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Full Discussion: awk getline problem
Top Forums Shell Programming and Scripting awk getline problem Post 302743891 by yifangt on Thursday 13th of December 2012 02:15:21 PM
Old 12-13-2012
The interesting part is the script works with another fasta file in which each sequence line/row has more 120bp wide.
Code:
>S94D_ctg_8004 Average coverage: 402.95
ATAATGCCTGTGAATATGACATGTGTTCCTGTTTCTACATCAGACTACTATTCTTGCATATCCCGCATCAGTCACTTATGATAAGGCACCTTTAAGTCGCCACTGTGATATTGGTTGTGT
CTTGCATATGATTTCTAGCATGTACTGCTTCTAATTTGTTGAAACGCCATACAGTTTGAACTTGGCAGAGTGATATTGGTTGCATCTTTCATATGGTGTCTAGCTTGCAGTGCTTCTAAT
TT
>S94D_ctg_8022 Average coverage: 212.74
CGTTGTCTGTGTGACATTTAAGAGTGTTTTGTGCAGTGCAACAAAAGGTCACAATGGCAACGAGGTGAAGTAGATAACCCTGTTTACACAGAGGTGCAAAGGAAACAACTAGTGGTCAAT
AACCCTGTTTACCAGCACCATGTGCATCTACCGATGTACTGGGGTGATGCACAGTCTGTTG
>S94D_ctg_8062 Average coverage: 710.87
ATGAATTTCAGACGAGTTTTGGATTTACTAGAATTTAAAAACCAGGCATCTCAATGTTTTGCCGGCAATCAACGGTGCCCTGGTGTTTGAAATTCATTCCCATTTCTTGCATGGGACCTA
AGCATGCACCCAAGGACA
>S94D_ctg_9034 Average coverage: 37.84
AGATTATTTTGTCTGCCATGTATAATTTTGGTTGATGTTTAGCCTGTTGTGCTTAACATGCTTCTCGACGTACCTACACAGGACAATTTGGGAACGACTGCTGTTTTCCATCGAGGTTAG
TTTCATCCCATGGCTTATATCTGCTCAATGTTCAGGATATCGGTAGCCGGTACCATATAGGCCGGCGGCTGATAGGAGACTAATCGGTGAATCGGACT

I thought the script may be related to the newline, but I did check and could not find any abnormal. Not sure the EOL is really the same of the two files. I will check it. Thank you both!
 

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LEARN ABOUT DEBIAN

cobertura-check

COBERTURA-CHECK(1)					      General Commands Manual						COBERTURA-CHECK(1)

NAME

       cobertura-check -- show which classes do not have adequate test coverage

SYNOPSIS

       cobertura-check	[--branch  0..100]   [--datafile  file]   [--line  0..100]   [--regex regex:branchrate:linerate]  [--packagebranch 0..100]
       [--packageline 0..100]  [--totalbranch 0..100]  [--totalline 0..100]

DESCRIPTION

       cobertura-check can be run after your JUnit tests to show which classes do not have adequate test coverage.

OPTIONS

       If no parameters are specified then all values will be set to 50%.

       --branch 0..100
		 Specify the minimum acceptable branch coverage rate needed by each class. This should be an integer  value  between  0  and  100.
		 Default value is 0.

       --datafile file
		 Specify the name of the file containing metadata about your classes. Default value: "./cobertura.ser".

       --line 0..100
		 Specify  the  minimum	acceptable  line  coverage  rate  needed by each class. This should be an integer value between 0 and 100.
		 Default value is 0.

       --regex regex:branchrate:linerate
		 For finer grained control, you can optionally specify minimum branch and line coverage rates for  individual  classes	using  any
		 number of regular expressions.

       --packagebranch 0..100
		 Specify the minimum acceptable average branch coverage rate needed by each package. This should be an integer value between 0 and
		 100. Default value is 0.

       --packageline 0..100
		 Specify the minimum acceptable average line coverage rate needed by each package. This should be an integer value between  0  and
		 100. Default value is 0.

       --totalbranch 0..100
		 Specify  the  minimum	acceptable  average branch coverage rate needed by the project as a whole. This should be an integer value
		 between 0 and 100. Default value is 0.

       --totalline 0..100
		 Specify the minimum acceptable average line coverage rate needed by the project as a whole.  This  should  be	an  integer  value
		 between 0 and 100. Default value is 0.

SEE ALSO

       junit(1), cobertura-instrument(1), cobertura-report(1), cobertura-merge(1).

AUTHOR

       This  manual  page  was	written  by  Miguel  Landaeta <miguel@miguel.cc> for the Debian system (but may be used by others).  Permission is
       granted to copy, distribute and/or modify this document under the terms of the terms of GNU General Public License, Version 2 or any  later
       version published by the Free Software Foundation.

       On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common-licenses/GPL.

																COBERTURA-CHECK(1)
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