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 CENTOS
tpm_quote_tools
TPM QUOTE
TOOLS(8) TPM QUOTE TOOLS(8)
NAME
TPM Quote Tools
PROGRAMS
tpm_mkuuid, tpm_mkaik, tpm_loadkey, tpm_unloadkey, tpm_getpcrhash, tpm_updatepcrhash, tpm_getquote, tpm_verifyquote
DESCRIPTION
TPM Quote Tools is a collection of programs that provide support for TPM based attestation using the TPM quote operation.
A TPM contains a set of Platform Configuration Registers (PCRs). In a well configured machine, some of these registers are set to known
values during the boot up process or at other times. For example, a PCR might contain the hash of a boot loader in memory before it is
run.
The TPM quote operation is used to authoritatively verify the contents of a TPM's Platform Configuration Registers (PCRs). During provi-
sioning, a composite hash of a selected set of PCRs is computed. The TPM quote operation produces a composite hash that can be compared
with the one computed while provisioning.
To use the TPM quote operation, keys must be generated. During provisioning, an Attestation Identity Key (AIK) is generated for each TPM,
and the public part of the key is made available to entities that validate quotes.
The TPM quote operation returns signed data and a signature. The data that is signed contains the PCRs selected for the operation, the
composite hash for the selected PCRs, and a nonce provided as input, and used to prevent replay attacks. At provisioning time, the data
that is signed is stored, not just the composite hash. The signature is discarded.
An entity that wishes to evaluate a machine generates a nonce, and sends it along with the set of PCR used to generate the composite PCR
hash at provisioning time. For this use of the TPM quote operation, the signed data is ignored, and the signature returned is used to val-
idate the state of the TPM's PCRs. Given the signature, the evaluating entity replaces the nonce in the signed data generated at provi-
sioning time, and checks to see if the signature is valid for the data. If so, this check ensures the selected PCRs contain values that
match the ones measured during provisioning.
A typical scenario for an enterprise using these tools follows. The tools expect AIKs to be referenced via one enterprise-wide Universally
Unique Identifier (UUID). The program tpm_mkuuid creates one.
For each machine being checked, an AIK is created using tpm_mkaik. The key blob produced is bound to the UUID on its machine using
tpm_loadkey. The public key associated with the AIK is sent to the entities that verify quotes. Finally, the expected PCR composite hash
is obtained using tpm_getpcrhash. When the expected PCR values change, a new hash can be generated with tpm_updatepcrhash.
The program to obtain a quote, and thus measure the current state of the PCRs is tpm_getquote. The program that verifies the quote
describes the same PCR composite hash as was measured initially is tpm_verifyquote.
SEE ALSO
tpm_mkuuid(8), tpm_mkaik(8), tpm_loadkey(8), tpm_unloadkey(8), tpm_getpcrhash(8), tpm_updatepcrhash(8), tpm_getquote(8), tpm_verifyquote(8)
Oct 2010 TPM QUOTE TOOLS(8)