10-08-2012
jim, thanks for taking a look.
Using the code you provide, I get the following in terminal:
Quote:
awk: illegal primary in regular expression >m.54555 g.54555 ORF g.54555 m.54555 type:internal len:137 (+) comp1001102_c0_seq1:3-416(+) at ) comp1001102_c0_seq1:3-416(+)
input record number 3, file source.txt
source line number 3
cat newfile returns:
Quote:
> comp100001_c0_seq1
comp1002314_c0_seq1
>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(+)
Just to verify, here are the input files:
Quote:
$ cat source.txt
>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
$ cat ID.txt
comp100001_c0_seq1
comp1002314_c0_seq1
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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)