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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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RE_COMP(3)						     Linux Programmer's Manual							RE_COMP(3)

NAME
re_comp, re_exec - BSD regex functions SYNOPSIS
#define _REGEX_RE_COMP #include <sys/types.h> #include <regex.h> char *re_comp(char *regex); int re_exec(char *string); DESCRIPTION
re_comp() is used to compile the null-terminated regular expression pointed to by regex. The compiled pattern occupies a static area, the pattern buffer, which is overwritten by subsequent use of re_comp(). If regex is NULL, no operation is performed and the pattern buffer's contents are not altered. re_exec() is used to assess whether the null-terminated string pointed to by string matches the previously compiled regex. RETURN VALUE
re_comp() returns NULL on successful compilation of regex otherwise it returns a pointer to an appropriate error message. re_exec() returns 1 for a successful match, zero for failure. CONFORMING TO
4.3BSD. NOTES
These functions are obsolete; the functions documented in regcomp(3) should be used instead. SEE ALSO
regcomp(3), regex(7), GNU regex manual COLOPHON
This page is part of release 3.44 of the Linux man-pages project. A description of the project, and information about reporting bugs, can be found at http://www.kernel.org/doc/man-pages/. GNU
1995-07-14 RE_COMP(3)
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