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Full Discussion: read regex from ID file, print regex and line below from source file
Top Forums UNIX for Dummies Questions & Answers read regex from ID file, print regex and line below from source file Post 302712149 by pathunkathunk on Monday 8th of October 2012 07:45:53 PM
Old 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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LEARN ABOUT DEBIAN

gd_get_string

gd_get_string(3)						      GETDATA							  gd_get_string(3)

NAME

       gd_get_string -- retrieve a string from a dirfile database

SYNOPSIS

       #include <getdata.h>

       size_t gd_get_string(DIRFILE *dirfile, const char *field_code, size_t len, char *data_out);

DESCRIPTION

       The  gd_get_string() function queries a dirfile(5) database specified by dirfile for the string scalar field_code, which should not contain
       a representation suffix.  The first len characters of the string scalar are stored in the user-supplied buffer data_out.

       The dirfile argument must point to a valid DIRFILE object previously created by a call to gd_open(3).

       If len equals zero, or if data_out equals NULL, no data will be copied to data_out, but the length of the string scalar will still  be  re-
       turned  by gd_get_string().  Otherwise, the argument data_out must point to a valid memory location of sufficient size to hold at least len
       characters.  If the length of the string scalar is greater than len, data_out will not be NULL-terminated.

RETURN VALUE

       On success, gd_get_string() returns the actual length of the specified string scalar, including the trailing NULL character.  A return val-
       ue greater than len indicates that the output string is not null terminated.

       On error, it returns 0 and sets the dirfile error to a non-zero value.  Possible error values are:

       GD_E_BAD_CODE
	       The field specified by field_code was not found in the database.

       GD_E_BAD_DIRFILE
	       An invalid dirfile was supplied.

       GD_E_BAD_FIELD_TYPE
	       The  supplied field_code referred to a field of type other than STRING.	The caller should use gd_getdata(3), or gd_get_constant(3)
	       instead.

       GD_E_BAD_TYPE
	       An invalid return_type was specified.

       GD_E_INTERNAL_ERROR
	       An internal error occurred in the library while trying to perform the task.  This indicates a bug in the  library.   Please  report
	       the incident to the maintainer.

       The  dirfile error may be retrieved by calling gd_error(3).  A descriptive error string for the last error encountered may be obtained from
       a call to gd_error_string(3).

SEE ALSO

       dirfile(5), gd_open(3), gd_error(3), gd_error_string(3), gd_put_string(3)

Version 0.7.0							    25 May 2010 						  gd_get_string(3)
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