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Top Forums UNIX for Dummies Questions & Answers read regex from ID file, print regex and line below from source file Post 302712145 by pathunkathunk on Monday 8th of October 2012 07:12:09 PM
Old 10-08-2012
read regex from ID file, print regex and line below from source file

I have a file of protein sequences with headers (my source file). Based on a list of IDs (which are included in some of the headers), I'd like to print out only the specified sequences, with only the ID as header.

In other words, I'd like to search source.txt for the terms in IDs.txt, and print the ID as well as the sequence. Ideally the process would continue even if an ID is not found in the source file. All headers in source.txt are of similar format.

source.txt
Quote:
>m.49518 g.49518 ORF g.49518 m.49518 type:internal len:169 (-) comp100001_c0_seq1:3-509(-)
FHPPVSDSCKRCDMYKNQIKIAPENEKIQLNADHELHLRKAESARNGMNNDVELCKTDPNKVTVIAFDLMKTLSTPSLSVGVAYYKRQLSTYNLGIHNLT TNDAYMYVWNESMASRGPQEIGSCLLHFIKNYVHTEQLIMYSDQCGGQNRNIKMALICNFVVGSNDYLP
>m.54555 g.54555 ORF g.54555 m.54555 type:internal len:137 (+) comp1001102_c0_seq1:3-416(+)
YGDLDDSALDAEGPAGPVYRFSRRKSDTKSDDNSQSNGEGVMMMINGELVKVEQLKREEIINCTCGYTEEDGLMIQCDLCLCWQHGHCNGIEREKDVPEK YICYICSHPYRQRPSRKYIHDQDWIKEGKLVSLTKRK
>m.54557 g.54557 ORF g.54557 m.54557 type:internal len:113 (+) comp1002314_c0_seq1:2-343(+)
SIKARQIYDSRGNPTVEVDLVTENGLFRAAVPSGASTGVHEALELRDNDKSMYHGKSVFKAVDNINSIIAPELLKANIEVTEQAEIDNFLLKLDGTPNKS KLGANAILGVSLA
IDs.txt
Quote:
comp100001_c0_seq1
comp1002314_c0_seq1
desired output:
Quote:
>comp100001_c0_seq1
FHPPVSDSCKRCDMYKNQIKIAPENEKIQLNADHELHLRKAESARNGMNNDVELCKTDPNKVTVIAFDLMKTLSTPSLSVGVAYYKRQLSTYNLGIHNLT TNDAYMYVWNESMASRGPQEIGSCLLHFIKNYVHTEQLIMYSDQCGGQNRNIKMALICNFVVGSNDYLP
>comp1002314_c0_seq1
SIKARQIYDSRGNPTVEVDLVTENGLFRAAVPSGASTGVHEALELRDNDKSMYHGKSVFKAVDNINSIIAPELLKANIEVTEQAEIDNFLLKLDGTPNKS KLGANAILGVSLA
I am able to pull out the sequences based on the ID one-by-one, but this is slow and doesn't give me the header.
Code:
awk '/comp51893_c0_seq1/ { getline; print $0 }' source.txt

I also tried extracting the entire header and the sequence by modifying a script I had for a sequence file with different header type, but again it's one-by-one it only prints the header.
Code:
awk '{lines[NR] = $0} /comp47911_c0_seq1/ {print lines [NR]; print lines [NR+1]}' source.txt

As is probably clear, I'm still pretty low on the learning curve. Any help would be really appreciated!
 

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cgiSetHeader(3) 						Programmer's Manual						   cgiSetHeader(3)

NAME
cgiSetHeader - Specify an additional HTTP header SYNOPSYS
#include <cgi.h> int cgiSetHeader (char *name, char *value); DESCRIPTION
With the cgiSetHeader routine you may specify additional HTTP header lines such as Expires: or Pragma:. The order of header lines withing the HTTP header has no significance. You may call this routine multiple times to set multiple headers. They will be printed in the same order as specified, however, after the Content-type: header. This routine will only add the header to the internal stack, not print it. They will be printed by cgiHeader(3). This routine does some syntax checking before accepting a new header. The name of a header must not contain any newline, space or colon, otherwise it will be truncated. The value must not contain any newline, otherwise it will be truncated as well. To set a cookie in your program you'll need to manually add additional header lines. Please take a look at cgitest.c. Basically, you'll need to add the following code: cgiSetHeader ("Set-Cookie", "Version=1; name=value; Path=/"); cgiHeader(); Please read the included file cookies.txt as well. RETURN VALUE
On success 1 is returned, otherwise 0. AUTHOR
This CGI library is written by Martin Schulze <joey@infodrom.org>. If you have additions or improvements please get in touch with him. SEE ALSO
cgiHeader(3), cgiGetCookies(3), cgiGetCookie(3), cgiInit(3). CGI Library 6 April 2008 cgiSetHeader(3)
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