Removing a portion of data in a file

Shell Programming and Scripting
1

Hi,
I have a folder that contains many (multiple) files

1.fasta
2.fasta
3.fasta
4.fasta
5.fasta
.
.
100's of files

Each such file have data in the following format
for example:
vi 1.fasta

Code:

>AB_1
MLKKPIIIGVTGGSGGGKTSVSRAILDSFPNARIAMIQHDSYYKDQSHMSFEERVKTNYDHPLAFDTDFM
IQQLKELLAGRPVDIPIYDYKKHTRSNTTFRQDPQDVIIVEGILVLEDERLRDLMDIKLFVDTDDDIRII
RRIKRDMMERGRSLESIIDQYTSVVKPMYHQFIEPSKRYADIVIPEGVSNVVAIDVINSKIASILGEV
>AB_2
MRARLIYNPTSGQELMRKSVPEVLDILEGFGYETSAFQTTAKKNSALNEARRAAKAGFDLLIAAGGDGTI
NEVVNGIAPLKKRPKMAIIPTGTTNDFARALKVPRGNPSQAAKLIGKNQTIQMDIGRAKKDTYFINIAAA
GSLTELTYSVPSQLKTMFGYLAYLAKGVELLPRVSNVPVKITHDKGVFEGQVSMIFAAITNSVGGFEMIA
PDAKLDDGMFTLILIKTANLFEIVHLLRLILDGGKHITDRRVEYIKTSKIVIEPQCGKRMMINLDGEYGG
DAPITLENLKNHITFFADTDLISDDALVLDQDELEIEEIVKKFAHEVEDLEQELEE
>AB_3
MTGYDDFNYALSALKLGADDYLLKPFSKADVEDMLGKLRKKLELSKKTETIQELVEQPQKEVSAIAMAIH
ERLADSDLTLKSLAQQLGFSPNYLSVLIKKELGMPFQDYLVQERLKKAKLFLLTSNLKIYEIAEQVGFED
MNYFSQRFKQLVGVTPSQYKKGGQA
>AB_4 
MRARLIYNPTSGQELMRKSVPEVLDILEGFGYETSAFQTTAKKNSALNEARRAAKAGFDLLIAAGGDGTI
NEVVNGIAPLKKRPKMAIIPTGTTNDFARALKVPRGNPSQAAKLIGKNQTIQMDIGRAKKDTYFINIAAA
GSLTELTYSVPSQLKTMFGYLAYLAKGVELLPRVSNVPVKITHDKGVFEGQVSMIFAAITNSVGGFEMIA
PDAKLDDGMFTLILIKTANLFEIVHLLRLILDGGKHITDRRVEYIKTSKIVIEPQCGKRMMINLDGEYGG
DAPITLENLKNHITFFADTDLISDDALVLDQDELEIEEIVKKFAHEVEDLEQELEE
>AB_5  
MRARLIYNPTSGQELMRKSVPEVLDILEGFGYETSAFQTTAKKNSALNEARRAAKAGFDLLIAAGGDGTI
NEVVNGIAPLKKRPKMAIIPTGTTNDFARALKVPRGNPSQAAKLIGKNQTIQMDIGRAKKDTYFINIAAA
GSLTELTYSVPSQLKTMFGYLAYLAKGVELLPRVSNVPVKITHDKGVFEGQVSMIFAAITNSVGGFEMIA
PDAKLDDGMFTLILIKTANLFEIVHLLRLILDGGKHITDRRVEYIKTSKIVIEPQCGKRMMINLDGEYGG
DAPITLENLKNHITFFADTDLISDDALVLDQDELEIEEIVKKFAHEVEDLEQELEE

I would like to edit these files such a way that the data below
>AB_1 is removed (including the header) and have an output file like'

>AB_2
MRARLIYNPTSGQELMRKSVPEVLDILEGFGYETSAFQTTAKKNSALNEARRAAKAGFDLLIAAGGDGTI
NEVVNGIAPLKKRPKMAIIPTGTTNDFARALKVPRGNPSQAAKLIGKNQTIQMDIGRAKKDTYFINIAAA
GSLTELTYSVPSQLKTMFGYLAYLAKGVELLPRVSNVPVKITHDKGVFEGQVSMIFAAITNSVGGFEMIA
PDAKLDDGMFTLILIKTANLFEIVHLLRLILDGGKHITDRRVEYIKTSKIVIEPQCGKRMMINLDGEYGG
DAPITLENLKNHITFFADTDLISDDALVLDQDELEIEEIVKKFAHEVEDLEQELEE
>AB_3
MTGYDDFNYALSALKLGADDYLLKPFSKADVEDMLGKLRKKLELSKKTETIQELVEQPQKEVSAIAMAIH
ERLADSDLTLKSLAQQLGFSPNYLSVLIKKELGMPFQDYLVQERLKKAKLFLLTSNLKIYEIAEQVGFED
MNYFSQRFKQLVGVTPSQYKKGGQA
>AB_4 
MRARLIYNPTSGQELMRKSVPEVLDILEGFGYETSAFQTTAKKNSALNEARRAAKAGFDLLIAAGGDGTI
NEVVNGIAPLKKRPKMAIIPTGTTNDFARALKVPRGNPSQAAKLIGKNQTIQMDIGRAKKDTYFINIAAA
GSLTELTYSVPSQLKTMFGYLAYLAKGVELLPRVSNVPVKITHDKGVFEGQVSMIFAAITNSVGGFEMIA
PDAKLDDGMFTLILIKTANLFEIVHLLRLILDGGKHITDRRVEYIKTSKIVIEPQCGKRMMINLDGEYGG
DAPITLENLKNHITFFADTDLISDDALVLDQDELEIEEIVKKFAHEVEDLEQELEE
>AB_5  
MRARLIYNPTSGQELMRKSVPEVLDILEGFGYETSAFQTTAKKNSALNEARRAAKAGFDLLIAAGGDGTI
NEVVNGIAPLKKRPKMAIIPTGTTNDFARALKVPRGNPSQAAKLIGKNQTIQMDIGRAKKDTYFINIAAA
GSLTELTYSVPSQLKTMFGYLAYLAKGVELLPRVSNVPVKITHDKGVFEGQVSMIFAAITNSVGGFEMIA
PDAKLDDGMFTLILIKTANLFEIVHLLRLILDGGKHITDRRVEYIKTSKIVIEPQCGKRMMINLDGEYGG
DAPITLENLKNHITFFADTDLISDDALVLDQDELEIEEIVKKFAHEVEDLEQELEE

Like wise I would it to all the files in the folder.
Please let me know the best way to do it in awk or sed/
LA

2

This is just an observation, but why do most of your question look the same?

Did you learn nothing from previous answers?

Like this one, which seems to me to be the same question...

3

A perl one (test it with backups!):

perl -ni -e '$a=0 unless $ARGV eq $lf;$lf=$ARGV;if( /^>AB_2/){$a=1};print unless !$a;' *fasta
4

Dear Scottn,
Sorry for the confusion. I am using only the same type example data but this time it was different question.
LA

---------- Post updated at 12:45 PM ---------- Previous update was at 12:44 PM ----------

Sorry the perl code didn't work

5

The perl code works for the example provide

6

Dear Klash xx

It worked..sorry it was my mistake....I didn't realize I have to target the second header.
LA

7 
for f in *.fasta; do
    printf '/^>/;/^>/-d\nw\nq\n' | ed -s "$f"
done
2 Likes