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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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LEARN ABOUT DEBIAN
interface-order
INTERFACE-ORDER(5) resolvconf INTERFACE-ORDER(5) NAME
interface-order - resolvconf configuration file DESCRIPTION
The file /etc/resolvconf/interface-order is used to control the order in which resolvconf nameserver information records are processed by those resolvconf update scripts that consult this file. (The name of the file is apt because a resolvconf nameserver information record is named after the interface with which it is associated.) The file contains a sequence of shell glob patterns, one per line. The position of a record in the order is the point at which its name first matches a pattern. Patterns may not contain whitespace, slashes or initial dots or tildes. Blank lines and lines beginning with a '#' are ignored. Resolvconf update scripts in /etc/resolvconf/update.d/ that consult this file include the current default versions of dnsmasq, pdnsd and libc. (Actually they don't read the file directly; they call the utility program /lib/resolvconf/list-records which lists records in the specified order and omits the names of empty records.) EXAMPLE
# /etc/resolvconf/interface-order # Use nameservers on the loopback interface first. lo* # Next use records for Ethernet interfaces eth* # Next use records for Wi-Fi interfaces wlan* # Next use records for PPP interfaces ppp* # Last use other interfaces * AUTHOR
Resolvconf was written by Thomas Hood <jdthood@gmail.com>. COPYRIGHT
Copyright (C) 2004, 2011 Thomas Hood This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICU- LAR PURPOSE. SEE ALSO
resolvconf(8) resolvconf 18 May 2011 INTERFACE-ORDER(5)