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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 OPENSOLARIS

adjmsg

adjmsg(9F)						   Kernel Functions for Drivers 						adjmsg(9F)

NAME

       adjmsg - trim bytes from a message

SYNOPSIS

       #include <sys/stream.h>

       int adjmsg(mblk_t *mp, ssize_t len);

INTERFACE LEVEL

       Architecture independent level 1 (DDI/DKI).

PARAMETERS

       mp     Pointer to the message to be trimmed.

       len    The number of bytes to be removed.

DESCRIPTION

       The  adjmsg()  function	removes  bytes	from a message. |len| (the absolute value of len) specifies the number of bytes to be removed. The
       adjmsg() function only trims bytes across message blocks of the same type.

       The adjmsg() function finds the maximal leading sequence of message blocks of the same type as that of mp and starts removing bytes  either
       from  the  head	of that sequence or from the tail of that sequence. If len is greater than 0, adjmsg() removes bytes from the start of the
       first message block in that sequence. If len is less than 0, it removes bytes from the end of the last message block in that sequence.

       The adjmsg() function fails if |len| is greater than the number of bytes in the maximal leading sequence it finds.

       The adjmsg() function may remove any except the first zero-length message block created during adjusting. It  may  also	remove	any  zero-
       length message blocks that occur within the scope of |len|.

RETURN VALUES

       The adjmsg() function returns:

       1    Successful completion.

       0    An error occurred.

CONTEXT

       The adjmsg() function can be called from user, interrupt, or kernel context.

SEE ALSO

       STREAMS Programming Guide

SunOS 5.11							    16 Jan 2006 							adjmsg(9F)
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