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  • faidx usage and non specific hits

    Hi All,

    I am using pyfaidx to extract fasta sequence from a multifasta file using a list of locus tags.

    List.txt
    JFCCLHHB_00692
    CKEMPBAI_00693
    FBNBCCDE_01742
    OMPPMJLG_02124
    GKEHKBJF_02074

    file.fasta
    >NOLHFCLD_00001 Magnesium-transporting ATPase, P-type 1
    atgc
    >NOLHFCLD_00003 Serine transporter
    atgc

    my command is
    xargs faidx file.fasta < list.txt > out.fas

    my problem is that faidix is being pretty non-specific in the output. Im getting hits back which I know I shouldnt and I was wondering would the underscore have anything to do with this?
    Last edited by SeqTroubles; 06-21-2017, 05:54 AM.

  • #2
    Are you referring to samtools faidx or something else?

    Comment


    • #3
      Originally posted by GenoMax View Post
      Are you referring to samtools faidx or something else?
      pyfaidx. Ill change my description now.

      Comment


      • #4
        Tested and appears to work fine. Fasta ID's need to match exactly (unless you want to try reg exp/wild cards).

        Code:
        $ more list.fa
        >JFCCLHHB_00692
        AGCTCGAT
        >CKEMPBAI_00693
        ACGCTG
        >FBNBCCDE_01742
        ACGATCAC
        >OMPPMJLG_02124
        ACGCTCGCTGC
        >GKEHKBJF_02074
        AGCTCGC
        
        $ more list.txt
        JFCCLHHB_00692
        CKEMPBAI_00693
        GKEHKBJF_02074
        
        $ xargs faidx list.fa < list.txt
        >JFCCLHHB_00692
        AGCTCGAT
        >CKEMPBAI_00693
        ACGCTG
        >GKEHKBJF_02074
        AGCTCGC

        Comment


        • #5
          Originally posted by GenoMax View Post
          Tested and appears to work fine. Fasta ID's need to match exactly (unless you want to try reg exp/wild cards).

          Code:
          $ more list.fa
          >JFCCLHHB_00692
          AGCTCGAT
          >CKEMPBAI_00693
          ACGCTG
          >FBNBCCDE_01742
          ACGATCAC
          >OMPPMJLG_02124
          ACGCTCGCTGC
          >GKEHKBJF_02074
          AGCTCGC
          
          $ more list.txt
          JFCCLHHB_00692
          CKEMPBAI_00693
          GKEHKBJF_02074
          
          $ xargs faidx list.fa < list.txt
          >JFCCLHHB_00692
          AGCTCGAT
          >CKEMPBAI_00693
          ACGCTG
          >GKEHKBJF_02074
          AGCTCGC
          Thanks GenoMax.

          I have two lists of tags and one list work perfect but when I execute the second it would appear its just copying all the information from the input fasta. Really weird. Ive already looked over all my data to ensure its valid so I cannot see where the issue is at present.

          In actuality Im running a loop to execute this search looks like
          for f in *.fna; do
          f=$(basename $f .fna); xargs faidx $f.fna < tags.txt > $PWD/out/$f.fas; done
          Last edited by SeqTroubles; 06-21-2017, 08:34 AM.

          Comment


          • #6
            Examine your ID file (something like cat -vet yourFile) to see if there are any non-printable characters that could be causing potential issues.

            Comment

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