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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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BCP(1)							 Boost C++ Libraries Documentation						    BCP(1)

NAME
bcp - extract subsets of Boost SYNOPSIS
bcp --list [options] module-list bcp [options] module-list output-path bcp --report [options] module-list html-file bcp --help DESCRIPTION
Copies all the files, including dependencies, found in module-list to output-path. output-path must be an existing path. With --list, prints the list of all the files in module-list, including dependencies. With --report, writes the HTML report to html-file. With --help, prints a quick usage reminder. It is useful for Boost authors who want to distribute their library separately from Boost and for Boost users who want to distribute a sub- set of Boost with their application. module-list When the --scan option is not used, a list of Boost files or library names to copy. It can be: - The name of a tool: for example "build" will find "tools/build". - The name of a library: for example "regex". - The title of a header: for example "scoped_ptr" will find "boost/scoped_ptr.hpp". - The name of a header: for example "scoped_ptr.hpp" will find "boost/scoped_ptr.hpp". - The name of a file: for example "boost/regex.hpp". When the --scan option is used, a list of (probably non-boost) files to scan for Boost dependencies, the files in the module list are not therefore copied/listed. File dependencies C++ source files are scanned for #includes, all #includes present in the Boost source tree will then be scanned for their dependencies and so on. C++ source files are associated with the name of a library, if that library has source code (and possibly build data), then include that source in the dependencies. C++ source files are checked for dependencies on Boost.Test (for example to see if they use cpp_main as an entry point). HTML files are scanned for immediate dependencies (images and style sheets, but not links). HTML report contains: - all the licenses in effect, plus the files using each license, and the copyright holders using each license - any files with no recognizable license (please report these to the Boost mailing lists) - any files with no recognizable copyright holders (please report these to the Boost mailing lists) - all the copyright holders and the files on which they hold copyright - file dependency information - indicates the reason for the inclusion of any particular file in the dependencies found OPTIONS
--boost=path sets the location of the Boost tree to path --scan treat the module list as a list of (possibly non-boost) files to scan for Boost dependencies --cvs only copy files under CVS version control --unix-lines make sure that all copied files use Unix style line endings EXAMPLES
bcp scoped_ptr /foo Copies boost/scoped_ptr.hpp and dependencies to /foo. bcp boost/regex.hpp /foo Copies boost/regex.hpp and all dependencies including the regex source code (in libs/regex/src) and build files (in libs/regex/build) to /foo. Does not copy the regex documentation, test or example code. bcp regex /foo Copies the full regex lib (in libs/regex) including dependencies (such as the Boost.Test source required by the regex test programs) to /foo. bcp regex config build /foo Copies the full regex lib (in libs/regex) plus the config lib (libs/config) and the build system (tools/build) to /foo including all the dependencies. bcp --scan --boost=/boost foo.cpp bar.cpp boost Scans the [non-boost] files foo.cpp and bar.cpp for Boost dependencies and copies those dependencies to the sub-directory boost. bcp --report regex.hpp boost-regex-report.html Creates a HTML report called boost-regex-report.html for the Boost module regex.hpp. AUTHORS
Author of bcp is John Maddock. Author of this manpage is Domenico Andreoli, who copied stuff from bcp --help and the HTML documentation. Boost C++ Libraries March 2006 BCP(1)
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