_rows[0].strip("\n"),file=f4)
row_count=0
for i in ls_xijie_result:
    row_count += 1
    print(i,end=",",file=f4)
    print(f3_rows[row_count].strip("\n"),file=f4)
f4.close()

结果如下

在excel中，复制为转置之后，再排序一下，就可以很直观的分析了！