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  • fefe89
    replied
    Thank's again. It works perfectly

    Leave a comment:


  • rhinoceros
    replied
    Originally posted by fefe89 View Post
    Thank you very much. It seems really perfect for my problem.

    But, how can I work with that kind of file (dmp)?

    Sorry but I'm really new of this world
    It's a tab separated text file. First column is Gi and second column is tax id. For example:

    Code:
    grep -m1 -w ^74664614 gi_taxid_prot.dmp
    Looks for line in which first column is exactly 74664614 and prints the first (I think also only) occurrence. The same with awk:

    Code:
    awk '$1 == 74664614 {print;exit}' gi_taxid_prot.dmp
    Also check the edit in my previous answer.

    Leave a comment:


  • fefe89
    replied
    Thank you very much. It seems really perfect for my problem.

    But, how can I work with that kind of file (dmp)?

    Sorry but I'm really new of this world

    Leave a comment:


  • rhinoceros
    replied
    You don't need blast for connecting GI/Accession to Taxonomy ID. This file links Prot GI to TaxID and this file does the same with Nucl GIs. Alternatively, if you don't want to download the big map files, you can use e.g. Entrez Direct, for example:

    Code:
    esearch -db protein -query ProtGiNumber | elink -target taxonomy | efetch -format xml | xtract -element TaxId | cut -f1
    Last edited by rhinoceros; 08-10-2014, 11:45 PM.

    Leave a comment:


  • fefe89
    started a topic Blast from accession number

    Blast from accession number

    Hey guys,

    I have a list of all the genes I have with the respective GI and accession number.

    What I would like to do is to make a blast using these accession number instead of the fasta sequence (as I ususally do with blast+), in order to have all the info (and particularly the taxonimy ID).

    Is it possible? How can I do?

    Thank you in advance

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