11-05-2009
Hi,
I just found out that the code that you suggested also will print out the content of seq_81,seq_800,etc
Do you have any idea just only specific and only print out the content that matched with seq_8?
Thanks a lot ^^
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1. Shell Programming and Scripting
Hi,
I got a long list of contents:
>sequence_1
ASSSSSSSSSSSDDDDDDDDDDDCCCCCCC
ASDSFDFFDFDFFWERERERERFSDFESFSFD
>sequence_2
ASDFDFDFFDDFFDFDSFDSFDFSDFSDFDSFASDSADSADASD
ASDFFDFDFASFASFASFAFSFFSDASFASFASFAFS
>sequence_3
VEDFGSDGSDGSDGSDGSDGSDGSDG
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My input file:
>sequence_1
ASSSSSSSSSSSDDDDDDDDDDDCCCCCCC
ASDSFDFFDFDFFWERERERERFSDFESFSFD
>sequence_2
ASDFDFDFFDDFFDFDSFDSFDFSDFSDFDSFASDSADSADASD
ASDFFDFDFASFASFASFAFSFFSDASFASFASFAFS
>sequence_3
VEDFGSDGSDGSDGSDGSDGSDGSDG
dDFSDFSDFSDFSDFSDFSDFSDFSDF
SDGFDGSFDGSGSDGSDGSDGSDGSDG
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3. Shell Programming and Scripting
My input:
Data name: ABC001
Data length: 1000
Detail info
Data Direction Start_time End_time Length
1 forward 10 100 90
1 forward 15 200 185
2 reverse 50 500 450
Data name: XFG110
Data length: 100
Detail info
Data Direction Start_time End_time Length
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Input file:
#abc_1
SAASFASFGGDSGDSGDSGSDGSDGSDGSDGSDGSDGSDGDS
Output file:
FASFGGDSGDS
I just want to print out the read from position 5 until position 15 from the data.
Below is the code that I just try but it is failed to get my desired output:
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Input file:
>position_10 sample:68711 coords:5453-8666 number:3 type:complete len:344
MSINQYSSDFHYHSLMWQQQQQQQQHQNDVVEEKEALFEKPLTPSDVGKLNRLVIPKQHA
ERYFPLAAAAADAVEKGLLLCFEDEEGKPWRFRYSYWNSSQSYVLTKGWSRYVKEKHLDA
NRTS*
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Input file 1:
>pattern_5
GAATTCGTTCATGTAGGTTGASDASFGDSGRTYRYGHDGSDFGSDGGDSGSDGSDFGSDF
ATTTAATTATGATTCATACGTCATATGTTATTATTCAATCGTATAAAATTATGTGACCTT
SDFSDGSDFKSDAFLKJASLFJASKLFSJAKJFHASJKFHASJKFHASJKFHSJAKFHAW
>pattern_1
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HS04636 PROGRAM source 836 7001 + ID=g1
HS04636 PROGRAM beginner 836 7001 + ID=g1.t1;Parent=g1
HS04636 PROGRAM position 836 836 + Parent=g1.t1
HS04636 PROGRAM type 836 1017 + Parent=g1.t1
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Input:
21 templeta parent 35718 36554 . - . ID=parent_cluster_50.21.11; Name=Partial%20parent%20for%20training%20set;
21 templeta kids 35718 36554 . - . ID=_52; Parent=parent_cluster_5085.21.11;
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data.txt has several information like the below..
<SERVER>:WEB:MYDOM01:/tmp/cong/MYDOM01,/tmp/app/MYDOM01
<WEBER>:CANES:https-web01,https-web02:/web/apps/https-web01/config
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LEARN ABOUT FREEBSD
atf-sh
ATF-SH(1) BSD General Commands Manual ATF-SH(1)
NAME
atf-sh [-s shell] -- interpreter for shell-based test programs
SYNOPSIS
atf-sh script
DESCRIPTION
atf-sh is an interpreter that runs the test program given in script after loading the atf-sh(3) library.
atf-sh is not a real interpreter though: it is just a wrapper around the system-wide shell defined by ATF_SHELL. atf-sh executes the inter-
preter, loads the atf-sh(3) library and then runs the script. You must consider atf-sh to be a POSIX shell by default and thus should not
use any non-standard extensions.
The following options are available:
-s shell Specifies the shell to use instead of the value provided by ATF_SHELL.
ENVIRONMENT
ATF_LIBEXECDIR Overrides the builtin directory where atf-sh is located. Should not be overridden other than for testing purposes.
ATF_PKGDATADIR Overrides the builtin directory where libatf-sh.subr is located. Should not be overridden other than for testing purposes.
ATF_SHELL Path to the system shell to be used in the generated scripts. Scripts must not rely on this variable being set to select a
specific interpreter.
EXAMPLES
Scripts using atf-sh(3) should start with:
#! /usr/bin/env atf-sh
Alternatively, if you want to explicitly choose a shell interpreter, you cannot rely on env(1) to find atf-sh. Instead, you have to hardcode
the path to atf-sh in the script and then use the -s option afterwards as a single parameter:
#! /path/to/bin/atf-sh -s/bin/bash
ENVIRONMENT
ATF_SHELL Path to the system shell to be used in the generated scripts.
SEE ALSO
atf-sh(3)
BSD
September 27, 2014 BSD