Question: Remove gene features from a given list
0
gravatar for arunprasanna83
5 months ago by
arunprasanna8330 wrote:

Hello,

Is there a tool that can help me remove the entire features for a given list of genes? i.e from this gff3-version, I want to remove all the features related to g1 (start to end).

# start gene g1 
scaffold1size1833262    AUGUSTUS    gene    1   1168    0.56    +   .   ID=g1 
scaffold1size1833262    AUGUSTUS    transcript  1   1168    0.56    +   .   ID=g1.t1;Parent=g1 
scaffold1size1833262    AUGUSTUS    intron  1   563 0.91    +   .   Parent=g1.t1 
scaffold1size1833262    AUGUSTUS    CDS 564 676 0.91    +   2   ID=g1.t1.cds;Parent=g1.t1 
scaffold1size1833262    AUGUSTUS    exon    564 1168    .   +   .   Parent=g1.t1 
scaffold1size1833262    AUGUSTUS    stop_codon  674 676 .   +   0   Parent=g1.t1 
scaffold1size1833262    AUGUSTUS    transcription_end_site  1168    1168    .   +   .   Parent=g1.t1
# protein sequence = [SGFLRPVEADVNLTVCSKDTGKAADKGGSTSFPISM]
# Evidence for and against this transcript:
# % of transcript supported by hints (any source): 33.3
# CDS exons: 0/1
# CDS introns: 0/1
# 5'UTR exons and introns: 0/0
# 3'UTR exons and introns: 1/1
#      W:   1 
# hint groups fully obeyed: 40
#      W:  40 
# incompatible hint groups: 14
#      W:  14 
# end gene g1
gff3 annotation gene • 193 views
ADD COMMENTlink written 5 months ago by arunprasanna8330

Have you looked at some combination of grep -v -w to eliminate lines with g1*?

ADD REPLYlink written 5 months ago by genomax73k

the problem is, it will remove all the lines with g1 but leaves the traces like lines from # protein sequence till # W: 14. This would make the gff3 file untidy.

ADD REPLYlink written 5 months ago by arunprasanna8330
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