Adding "#" before the first 8 lines corresponding to STRING
The question is a bit confusing, so I'll just show you an example.
Let's say I have the following case:
$ grep -P "locus_tag\tM715_1000193188" Genome.tbl -B1 -A8
193188 193066 gene
locus_tag M715_1000193188
193188 193066 mRNA
product hypothetical protein
protein_id gnl|CorradiLab|M715_1000193188
transcript_id gnl|CorradiLab|M715_mrna1000193188
193188 193066 CDS
product hypothetical protein
protein_id gnl|CorradiLab|M715_1000193188
transcript_id gnl|CorradiLab|M715_mrna1000193188
I want to add "#" on the 8 lines following "locus_tag M715_1000193188" so that the modified file looks like this:
193188 193066 gene
locus_tag M715_1000193188
#193188 193066 mRNA
# product hypothetical protein
# protein_id gnl|CorradiLab|M715_1000193188
# transcript_id gnl|CorradiLab|M715_mrna1000193188
#193188 193066 CDS
# product hypothetical protein
# protein_id gnl|CorradiLab|M715_1000193188
# transcript_id gnl|CorradiLab|M715_mrna1000193188
Essentially I have a file with ~ 3000 different locus tags, and for 300 of them I need to comment out the mRNA and CDS functions, so 8 lines following the locus_tag line.
Any possible way to do this with sed? There are other types of information in the file that must be left untouched.
Thanks, Adrian
If you can use awk
this should do:
awk 'f&&f-- {$0="#"$0} /locus_tag/ {f=8} 1' file
193188 193066 gene
locus_tag M715_1000193188
#193188 193066 mRNA
# product hypothetical protein
# protein_id gnl|CorradiLab|M715_1000193188
# transcript_id gnl|CorradiLab|M715_mrna1000193188
#193188 193066 CDS
# product hypothetical protein
# protein_id gnl|CorradiLab|M715_1000193188
# transcript_id gnl|CorradiLab|M715_mrna1000193188
sed supports the Addresses range , which can do what you want here.
sed -e '/locus_tag\tM715_1000193188/,+8s/^/#/' file
As noted in the comments, this range address format has the GNU sed specification.
$ cat tst.awk
BEGIN { split(tags,tmp); for (i in tmp) tagsA[tmp[i]] }
c&&c-- { $0 = "#" $0 }
($(NF-1) == "locus_tag") && ($NF in tagsA) { c=8 }
{ print }
$ awk -v tags="M715_1000193188 M715_1000193189 M715_1000193190" -f tst.awk file
193188 193066 gene
locus_tag M715_1000193188
#193188 193066 mRNA
# product hypothetical protein
# protein_id gnl|CorradiLab|M715_1000193188
# transcript_id gnl|CorradiLab|M715_mrna1000193188
#193188 193066 CDS
# product hypothetical protein
# protein_id gnl|CorradiLab|M715_1000193188
# transcript_id gnl|CorradiLab|M715_mrna1000193188
Just list all 300 locus tag values you care about as shown above for 3 examples.
This might work for you (GNU sed):
sed 's/.*/\\#locus_tag\\s*&#,+9{\\#locus_tag\\s*&#n;s|^|#|}/' tag_file |
sed -i -f - file
This creates a sed script from the tag file and appends #
to eight lines after the tag matches.