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Shell Programming and Scripting
extracting substrings
Post 302263158 by smriti_shridhar on Monday 1st of December 2008 01:34:05 AM
12-01-2008
extracting substrings
Hi guys,
I am stuck in this problem. Please help.
I have two files.
FILE1 (with records starting from '>' )
>TC1723_3 similar to Scific_A7Q9Q3
EMSPSQDYCDDYFKLTYPCTAGAQYYGRGALPVYWNYNYGAIGEALKLDLLNHPEYIEQN
ATMAFQAAIWRWMNPMKKGQPSAHDAFVGNWKP
>TC214_2 similar to Quiet_Ref100_Q8W2B2 Cluster; Capsule catabar holesome, partial (58%)
S**ELSSCY*QRRKMRYSFLIFLTLALLLTTSSAQQCGKQAGGRVCANKLCCSQYGFCGS
SRNYCGAGCQSNCRSVASGNTESEAANAHRKNLPGHSN*SCYSF*FTMNIIMFHVC*LLR
TTNKN
FILE2 ( with 3 columns, col1 is ID col2 and col3 are the substring co-ordinates). It is a single space separated file but shown with '-' for clarity
TC1723_3 - 10 - 40
TC214_2 - 5 - 115
I need the OUTPUT FILE as -
>TC1723_3 similar to Scific_A7Q9Q3 (Region 10 - 40 of 95)
DYFKLTYPCTAGAQYYGRGALPVYWNYNYGA
>TC214_2 similar to Quiet_Ref100_Q8W2B2 Cluster; n=1; Capsule catabar holesome, partial (58%) (Region 5 - 115 of 125)
SSCY*QRRKMRYSFLIFLTLALLLTTSSAQQCGKQAGGRVCANKLCCSQYGFCGSSRNYC
GAGCQSNCRSVASGNTESEAANAHRKNLPGHSN*SCYSF*FTMNIIMFHV
where (Region 10 - 40 of 95) represents region of substring and 95 is the total length of the subsring following the line beginning with '>'
Thanks in advance.
I am stuck in this problem. Please help.
I have two files.
FILE1 (with records starting from '>' )
>TC1723_3 similar to Scific_A7Q9Q3
EMSPSQDYCDDYFKLTYPCTAGAQYYGRGALPVYWNYNYGAIGEALKLDLLNHPEYIEQN
ATMAFQAAIWRWMNPMKKGQPSAHDAFVGNWKP
>TC214_2 similar to Quiet_Ref100_Q8W2B2 Cluster; Capsule catabar holesome, partial (58%)
S**ELSSCY*QRRKMRYSFLIFLTLALLLTTSSAQQCGKQAGGRVCANKLCCSQYGFCGS
SRNYCGAGCQSNCRSVASGNTESEAANAHRKNLPGHSN*SCYSF*FTMNIIMFHVC*LLR
TTNKN
FILE2 ( with 3 columns, col1 is ID col2 and col3 are the substring co-ordinates). It is a single space separated file but shown with '-' for clarity
TC1723_3 - 10 - 40
TC214_2 - 5 - 115
I need the OUTPUT FILE as -
>TC1723_3 similar to Scific_A7Q9Q3 (Region 10 - 40 of 95)
DYFKLTYPCTAGAQYYGRGALPVYWNYNYGA
>TC214_2 similar to Quiet_Ref100_Q8W2B2 Cluster; n=1; Capsule catabar holesome, partial (58%) (Region 5 - 115 of 125)
SSCY*QRRKMRYSFLIFLTLALLLTTSSAQQCGKQAGGRVCANKLCCSQYGFCGSSRNYC
GAGCQSNCRSVASGNTESEAANAHRKNLPGHSN*SCYSF*FTMNIIMFHV
where (Region 10 - 40 of 95) represents region of substring and 95 is the total length of the subsring following the line beginning with '>'
Thanks in advance.
Last edited by smriti_shridhar; 12-01-2008 at 02:38 AM.. Reason: formatting
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ldns-walk
ldns-walk(1) General Commands Manual ldns-walk(1) NAME
ldns-walk - Retrieve the contents of a DNSSEC signed zone SYNOPSIS
ldns-walk [ OPTION ] ZONE DESCRIPTION
ldns-walk is used to retrieve the contents of a DNSSEC signed zone. It does this through NSEC-walking (following the chain of NSEC records) and 'guessing' the next non-existent owner name for each NSEC. Note that it might get stuck on some wildcard records when used through a caching forwarder. This problem can be circumvented by querying the authoritative nameserver directly (with the @ argument). Of course the nameserver that is used must be DNSSEC-aware. OPTIONS
-4 Use only IPv4. -6 Use only IPv6. -f Do a 'full' zone walk; by default, ldns-walk will only show the names, and types present at those names. If this option is given, all resource records will be printed. -s name Start the walk with this owner name. Useful when continuing the walk for a large zone. -v verbosity Verbosity level [1-5]. @ nameserver Send the queries to this nameserver. BUGS
The full zone walk function is not complete yet, it does not correctly print delegation records AUTHOR
Written by Jelte Jansen as an example for ldns usage. REPORTING BUGS
Report bugs to <ldns-team@nlnetlabs.nl>. COPYRIGHT
Copyright (C) 2005 NLnet Labs. This is free software. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PUR- POSE. 21 Nov 2005 ldns-walk(1)