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https://github.com/Priyatham-sai-chand/compara-deep-learning.git
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48 lines
1.2 KiB
Python
48 lines
1.2 KiB
Python
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from ftplib import FTP
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from req_data import get_data_file
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#This wil download all the fasta files for the coding sequences. To change the directory, change the argument in the get_data_file argument.
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host ="ftp.ensembl.org"
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user = "anonymous"
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password = ""
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print("Connecting to {}".format(host))
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ftp = FTP(host)
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ftp.login(user, password)
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print("Connected to {}".format(host))
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l=ftp.nlst("/pub/release-96/fasta")
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lt=[]
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for x in l:
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y=ftp.nlst(x+"/cds")
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for z in y:
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if z.endswith(".cds.all.fa.gz"):
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lt.append(z)
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base_link="ftp://ftp.ensembl.org"
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with open("seq_link.txt","w") as file:
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for x in lt:
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file.write(base_link+x)
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file.write("\n")
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l=ftp.nlst("/pub/release-96/gtf")
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lt=[]
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for x in l:
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y=ftp.nlst(x)
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for z in y:
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if z.endswith(".96.gtf.gz"):
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lt.append(z)
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base_link="ftp://ftp.ensembl.org"
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with open("gtf_link.txt","w") as file:
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for x in lt:
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file.write(base_link+x)
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file.write("\n")
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ch=input("Do you want to download the data?[y/n]")
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if ch=='y':
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print("Downloading Data.................")
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get_data_file("gtf_link.txt","data")
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get_data_file("seq_link.txt","geneseq")
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print("Download Complete.................")
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