Inserting a string after placing the last underscore in a header if a fasta file

Question

[timmers]

I'm having trouble with my syntax in trying to remove the last '_' in the header to replace with the string ':size=' and then add a ';' after the number. Original file looks like this:

 >ART01B_100_M7_ID100005_1
TAAGAGGAGGAATTTTTCATAGAGGATTGTCTGTAGACTTAGTAATTTTTTCTCTTCATTTAGCTGGAATTTCTTCTCTT
TTAGGGGCTGTAAATTTTATTACTACAATTCTTAATTGTCGATCTTTAGGGGTTTGGTGAGATGAATTGCCCTTATTTGT
>PAG05A_100_M7_ID102325_189
TAAGAGGAGGAATTTTTCATAGAGGATTGTCTGTAGACTTAGTAATTTTTTCTCTTCATTTAGCTGGAATTTCTTCTCTT
TTAGGGGCTGTAAATTTTATTACTACAATTCTTAATTGTCGATCTTTAGGGGTTTGGTGAGATGAATTGCCCTTATTTGT
>KIN05B_100_M7_ALT_ID230005_46
TAAGAGGAGGAATTTTTCATAGAGGATTGTCTGTAGACTTAGTAATTTTTTCTCTTCATTTAGCTGGAATTTCTTCTCTT
TTAGGGGCTGTAAATTTTATTACTACAATTCTTAATTGTCGATCTTTAGGGGTTTGGTGAGATGAATTGCCCTTATTTGT

and am trying to make it look like the following:

>ART01B_100_M7_ID100005;size=1;
TAAGAGGAGGAATTTTTCATAGAGGATTGTCTGTAGACTTAGTAATTTTTTCTCTTCATTTAGCTGGAATTTCTTCTCTT
TTAGGGGCTGTAAATTTTATTACTACAATTCTTAATTGTCGATCTTTAGGGGTTTGGTGAGATGAATTGCCCTTATTTGT
>PAG05A_100_M7_ID102325;size=189;
TAAGAGGAGGAATTTTTCATAGAGGATTGTCTGTAGACTTAGTAATTTTTTCTCTTCATTTAGCTGGAATTTCTTCTCTT
TTAGGGGCTGTAAATTTTATTACTACAATTCTTAATTGTCGATCTTTAGGGGTTTGGTGAGATGAATTGCCCTTATTTGT
>KIN05B_100_M7_ALT_ID230005;size=46;
TAAGAGGAGGAATTTTTCATAGAGGATTGTCTGTAGACTTAGTAATTTTTTCTCTTCATTTAGCTGGAATTTCTTCTCTT
TTAGGGGCTGTAAATTTTATTACTACAATTCTTAATTGTCGATCTTTAGGGGTTTGGTGAGATGAATTGCCCTTATTTGT

Thanks!

[WouterDeCoster]

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[WouterDeCoster]

I'm having trouble with my syntax

Please show us what you tried, we'd be happy to put you on the right track.

[timmers]

I seem to keep removing everything in the line and just replacing with ';size=. These are three of the attempts that do this: sed '/>/ s/(.)_.$/;size=/g' , sed '/>/ s/(.)_/;size=/g', sed '/>/ s/(.)_./;size=/g'. I'm missing something to indicate not to remove everything before that last _ but to replace it with ;size=. I know how to add just the ';' at the end which is sed 's/$/;/' so if the first replacement part is fixed then I can add that sed function to finish up the header but if it's possible to do all at once, great.

Answer 1

[vkkodali_ncbi]

Try this:

vamsi@cistron:~$ cat temp.txt
 >ART01B_100_M7_ID100005_1
TAAGAGGAGGAATTTTTCATAGAGGATTGTCTGTAGACTTAGTAATTTTTTCTCTTCATTTAGCTGGAATTTCTTCTCTT
TTAGGGGCTGTAAATTTTATTACTACAATTCTTAATTGTCGATCTTTAGGGGTTTGGTGAGATGAATTGCCCTTATTTGT
>PAG05A_100_M7_ID102325_189
TAAGAGGAGGAATTTTTCATAGAGGATTGTCTGTAGACTTAGTAATTTTTTCTCTTCATTTAGCTGGAATTTCTTCTCTT
TTAGGGGCTGTAAATTTTATTACTACAATTCTTAATTGTCGATCTTTAGGGGTTTGGTGAGATGAATTGCCCTTATTTGT
>KIN05B_100_M7_ALT_ID230005_46
TAAGAGGAGGAATTTTTCATAGAGGATTGTCTGTAGACTTAGTAATTTTTTCTCTTCATTTAGCTGGAATTTCTTCTCTT
TTAGGGGCTGTAAATTTTATTACTACAATTCTTAATTGTCGATCTTTAGGGGTTTGGTGAGATGAATTGCCCTTATTTGT

vamsi@cistron:~$ sed 's/\(>.*\)_\([0-9]*\)/\1;size=\2/g' temp.txt
 >ART01B_100_M7_ID100005;size=1
TAAGAGGAGGAATTTTTCATAGAGGATTGTCTGTAGACTTAGTAATTTTTTCTCTTCATTTAGCTGGAATTTCTTCTCTT
TTAGGGGCTGTAAATTTTATTACTACAATTCTTAATTGTCGATCTTTAGGGGTTTGGTGAGATGAATTGCCCTTATTTGT
>PAG05A_100_M7_ID102325;size=189
TAAGAGGAGGAATTTTTCATAGAGGATTGTCTGTAGACTTAGTAATTTTTTCTCTTCATTTAGCTGGAATTTCTTCTCTT
TTAGGGGCTGTAAATTTTATTACTACAATTCTTAATTGTCGATCTTTAGGGGTTTGGTGAGATGAATTGCCCTTATTTGT
>KIN05B_100_M7_ALT_ID230005;size=46
TAAGAGGAGGAATTTTTCATAGAGGATTGTCTGTAGACTTAGTAATTTTTTCTCTTCATTTAGCTGGAATTTCTTCTCTT
TTAGGGGCTGTAAATTTTATTACTACAATTCTTAATTGTCGATCTTTAGGGGTTTGGTGAGATGAATTGCCCTTATTTGT

By default, sed is 'greedy' so \1 will always include everything until the last underscore.

[timmers]

Yes that works thanks!

[vkkodali_ncbi]

Sorry, did not notice the trailing semi-colon; if you change the sed statement to something like this, you can add it with a single command:

sed 's/\(>.*\)_\([0-9]*\)/\1;size=\2;/g'

[Ram]

I'd recommend --extended-regexp while working with backreferences, it removes the need for backslashes in the match expression.

sed -r 's/(>.*)_([0-9]*)/\1;size=\2;/g' temp.txt

[WouterDeCoster]

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