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rmes.format
Result Display



Description Usage Options Input file Output file Examples

Description

The program rmes.format is a useful tool to present in a table the words (and their statistical properties) in increasing order of the statistic stat.

Usage

rmes.format -h
or 
rmes.format  [-hmin <hmin>] [-hmax <hmax>]
             [-moins <moins>] [-plus <plus>] 
             [-conj | -pal]
             [-english]
             < Input-file
             > Output-file

Options

-h
gives only the syntax of the command.
-hmin <hmin>
When set, <hmin> corresponds to the minimal length of words for which the results need to be displayed.
By default, <hmin> is the smaller length of words analyzed in the input file.
Ignored when the results have been obtained on families of words.
-hmax <hmax>
When set, <hmax> corresponds to the maximal length of words for which the results need to be displayed.
By default, <hmax> is the larger length of words analyzed in the input file.
Ignored when the results have been obtained on families of words.
-moins <moins>
When set, <moins> is the negative value of statistic up to which results are displayed: only words for which the statistic is less or equal than <moins> will be displayed. If <moins> is a positive value, its opposite will be considered.
By default, <moins> is equal to -3.
-plus <plus>
When set, <plus> is the positive value of statistic from which results are displayed: only words for which the statistic is greater or equal than <plus> will be displayed. If <plus> is a negative value, its opposite will be considered.
By default, <plus> is equal to +3.
Note: all the results are displayed when both -moins and -plus are set to 0.
-conj or -pal
When -conj is set, information about the conjugate of each word are also displayed.
The conjugate of a word W is the corresponding word read on the complementary strand. It is obtained by replacing the letters of W by the complementary letters (a by t and c by g, and vice versa), and then by reversing the letters. For instance, acg is the conjugate of cgt.
When -pal is set, only results of palindromic (or pseudo-palindromic) words are displayed. A palindromic word is a word with even length that is identical to its conjugate. A pseudo-palindromic word is a word with odd length that is identical (except its middle letter) to its conjugate.
Ignored when the results have been obtained on families of words.
-english or -eng
When set, the output are in english.
By default, they are in french.

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Input file

The standard input file of rmes.format should be a file created by one of the R'MES programs rmes.gaussien, rmes.poisson or rmes.poisson.composee.
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Output file

The standard output file of rmes.format contains as many table as the word lengths specified by the options -hmin and -hmax (in case of families of words a unique table is displayed).

The structure of each table depends on the program used to create the input file.

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Examples

1- List of the 4-words having a statistic less than -7 or greater than 10 in the lambda genome under M1. The input file lambda.gaussien.4_1.0 has been previously obtained by rmes.gaussien.
The table lambda.gaussien.4_1.0.en.out is in english. 
rmes.gaussien -o lambda.gaussien.4_1 -seq lambda -m 1 -hmin 4 

rmes.format -english -hmin 4 -moins -7 -plus 10
            <lambda.gaussien.4_1.0 
            >lambda.gaussien.4_1.0.en.out
2- List of the 4-words having a statistic less than -6.5 or greater than 9.5 in the lambda genome under M1. For each listed word, the information on its conjugate is given. The input file lambda.gaussien.4_1.0 has been previously obtained by rmes.gaussien. 
rmes.format -hmin 4 -moins -6.5 -plus 9.5 -conj 
            <lambda.gaussien.4_1.0 
            >lambda.gaussien.4_1.0.conj.out
3- List of the statistics of all the palindromes of length 4 in the lambda genome under M1. The input file lambda.gaussien.4_1.0 has been previously obtained by rmes.gaussien. 
rmes.format -hmin 4 -moins 0 -plus 0 -pal 
            <lambda.gaussien.4_1.0 
            >lambda.gaussien.4_1.0.pal.out
4- List of the 7-words having a statistic greater than 5 in absolute value in the lambda genome under M1. The input file lambda.pc.7-8_1.0 has been previously obtained by rmes.poisson.composee. 
rmes.format -hmin 7 -hmax 7 -moins -5 -plus 5
            <lambda.pc.7-8_1.0 
            >lambda.pc.7_1.0.out
5- List of the 7-words having a statistic, related to the number of clumps, greater than 5 in absolute value in the lambda genome under M1. The input file lambda.p.7_1.0 has been previously obtained by rmes.poisson. 
rmes.format -hmin 7 -hmax 7 -moins -5 -plus 5 
            <lambda.p.7_1.0 
            >lambda.p.7_1.0.out

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