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!
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!