Delete specific strings in a file

UNIX for Beginners Q & A UNIX for Dummies Questions & Answers
1

Hi,
My file has a numerous sttrings.I want to retain those strings which start with stt and delete entries with >C
For eg:
my infile is

>C4603985
ATGFFGTGFAGGHTGHTAHGHATAGGTHTTHAHAGHGCHATCACCTGCGATATGGGGGCCACCATAGATAGTAAAGATGGTTCTTACCFAGATGFFGTGFAGGHTGHTAHGHATAGGTFAGATGFFGTGFAGGHTGHTAHGHATAGGTFAGATGFFGTGFAGGHTGH>C3914137
CATCTTGFFGTGFAGGHTGHTAHGHATAGGTHTTHAHAGHGCHTTATTAGGGAAGAAACCTTCATTCTCTTTTTAATTTTCTTTTTCAAGATGCAATTGFFGTGFAGGHTGHTAHGHATAGGTHTTHAHAGHGCHCTGTATCACCAGTTATATATAGATTGCATCTTGATATAGATATAGTG
>stt4468869
SQAERTYUVSAASSFFAGATGFFGTGFAGGHTGHTAHGHATAGGTHTTHAHAGHGCHAHAHGHACTHTGHTGGHCAHAANGGGATATAACCAGGTGGAAGGTAGACTACTTTGATAGTTTTTCTCCAGTNGNGCANAAGTTAGTAACAGTGAGAATTTTCTTAGCAATCGCAG
>C4913369
GTERTYUVSAASSFFAGATGFFGTGFAGGHTGHTAHGHATAGGTTGCVTCABGCGBATBAAGATBTBTHYHBHHTAGCGCCCTACGTACGATGCAGTAAATTCCGTAACGTAGTGGTTGAGATATCTCAGTAAGCTTCACGTTGACGTTAGTTBTBTAATCGCCCGTGATGDDDGTGTTAGAATGTTTAAAGGATATACAT
>stt4688097
GCDDDDCJJJJAWDDDDFFFFFCTCATATCGCAGGTGATTCCAACAGATCGCATGAGAGGTATGTCCGAGAGGCAAATCATTCTTTTCGGCTCTATGGATCCGAAGGACCTGCGAAAAGGGCAAAACCGACCTCGGACGAGATTGTGTTTACGGACGAGCATGAGAGGTATGTCCGAGAGGCAAATCATTCTTTTCGGCTCTATGGATCCGAAG

My outfile should look like

>stt4468869
SQAERTYUVSAASSFFAGATGFFGTGFAGGHTGHTAHGHATAGGTHTTHAHAGHGCHAHAHGHACTHTGHTGGHCAHAANGGGATATAACCAGGTGGAAGGTAGACTACTTTGATAGTTTTTCTCCAGTNGNGCANAAGTTAGTAACAGTGAGAATTTTCTTAGCAATCGCAG
>stt4688097
GCDDDDCJJJJAWDDDDFFFFFCTCATATCGCAGGTGATTCCAACAGATCGCATGAGAGGTATGTCCGAGAGGCAAATCATTCTTTTCGGCTCTATGGATCCGAAGGACCTGCGAAAAGGGCAAAACCGACCTCGGACGAGATTGTGTTTACGGACGAGCATGAGAGGTATGTCCGAGAGGCAAATCATTCTTTTCGGCTCTATGGATCCGAAG

Any suggestions?:wall:

2

Try

 
 $ cat  tmp
 >C4603985
 ATGFFGTGFAGGHTGHTAHGHATAGGTHTTHAHAGHGCHATCACCTGCGATATGGGGGCCACCATAGATAGTAAAGATGGTTCTTACCFAGATGFFGTGFAGGHTGHTAHGHATAGGTFAGATGFFGTGFAGGHTGHTAHGHATAGGTFAGATGFFGTGFAGGHTGH>C3914137
 CATCTTGFFGTGFAGGHTGHTAHGHATAGGTHTTHAHAGHGCHTTATTAGGGAAGAAACCTTCATTCTCTTTTTAATTTTCTTTTTCAAGATGCAATTGFFGTGFAGGHTGHTAHGHATAGGTHTTHAHAGHGCHCTGTATCACCAGTTATATATAGATTGCATCTTGATATAGATATAGTG
 >stt4468869
 SQAERTYUVSAASSFFAGATGFFGTGFAGGHTGHTAHGHATAGGTHTTHAHAGHGCHAHAHGHACTHTGHTGGHCAHAANGGGATATAACCAGGTGGAAGGTAGACTACTTTGATAGTTTTTCTCCAGTNGNGCANAAGTTAGTAACAGTGAGAATTTTCTTAGCAATCGCAG
 >C4913369
 GTERTYUVSAASSFFAGATGFFGTGFAGGHTGHTAHGHATAGGTTGCVTCABGCGBATBAAGATBTBTHYHBHHTAGCGCCCTACGTACGATGCAGTAAATTCCGTAACGTAGTGGTTGAGATATCTCAGTAAGCTTCACGTTGACGTTAGTTBTBTAATCGCCCGTGATGDDDGTGTTAGAATGTTTAAAGGATATACAT
 >stt4688097
 GCDDDDCJJJJAWDDDDFFFFFCTCATATCGCAGGTGATTCCAACAGATCGCATGAGAGGTATGTCCGAGAGGCAAATCATTCTTTTCGGCTCTATGGATCCGAAGGACCTGCGAAAAGGGCAAAACCGACCTCGGACGAGATTGTGTTTACGGACGAGCATGAGAGGTATGTCCGAGAGGCAAATCATTCTTTTCGGCTCTATGGATCCGAAG
 
