sed command to extract sequence

Hi,

I have a fasta file, like this:

>TRINITY_DN100000_c1_g1::TRINITY_DN100000_c1_g1_i3::g.3039::m.3039 TRINITY_DN100000_c1_g1::TRINITY_DN100000_c1_g1_i3::g.3039  ORF type:complete len:100 (-) TRINITY_DN100000_c1_g1_i3:1027-1326(-)
MVWIKFRGLHRVLTSTPLVKSGKTPSQTWAFLDISVELIVFLFLNVHKSPMPHFKIYSEA
FSEEWSLLWLQYSRHLIQKPKPWQIKIELLHLCCCNRLC*
>TRINITY_DN100000_c1_g6::TRINITY_DN100000_c1_g6_i2::g.84365::m.84365 TRINITY_DN100000_c1_g6::TRINITY_DN100000_c1_g6_i2::g.84365  ORF type:complete len:112 (-) TRINITY_DN100000_c1_g6_i2:379-714(-)
MEMMQEIIPFAREMLSARPSKGTMKVYLVGGTFAVLGIVSGMVEAACSLFPEQEESTLTK
LMEDCLTVTAQNQEPQTFIPEDDEQDAEMEAKAKDLPMFRQRRMSFRAHAS*

if I want to only keep the second header, like this (the amino acid sequence keep unchanged), how should I correct this command sed 's/::.*//' input > output:

>TRINITY_DN100000_c1_g1_i3
MVWIKFRGLHRVLTSTPLVKSGKTPSQTWAFLDISVELIVFLFLNVHKSPMPHFKIYSEA
FSEEWSLLWLQYSRHLIQKPKPWQIKIELLHLCCCNRLC*
>TRINITY_DN100000_c1_g6_i2
MEMMQEIIPFAREMLSARPSKGTMKVYLVGGTFAVLGIVSGMVEAACSLFPEQEESTLTK
LMEDCLTVTAQNQEPQTFIPEDDEQDAEMEAKAKDLPMFRQRRMSFRAHAS*

this command can only keep the first header >TRINITY_DN100000_c1_g1 if I want to keep the second header with the isoform information TRINITY_DN100000_c1_g1_i3, how should I correct this command?

rna-seq

• 1,678 views • link

updated 6.9 years ago by patelk26

• written 6.9 years ago by mxlsherry1992 •

1 answer

Try this: sed 's/::g.*(-)//' input.fasta | sed 's/>.*::/>/' > output.fasta

• 0 views • link

written 6.9 years ago by patelk26

Hi thanks! this command will give this:

    >g.122404  ORF type:internal len:253 (+) TRINITY_DN100000_c0_g1_i1:3-758(+)
    GIELKRFDMSEYMERHAVSRLIGAPPGYVGYEQGGLLTEAISKKPHCVLLLDEIEKAHPD
    IYNVLLQVMDHGTLTDNNGRKADFRNVIIIMTTNAGAETMNKATIGFTNPRQAGDEMGDI
    KRLFTPEFRNRLDAIVSFKPLDEQIILRVVDKFLLQLETQLAEKKVEVTFTDALRKHLAK
    KGFDPLMGARPMQRLIQEMIRKALADELLFGRLTEGGRLNVDLDDKGEVQLDIQPLPKKE
    ARSGKSDEPLLS
    >TRINITY_DN100000_c1_g1_i1
    LLTEAVTKKPHCVLLLDEIEKAHPDIFNVLLQVMDHGTLTDNNGRKADFRNVIIIMTTNA
    GAETMNKSTIGFTTQRQAGDEMADIKRLFTPEFRNRLDAI

Some of the sequences look good, but some still look messed up...if you know how to modify the command further..?

Thank you

• 0 views • link

written 6.8 years ago by mxlsherry1992 •