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  • liuhui
    Junior Member
    • Feb 2016
    • 3
    #1

    How to convert pfam output format?

    Dear all,
    Recently, I aligned my transcriptome sequences to the pfam database. Sometimes, one sequence will hit several pfam records. And I want to convert the pfam output format from

    TRINITY_GG_428_c0_g1_i1_orf1 PF13499.1 EF_hand_5
    TRINITY_GG_428_c0_g1_i1_orf1 PF00036.27 efhand
    TRINITY_GG_428_c0_g1_i1_orf1 PF13405.1 EF_hand_4
    TRINITY_GG_428_c0_g1_i1_orf1 PF13833.1 EF_hand_6
    TRINITY_GG_428_c0_g1_i1_orf1 PF13202.1 EF_hand_3
    TRINITY_GG_429_c0_g1_i1_orf1 PF00156.22 Pribosyltran
    TRINITY_GG_431_c5_g1_i1_orf1 PF00475.13 IGPD
    TRINITY_GG_461_c0_g1_i1_orf1 PF01208.12 URO-D
    TRINITY_GG_461_c0_g1_i1_orf1 PF12876.2 Cellulase-like

    to

    TRINITY_GG_428_c0_g1_i1_orf1 PF13499.1 EF_hand_5 | PF00036.27 efhand | PF13405.1 EF_hand_4 | PF13833.1 EF_hand_6 | PF13202.1 EF_hand_3
    TRINITY_GG_429_c0_g1_i1_orf1 PF00156.22 Pribosyltran
    TRINITY_GG_431_c5_g1_i1_orf1 PF00475.13 IGPD
    TRINITY_GG_461_c0_g1_i1_orf1 PF01208.12 URO-D | PF12876.2 Cellulase-like
    .
    Could you please share your code or any idea with me to solve this problem?
    Thank you very much!
    Tags: bioinfomatics, pfam
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