Editing headers

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

>AB_1 200bp
MLKKPIIIGVTGGSGGGKTSVSRAILDSFPNARIAMIQHDSYYKDQSHMSFEERVKTNYDHPLAFDTDFM
IQQLKELLAGRPVDIPIYDYKKHTRSNTTFRQDPQDVIIVEGILVLEDERLRDLMDIKLFVDTDDDIRII
RRIKRDMMERGRSLESIIDQYTSVVKPMYHQFIEPSKRYADIVIPEGVSNVVAIDVINSKIASILGEV
>AB_2 200bp
MRARLIYNPTSGQELMRKSVPEVLDILEGFGYETSAFQTTAKKNSALNEARRAAKAGFDLLIAAGGDGTI
NEVVNGIAPLKKRPKMAIIPTGTTNDFARALKVPRGNPSQAAKLIGKNQTIQMDIGRAKKDTYFINIAAA
GSLTELTYSVPSQLKTMFGYLAYLAKGVELLPRVSNVPVKITHDKGVFEGQVSMIFAAITNSVGGFEMIA
PDAKLDDGMFTLILIKTANLFEIVHLLRLILDGGKHITDRRVEYIKTSKIVIEPQCGKRMMINLDGEYGG
DAPITLENLKNHITFFADTDLISDDALVLDQDELEIEEIVKKFAHEVEDLEQELEE
>AB_3 200bp
MTGYDDFNYALSALKLGADDYLLKPFSKADVEDMLGKLRKKLELSKKTETIQELVEQPQKEVSAIAMAIH
ERLADSDLTLKSLAQQLGFSPNYLSVLIKKELGMPFQDYLVQERLKKAKLFLLTSNLKIYEIAEQVGFED
MNYFSQRFKQLVGVTPSQYKKGGQA
>AB_4 200bp
MRARLIYNPTSGQELMRKSVPEVLDILEGFGYETSAFQTTAKKNSALNEARRAAKAGFDLLIAAGGDGTI
NEVVNGIAPLKKRPKMAIIPTGTTNDFARALKVPRGNPSQAAKLIGKNQTIQMDIGRAKKDTYFINIAAA
GSLTELTYSVPSQLKTMFGYLAYLAKGVELLPRVSNVPVKITHDKGVFEGQVSMIFAAITNSVGGFEMIA
PDAKLDDGMFTLILIKTANLFEIVHLLRLILDGGKHITDRRVEYIKTSKIVIEPQCGKRMMINLDGEYGG
DAPITLENLKNHITFFADTDLISDDALVLDQDELEIEEIVKKFAHEVEDLEQELEE
>AB_5 200bp
MRARLIYNPTSGQELMRKSVPEVLDILEGFGYETSAFQTTAKKNSALNEARRAAKAGFDLLIAAGGDGTI
NEVVNGIAPLKKRPKMAIIPTGTTNDFARALKVPRGNPSQAAKLIGKNQTIQMDIGRAKKDTYFINIAAA
GSLTELTYSVPSQLKTMFGYLAYLAKGVELLPRVSNVPVKITHDKGVFEGQVSMIFAAITNSVGGFEMIA
PDAKLDDGMFTLILIKTANLFEIVHLLRLILDGGKHITDRRVEYIKTSKIVIEPQCGKRMMINLDGEYGG
DAPITLENLKNHITFFADTDLISDDALVLDQDELEIEEIVKKFAHEVEDLEQELEE

I would like to edit these files such a way that the data below so that the file will look like

>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

That is remove every thing after >AB_1 ..same with >AB_2....etc
Please let me know the best way to do it using awk or sed as I have to edit hundred's of files.
LA

2 
ls *.fasta | xargs sed -i .b 's/ [^ ]*bp//'

This will change your file as expected and it will keep a backup copy *.b of the original file
you can then rm *.b if you want to remove the backup of the initial files
or you can rollback to your initial file from the backup copy:

cat 3.fasta.b >3.fasta
3

Hi,
Actually there is a space between 200 and bp. The above code you suggested only removed the bp. I would like to remove the entire thing (200 bp). That is any thing after >AB_1 ... >AB_2..etc
LA

---------- Post updated at 06:00 PM ---------- Previous update was at 05:50 PM ----------

Hi
I think I got it now. I first ran your code and repeated the same code again why replacing bp with *\d.

ls *.fasta | xargs sed -i .b 's/ [^ ]*\d*//'

I think it worked

4

Not sure, if your file have space in the content not only in line ">"

Here is the command which will only remove the bp part in line ">"

ls *.fasta | xargs sed -i  '/>/ s/ .*//'

you can also run by (but both can't update the file directly. you need generate temp file, and rename it back.)

awk 'NF=1' 1.fasta
cut -f1 1.fasta
5

In your file, is the following :

>AB_1 200bp
MLKKPIIIGVTGGSGGGKTSVSRAILDSFPNARIAMIQHDSYYKDQSHMSFEERVKTNYDHPLAFDTDFM
IQQLKELLAGRPVDIPIYDYKKHTRSNTTFRQDPQDVIIVEGILVLEDERLRDLMDIKLFVDTDDDIRII
RRIKRDMMERGRSLESIIDQYTSVVKPMYHQFIEPSKRYADIVIPEGVSNVVAIDVINSKIASILGEV

1 long line or 4 lines ?