使用python批量下载ensembl数据库指定类型的文件

1. 通过python的ftplib批量下载ensembl中指定类型的文件，并且同一个物种的文件保存在一个文件夹中
2. 经常碰到没下载完就停止，遇到这种情况可再次执行脚本，之前下载的文件不会被覆盖。如再次执行，log和summary文件会有点问题，不过不影响下载
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   2021-03-25更新，增加下载gff3和gtf的功能

#!/usr/bin/python
import ftplib
import os

HOST='ftp.ensemblgenomes.org'

def mkdir(path):
    dir=os.path.exists(path)
    if not dir:
        os.makedirs(path)
        
def get_cdna_cds_pep():
    feature_lst=['cdna','cds','pep']
    DIRN='/pub/release-50/plants/fasta'
    logFile=open('download.log','a')
    ###链接主机，定义端口###
    try:
        ftp=ftplib.FTP(HOST)   
    except ftplib.error_perm:
        logFile.write("Can not contect %s\n" %HOST)
        return
    logFile.write("Connect %s successfully\n"%HOST)
    
    ###匿名登陆 f.login()###
    try:
        ftp.login() 
    except ftplib.error_perm:
        logFile.write("Fail to login\n")
        ftp.quit()
        return
    logFile.write("Login successfully\n")

    ###获取下载文件###
    species_lst=ftp.nlst(DIRN)
    for species in species_lst: #遍历每个物种的文件夹
        speciesName=species.split("/")[-1]
        mkdir(speciesName)
        for feature in feature_lst: #遍历每个物种文件夹中的pep, cdna, cds文件夹
            path=species+"/"+feature
            for file in ftp.nlst(path):
                outFilename=file.split("/")[-1]
                if 'fa.gz' in file and os.path.exists(outFilename) is False:
                    with open(speciesName+"/"+outFilename, 'wb') as outfile:
                        ftp.retrbinary('RETR %s' % file, outfile.write)
                        logFile.write("file %s is dowloaded successfully\n" %outFilename)
    logFile.close()

def get_gff_gtf():
    feature_lst=['gff3','gtf']
    DIRN='/pub/release-50/plants/'
    logFile=open('download.log','a')
    ###链接主机，定义端口###
    try:
        ftp=ftplib.FTP(HOST)   
    except ftplib.error_perm:
        logFile.write("Can not contect %s\n" %HOST)
        return
    logFile.write("Connect %s successfully\n"%HOST)
    
    ###匿名登陆 f.login()###
    try:
        ftp.login() 
    except ftplib.error_perm:
        logFile.write("Fail to login\n")
        ftp.quit()
        return
    logFile.write("Login successfully\n")

    ###获取下载文件###
    for feature in feature_lst:
        suffix="50."+feature+".gz" #下载文件后缀
        species_lst=ftp.nlst(DIRN+feature)
        for species in species_lst: #遍历每个物种的文件夹
            speciesName=species.split("/")[-1]
            mkdir(speciesName)
            for file in ftp.nlst(species):
                outFilename=file.split("/")[-1]
                if suffix in file and os.path.exists(outFilename) is False:
                    with open(speciesName+"/"+outFilename, 'wb') as outfile:
                        ftp.retrbinary('RETR %s' % file, outfile.write)
                        logFile.write("file %s is dowloaded successfully\n" %outFilename)
    logFile.close()

if __name__ == '__main__':
    #get_cdna_cds_pep()
    get_gff_gtf()