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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 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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X86DIS(1)							     libdisasm								 X86DIS(1)

NAME
x86dis - disassemble a bytestream of Intel x86 instructions SYNTAX
x86dis [-a offset|--addr=offset] [-r offset len|--range=offset len] [-e offset|--entry=offset] [-s name|--syntax=name] [-d name|--desc=name] [-f file|--file=file] [-o file|--out=file] [-l file|--log=file] [-p num|--pagesize=num] [-h|-?|--help] [-v|--version] DESCRIPTION
A command-line interface to the libdisasm disassembler library. OPTIONS
At least one option from the list -a, -e, -r must be given. -f, --file=file Read input bytes from file instead of stdin -o, --out=file Write output to file instead of stdout -l, --log=file Log errors to file instead of stderr -p, --pagesize=num Set page size for buffering STDIN to num (default 512K) -s, --syntax=name Set output syntax to name, where name is one of intel (Intel syntax), att (AT&T syntax), raw (libdisasm syntax) -d, --desc=name Print a description of syntax name -a, --addr=offset Disassemble single instruction at offset -e, --entry=offset Disassemble forward from offset -r, --range=offset len Disassemble len bytes starting at offset All offset and len parameters are expected to follow the conventions used in strtoul(3), where hexadecimal numbers have the prefix 0x, octal numbers have the prefix 0, and decimal numbers have no prefix. A value of 0 for len indicates that that range extends to the end of the file. EXAMPLES
cat `which ls` | x86dis -s intel -e 0x00 -r 0x00 -1 -a 0xEEEE x86dis -e 0 -s intel < bootsect.img x86dis -d -s raw -f a.out -e `readelf -h a.out | grep Entry | awk '{ printf( "0x%%x", strtonum($4) - 0x8048000 ) }` echo '55 89 e5 83 EC 08' | perl -ane 'foreach(@F){print pack("C",hex);}'| x86dis -e 0 -s att NOTES
x86dis performs no file format parsing, nor any verification that its input is in fact executable binary code. All offsets are assumed to be from the start of the file, with no load addresses applied. The intent is to provide a bytestream disassembler rather than an object file disassembler. Descriptions of the various output formats can be obtained using the -d option. AUTHORS
mammon_ <mammon_@users.sourceforge.net> SEE ALSO
bastard(1), libdisasm(7), x86_disasm(3), x86_format_insn(3), x86_init(3) mammon_ 0.21 X86DIS(1)
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