 $ awk '{ if ( $0~/>st/ ) {
 > a=1
 > }
 > if ( $0 ~/>C/ ) {
 > a=0}
 > if ( a==1)
 > print $0
 > }' tmp
 >stt4468869
 SQAERTYUVSAASSFFAGATGFFGTGFAGGHTGHTAHGHATAGGTHTTHAHAGHGCHAHAHGHACTHTGHTGGHCAHAANGGGATATAACCAGGTGGAAGGTAGACTACTTTGATAGTTTTTCTCCAGTNGNGCANAAGTTAGTAACAGTGAGAATTTTCTTAGCAATCGCAG
 >stt4688097
 GCDDDDCJJJJAWDDDDFFFFFCTCATATCGCAGGTGATTCCAACAGATCGCATGAGAGGTATGTCCGAGAGGCAAATCATTCTTTTCGGCTCTATGGATCCGAAGGACCTGCGAAAAGGGCAAAACCGACCTCGGACGAGATTGTGTTTACGGACGAGCATGAGAGGTATGTCCGAGAGGCAAATCATTCTTTTCGGCTCTATGGATCCGAAG
3

senhia83's script can be simplified a little bit to something like:

awk '
/^>/ { copy = ($0 ~ /^>stt/) }
copy' infile

As always, if you want to try this on a Solaris/SunOS system, change awk to /usr/xpg4/bin/awk , /usr/xpg6/bin/awk , or nawk .

4

You can try:

awk 'NF&&!/^C/{print ">"$0}' ORS="" RS=">"
5

Hello sa@@,

One more approach may help you, very slightly different from Don's and Senhia83's script. Enjoy learning :b:

awk '/^>stt/ {A=1} A{print} !/^>stt/ {A=0}' Input_file

Output will be as follows.

>stt4468869
SQAERTYUVSAASSFFAGATGFFGTGFAGGHTGHTAHGHATAGGTHTTHAHAGHGCHAHAHGHACTHTGHTGGHCAHAANGGGATATAACCAGGTGGAAGGTAGACTACTTTGATAGTTTTTCTCCAGTNGNGCANAAGTTAGTAACAGTGAGAATTTTCTTAGCAATCGCAG
>stt4688097
GCDDDDCJJJJAWDDDDFFFFFCTCATATCGCAGGTGATTCCAACAGATCGCATGAGAGGTATGTCCGAGAGGCAAATCATTCTTTTCGGCTCTATGGATCCGAAGGACCTGCGAAAAGGGCAAAACCGACCTCGGACGAGATTGTGTTTACGGACGAGCATGAGAGGTATGTCCGAGAGGCAAATCATTCTTTTCGGCTCTATGGATCCGAAG

Thanks,
R. Singh

6

@sa@@: your sample contains a multiline sequence

Shouldn't the input file be:

>C4603985
ATGFFGTGFAGGHTGHTAHGHATAGGTHTTHAHAGHGCHATCACCTGCGATATGGGGGCCACCATAGATAGTAAAGATGGTTCTTACCFAGATGFFGTGFAGGHTGHTAHGHATAGGTFAGATGFFGTGFAGGHTGHTAHGHATAGGTFAGATGFFGTGFAGGHTGH
>C3914137
CATCTTGFFGTGFAGGHTGHTAHGHATAGGTHTTHAHAGHGCHTTATTAGGGAAGAAACCTTCATTCTCTTTTTAATTTTCTTTTTCAAGATGCAATTGFFGTGFAGGHTGHTAHGHATAGGTHTTHAHAGHGCHCTGTATCACCAGTTATATATAGATTGCATCTTGATATAGATATAGTG
>stt4468869
SQAERTYUVSAASSFFAGATGFFGTGFAGGHTGHTAHGHATAGGTHTTHAHAGHGCHAHAHGHACTHTGHTGGHCAHAANGGGATATAACCAGGTGGAAGGTAGACTACTTTGATAGTTTTTCTCCAGTNGNGCANAAGTTAGTAACAGTGAGAATTTTCTTAGCAATCGCAG
>C4913369
GTERTYUVSAASSFFAGATGFFGTGFAGGHTGHTAHGHATAGGTTGCVTCABGCGBATBAAGATBTBTHYHBHHTAGCGCCCTACGTACGATGCAGTAAATTCCGTAACGTAGTGGTTGAGATATCTCAGTAAGCTTCACGTTGACGTTAGTTBTBTAATCGCCCGTGATGDDDGTGTTAGAATGTTTAAAGGATATACAT
>stt4688097
GCDDDDCJJJJAWDDDDFFFFFCTCATATCGCAGGTGATTCCAACAGATCGCATGAGAGGTATGTCCGAGAGGCAAATCATTCTTTTCGGCTCTATGGATCCGAAGGACCTGCGAAAAGGGCAAAACCGACCTCGGACGAGATTGTGTTTACGGACGAGCATGAGAGGTATGTCCGAGAGGCAAATCATTCTTTTCGGCTCTATGGATCCGAAG

--
@Ravinder. That works if there are no multiline sequences.

7

This is a protein sequence fasta file, pretty sure the sequences are in one line unless word wrapped

8

FASTA format