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Delete specific strings in a file

 
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# 1  
Old 01-10-2015
Delete specific strings in a file
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

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

My outfile should look like

Code:
>stt4468869
SQAERTYUVSAASSFFAGATGFFGTGFAGGHTGHTAHGHATAGGTHTTHAHAGHGCHAHAHGHACTHTGHTGGHCAHAANGGGATATAACCAGGTGGAAGGTAGACTACTTTGATAGTTTTTCTCCAGTNGNGCANAAGTTAGTAACAGTGAGAATTTTCTTAGCAATCGCAG
>stt4688097
GCDDDDCJJJJAWDDDDFFFFFCTCATATCGCAGGTGATTCCAACAGATCGCATGAGAGGTATGTCCGAGAGGCAAATCATTCTTTTCGGCTCTATGGATCCGAAGGACCTGCGAAAAGGGCAAAACCGACCTCGGACGAGATTGTGTTTACGGACGAGCATGAGAGGTATGTCCGAGAGGCAAATCATTCTTTTCGGCTCTATGGATCCGAAG


Any suggestions?Smilie
# 2  
Old 01-10-2015
Try
Code:
 
 $ 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

This User Gave Thanks to senhia83 For This Post:
sa@@
# 3  
Old 01-10-2015
senhia83's script can be simplified a little bit to something like:
Code:
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.
This User Gave Thanks to Don Cragun For This Post:
sa@@
# 4  
Old 01-10-2015
You can try:

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

This User Gave Thanks to pilnet101 For This Post:
sa@@
# 5  
Old 01-11-2015
Hello sa@@,

One more approach may help you, very slightly different from Don's and Senhia83's script. Enjoy learning Smilie
Code:
awk '/^>stt/ {A=1} A{print} !/^>stt/ {A=0}' Input_file

Output will be as follows.
Code:
>stt4468869
SQAERTYUVSAASSFFAGATGFFGTGFAGGHTGHTAHGHATAGGTHTTHAHAGHGCHAHAHGHACTHTGHTGGHCAHAANGGGATATAACCAGGTGGAAGGTAGACTACTTTGATAGTTTTTCTCCAGTNGNGCANAAGTTAGTAACAGTGAGAATTTTCTTAGCAATCGCAG
>stt4688097
GCDDDDCJJJJAWDDDDFFFFFCTCATATCGCAGGTGATTCCAACAGATCGCATGAGAGGTATGTCCGAGAGGCAAATCATTCTTTTCGGCTCTATGGATCCGAAGGACCTGCGAAAAGGGCAAAACCGACCTCGGACGAGATTGTGTTTACGGACGAGCATGAGAGGTATGTCCGAGAGGCAAATCATTCTTTTCGGCTCTATGGATCCGAAG

Thanks,
R. Singh
This User Gave Thanks to RavinderSingh13 For This Post:
sa@@
# 6  
Old 01-11-2015
@sa@@: your sample contains a multiline sequence

Shouldn't the input file be:
Code:
>C4603985
ATGFFGTGFAGGHTGHTAHGHATAGGTHTTHAHAGHGCHATCACCTGCGATATGGGGGCCACCATAGATAGTAAAGATGGTTCTTACCFAGATGFFGTGFAGGHTGHTAHGHATAGGTFAGATGFFGTGFAGGHTGHTAHGHATAGGTFAGATGFFGTGFAGGHTGH
>C3914137
CATCTTGFFGTGFAGGHTGHTAHGHATAGGTHTTHAHAGHGCHTTATTAGGGAAGAAACCTTCATTCTCTTTTTAATTTTCTTTTTCAAGATGCAATTGFFGTGFAGGHTGHTAHGHATAGGTHTTHAHAGHGCHCTGTATCACCAGTTATATATAGATTGCATCTTGATATAGATATAGTG
>stt4468869
SQAERTYUVSAASSFFAGATGFFGTGFAGGHTGHTAHGHATAGGTHTTHAHAGHGCHAHAHGHACTHTGHTGGHCAHAANGGGATATAACCAGGTGGAAGGTAGACTACTTTGATAGTTTTTCTCCAGTNGNGCANAAGTTAGTAACAGTGAGAATTTTCTTAGCAATCGCAG
>C4913369
GTERTYUVSAASSFFAGATGFFGTGFAGGHTGHTAHGHATAGGTTGCVTCABGCGBATBAAGATBTBTHYHBHHTAGCGCCCTACGTACGATGCAGTAAATTCCGTAACGTAGTGGTTGAGATATCTCAGTAAGCTTCACGTTGACGTTAGTTBTBTAATCGCCCGTGATGDDDGTGTTAGAATGTTTAAAGGATATACAT
>stt4688097
GCDDDDCJJJJAWDDDDFFFFFCTCATATCGCAGGTGATTCCAACAGATCGCATGAGAGGTATGTCCGAGAGGCAAATCATTCTTTTCGGCTCTATGGATCCGAAGGACCTGCGAAAAGGGCAAAACCGACCTCGGACGAGATTGTGTTTACGGACGAGCATGAGAGGTATGTCCGAGAGGCAAATCATTCTTTTCGGCTCTATGGATCCGAAG

--
@Ravinder. That works if there are no multiline sequences.
Last edited by Scrutinizer; 01-11-2015 at 02:35 AM..
# 7  
Old 01-11-2015
This is a protein sequence fasta file, pretty sure the sequences are in one line unless word wrapped
 
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