#11 fisher-test.pl errors - missing twotailed.pm

[Anonymous]

Originally created by: bsc6... (code.google.com)@gmail.com

What steps will reproduce the problem?
1. created mpileup successfully
2. created syn file successfully
3. fisher-test.pl fails (stops on line 9 and 10)

What is the expected output? What do you see instead?
fisher-test.pl fails (stops on line 9 and 10).

What version of the product are you using? On what operating system?
Popoolation2

Please provide any additional information below.

Receive the following error messages:

"Can't locate Text/NSP/Measures/2D/Fisher/twotailed.pm in @INC <@INC contains C:Popoolation2 C:Popoolation2/Modules C:/Perl64/site/lib C:/Perl64/lib > at C:/Popoolation2/Modules/FET.pm line 10
BEGIN failed--compilation aborted at C:/Popoolation/Modules/FET.pm line 10"

and

"Compilation failed in require at C:/Popoolation2/fisher-test.pl line 9
BEGIN failed--compilation aborted at C:/Popoolation2/fisher-test.pl"

I discovered that twotailed.pm was not located in the Popoolation2 directories, but found it at http://cpansearch.perl.org/src/TPEDERSE/Text-NSP-1.15/lib/Text/NSP/Measures/2D/Fisher2/twotailed.pm .  I placed twotail.pm into the Modules directory of Popoolation2 as well as Perl/site/lib

I still receive the same errors.

Any help to resolve this will be much appreciated!

[Anonymous]

Originally posted by: pip.grif... (code.google.com)@gmail.com

I also encountered this issue. My guess is that this module has been deprecated in the latest version of Perl, but I am not at all knowledgeable about Perl so that may be wrong. Hopefully it is not a problem to be using these modules still.

I guess you can put the whole NSP module into your directory to fix this. I added just the bits that popoolation needs for the Fisher's Exact Test, and that worked. I traced back the scripts required by first adding Text/NSP/Measures/2D/Fisher/twotailed.pm to the directory, looking at the next error message, then adding Fisher.pm in the Text/NSP/Measures/2D/ directory as required, and so on. All the source code for those scripts is here http://search.cpan.org/~tpederse/Text-NSP/

[Anonymous]

Originally posted by: RoKof... (code.google.com)@gmail.com

hi guys,
not sure if I understand, correctly, but this module needs to be installed manually as it never was part of the Perl standard distribution (more details also in the manual)
A simple guide for installing perl modules: http://www.cpan.org/modules/INSTALL.html
cheers ro

[Anonymous]

Originally posted by: fufu... (code.google.com)@gmail.com

I meet the same problem. I have installed manually the Perl. But it is not work.
Could you tell us how to improve it?
Thanks,
Fuyou

[Bernadette]

You will need to install the perl package (Text::NSP::Measures::2D::Fisher::twotailed). This fixed the problem for me.

1. Install cpanminus:

   sudo apt install cpanminus

2. Install perl package:

   cpanm Text::NSP::Measures::2D::Fisher::twotailed

Link to package: https://metacpan.org/pod/Text::NSP::Measures::2D::Fisher::twotailed