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  • Get Protein Sequences fasta file by using Entrez Gene Ids

    I want to get a protein sequences FASTA file for a given list of Entrez Gene IDs, which is shown as blow:

    Code:
    kurban@kurban-X550VC:~/Desktop$ more Triboliumcastaneum_tf_id.txt
    100141790
    100142111
    100142176
    100142203
    100142308
    654967
    655070
    655772
    655998
    how could i extract their corresponding protein sequences fasta file for these Tribolium castaneum gene id from ncbi? thanks.

  • #2
    Here's a hint:

    Use the efetch utilty :
    example for mrna:
    wget "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=100141790,100142111,100142176,100142203,100142308,654967,655070,655772,655998&rettype=fasta&retmode=text" -O out

    Getting the protein is the hard part.

    Full solution
    echo -e "100141790\n100142111\n100142176\n100142203\n100142308\n654967\n655070\n655772\n655998" | while read G; do curl -s "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=gene&db=protein&id=${G}" | grep -A 1 "<Link>" | grep "<Id>" | cut -d '>' -f 2 | cut -d '<' -f 1 | while read S ; do curl -s "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=protein&id=${S}&retmode=text&rettype=fasta" ; done; done


    from Pierre Lindenbaum's post at biostars:


    Note there are multiple isoforms

    Comment


    • #3
      thanks @Richard,
      the commend really works like a charm, but the total sequences i wanna extract are 519, so how could i change my file formation
      Code:
      100141790
      100142111
      100142176
      100142203
      100142308
      654967
      655070
      655772
      655998
      to this form: "100141790\n100142111\n100142176\n100142203\n100142308\n654967\n655070\n655772\n655998"?

      sorry , i am now at this.
      Last edited by kurban910; 07-03-2015, 09:50 AM.

      Comment

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