$ ls -1 *SNPtable*
2836_SNPtable_CLC_stringent.txt
2838_SNPtable_CLC_stringent.txt
2840_SNPtable_CLC_stringent.txt
5039_SNPtable_CLC_stringent.txt
$ cat script.pl
use warnings;
use strict;
@ARGV >= 1 or die qq[Usage: perl $0 file1 [file2] [file3] ...\n];
my $suffix_word = qq[Sample];
my $suffix_letter = qq[A];
my $argc = @ARGV;
my @header_in = split /\s+/, scalar <>;
my $header_out = "@header_in[0..2]" . qq[ ];
for ( 1 .. $argc ) {
$header_out .= join( qq[ ], map { $_ . qq[.] . $suffix_word . $suffix_letter } @header_in[3..$#header_in] ) . qq[ ];
++$suffix_letter;
}
printf "%s\n", $header_out;
while ( <> ) {
next if $. == 1;
print;
} continue {
close ARGV if eof;
}
$ perl script.pl
Usage: perl script.pl file1 [file2] [file3] ...
$ perl script.pl 2836_SNPtable_CLC_stringent.txt 2838_SNPtable_CLC_stringent.txt 2840_SNPtable_CLC_stringent.txt 5039_SNPtable_CLC_stringent.txt
chromo pos ref alleles.SampleA refAllele.SampleA refCount.SampleA refFreq.SampleA altAllele.SampleA altCount.SampleA altFreq.SampleA alleles.SampleB refAllele.SampleB refCount.SampleB refFreq.SampleB altAllele.SampleB altCount.SampleB altFreq.SampleB alleles.SampleC refAllele.SampleC refCount.SampleC refFreq.SampleC altAllele.SampleC altCount.SampleC altFreq.SampleC alleles.SampleD refAllele.SampleD refCount.SampleD refFreq.SampleD altAllele.SampleD altCount.SampleD altFreq.SampleD
chr1 30146 A A A 31 100 NA 0 NA
chr1 55217 G G G 2 100 NA 0 NA
chr1 55223 C C C 2 100 NA 0 NA
chr1 55987 C C C 19 100 NA 0 NA
chr1 62138 T T T 114 100 NA 0 NA
chr1 62233 A A A 110 100 NA 0 NA
chr1 64310 A A A 64 100 NA 0 NA
chr1 64321 A A A 17 100 NA 0 NA
chr1 64377 A A A 56 98 NA 1 NA
chr1 30146 A A A 10 100 NA 0 NA
chr1 55217 G G G 2 100 NA 0 NA
chr1 55987 C C C 8 100 NA 0 NA
chr1 62138 T C 0 0 C 10 100
chr1 62233 A A A 34 100 NA 0 NA
chr1 64310 A A A 37 100 NA 0 NA
chr1 64321 A A A 9 100 NA 0 NA
chr1 64377 A A A 27 100 NA 0 NA
chr1 65570 A C 0 0 C 2 100
chr1 30146 A A A 54 100 NA 0 NA
chr1 55217 G A/G 0 0 A 5 55
chr1 55223 C T/C 0 0 T 4 57
chr1 55987 C C C 17 100 NA 0 NA
chr1 56065 T T T 18 90 NA 2 NA
chr1 62138 T T/C T 19 70 C 8 29
chr1 62233 A G/A 0 0 G 16 66
chr1 64310 A A A 28 100 NA 0 NA
chr1 64321 A C 0 0 C 4 100
chr1 30146 A A A 23 100 NA 0 NA
chr1 55217 G G G 2 100 NA 0 NA
chr1 55223 C C C 2 100 NA 0 NA
chr1 55987 C C C 19 100 NA 0 NA
chr1 62138 T C 0 0 C 38 100
chr1 62233 A A A 108 100 NA 0 NA
chr1 64377 A A A 2 100 NA 0 NA
chr1 65570 A A A 3 100 NA 0 NA
chr1 66577 T T T 45 100 NA 0 NA
Hi ,
I want to read the data from 9 tables in oracle DB into 9 different files in the same connection instance (session). I am able to get data from one table to one file with below code :
X=`sqlplus -s user/pwd@DB <<eof
select col1 from table1;
EXIT;
eof`
echo $X>myfile
Can anyone... (2 Replies)
I'm pretty new to the database world and I've run into a mental block of sorts. I've been unable to find the answer anywhere. Here's my problem: I have several tables and everything is as normalized as possible (as I've been lead to understand normalization.) Normalization has lead to some... (1 Reply)
I've hunted and hunted but nothing seems to apply to what I need. Any help will be much appreciated!
My input file looks like (Unix):
marker,allele1,allele2
RS1002244,1,1
RS1002244,1,3
RS1002244,3,3
RS1003719,2,2
RS1003719,2,4
RS1003719,4,4
Most markers are listed 3 times but a few... (2 Replies)
Hi..
File 1:
1 aa rep
1 dd rep
1 kk rep
2 bb sad
2 ss sad
3 ee dam
File 2
1 apple fruit
2 mango tree
3 lilly flower
output:
1 aaple fruit aa,dd,kk rep (7 Replies)
Say I have two tables like below..
status
HId sName dName StartTime EndTime
1 E E 9:10 10:10
2 E F 9:15 10:15
3 G H 9:17 10:00
logic
Id devName capacity free Line
1 E 123 34 1
2 E 345 ... (3 Replies)
Hi all,
I have a complex (beyond my biological expertise) problem at hand.
I need to merge multiple files into 1 big matrix. Please help me with some code.
Inp1
Ang_0 chr1 98 T A
Ang_0 chr1 352 G A
Ang_0 chr1 425 C T
Ang_0 chr2 ... (1 Reply)
multiple files to load into different tables,
I have a script show below, but this script loads data from txt file into a table,
but i have multiple input files(xyzload.txt,xyz1load.txt,xyz2load.txt......) in the unix folder ,
can we load these files in diff tables (table 1, table2... (0 Replies)
multiple files to load into different tables,
I have a script show below, but this script loads data from txt file into a table,
but i have multiple input files(xyzload.txt,xyz1load.txt,xyz2load.txt......) in the unix folder ,
can we load these files in diff tables (table 1, table2... (1 Reply)
Hi,
Please excuse me , i have searched unix forum, i am unable to find what i expect ,
my query is , i have 2 files of same structure and having 1 similar field/column , i need to merge 2 tables/files based on the one matched field/column (that is field 1),
file 1:... (5 Replies)
Hello All,
just wanted to export multiple tables from oracle sql using unix shell script to csv file and the below code is exporting only the first table.
Can you please suggest why? or any better idea?
export FILE="/abc/autom/file/geo_JOB.csv"
Export= `sqlplus -s dev01/password@dEV3... (16 Replies)
Discussion started by: Hope
16 Replies
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)