https://github.com/riccardoscalco/flubud

Flubud calculates the Rohlin distance between alphabetical strings, according to a certain procedure of partitioning.
https://github.com/riccardoscalco/flubud

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Flubud calculates the Rohlin distance between alphabetical strings, according to a certain procedure of partitioning.

• Host: GitHub
• URL: https://github.com/riccardoscalco/flubud
• Owner: riccardoscalco
• License: gpl-3.0
• Created: 2012-03-29T14:33:45.000Z (over 12 years ago)
• Default Branch: master
• Last Pushed: 2012-10-10T12:59:53.000Z (about 12 years ago)
• Last Synced: 2024-10-05T09:41:47.403Z (about 2 months ago)
• Language: Haskell
• Homepage:
• Size: 1.74 MB
• Stars: 1
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.txt
  • License: LICENSE

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README

        
Flubud calculates the Rohlin distance between alphabetical strings, according

to a certain procedure of partitioning.

For details, see:

Burioni R , Scalco R , Casartelli M (2011) Rohlin Distance and the Evolution of

Influenza A Virus: Weak Attractors and Precursors. PLoS ONE 6(12): e27924.

doi:10.1371/journal.pone.0027924

Flags

-----

--s : The accepted difference between labels (optional, default to 1).

      

      Here there are some examples with the string "aababbac":

      s=1 --> [[1,2],[3],[4],[5,6],[7],[8]]

      s=2 --> [[1,2,4],[3,5,6],[7],[8]]

      s=3 --> [[1,2,4,7],[3,5,6],[8]]

--fasta : The fasta file to read as input (required).

          The file has to have the following format:

          - sequence must be of the same length;

          - the description line of the sequence must start with '>' and cannot

            start a new line (one line description);

          - empty lines are not allowed (note that some times there is an empty

            line at the end of the file);

          Here there is an example:

------------8<--------------------------------------------------------

>AEO08998 A/Ankara/01/2010 2010/12/ HA

MKAILVVLLYTFATANADTLCIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDKHNGKLCKLRGVAPLHLG

KCNIAGWILGNPECESLSTASSWSYIVETSSSDNGTCYPGDFINYEELREQLSSVSSFERFEIFPKTSSW

PNHDSNKGVTAACPHAGAKSFYKNLIWLVKKGNSYPKLSKSYINDKGKEVLVLWGIHHPSTSADQQSLYQ

NADAYVFVGTSKYSKKFKPEIAVRPKVRDQEGRMDYYWTLVEPGDKITFEATGNLLVPRYAFAMERNAGS

GIIISDTPVHDCNTTCQTPKGAINTSLPFQNIHPITIGKCPKYVKSTKLRLATGLRNVPSIQSRGLFGAI

AGFIEGGWTGMVDGWYGYHHQNEQGSGYAADLKSTQNAIDKITNKVNSVIEKMNTQFTAVGKEFNHLEKR

IENLNKKVDDGFLDIWTYNAELLVLLENERTLDYHDSNVKNLYEKVRSQLKNNAKEIGNGCFEFYHKCDN

TCMESVKNGTYDYPKYSEEAKLNREEIDGVKLESTRIYQILAIYSTVASSLVLIVSLGAISFWMCSNGSL

QCRICI

>AEM92338 A/District of Columbia/WRAIR0306/2010 2010/12/28 HA

MKAILVVLLYTFATANADTLCIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDKHNGKLCKLRGVAPLHLG

KCNIAGWILGNPECESLSTASSWSYIVETSSSDNGTCYPGDFIDYEELREQLSSVSSFERFEIFPKTSSW

PNHDSNKGVTAACPHAGAKSFYKNLIWLVKKGNSYPKLNKSYINDKGKEVLVLWGIHHPSTTADQQSLYQ

NADAYVFVGTSRYSKKFKPEIAIRPKVRDQEGRMNYYWTLVEPGDKITFEATGNLVVPRYAFAMERNAGS

GIIISDTPVHDCNTTCQTPKGAINTSLPFQNIHPITIGKCPKYVKSTKLRLATGLRNVPSIQSRGLFGAI

AGFIEGGWTGMVDGWYGYHHQNEQGSGYAADLKSTQNAIDKITNKVNSVIEKMNTQFTAVGKEFNHLEKR

IENLNKKVDDGFLDIWTYNAELLVLLENERTLDYHDSNVKNLYEKVRNQLKNNAKEIGNGCFEFYHKCDN

TCMESVKNGTYDYPKYSEEAKLNREEIDGVKLESTRIYQILAIYSTVASSLVLVVSLGAISFWMCSNGSL

QCRICI

>AEF28931 A/Guangdong/002/2011 2011/01/19 HA

MKAILVVMLYTFATANADTLCIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDKHNGKLCKLRGVAPLHLG

KCNIAGWILGNPECESLSTASSWSYIVETSSSDNGTCYPGDFIDYEELREQLSSVSSFERFEIFPKTSSW

PNHDSNKGVTAACPHAGAKGFYKNLIWLVKKGNSYPKLSKSYINDKGKEVLVLWGIHHPSTTADQQSLYQ

NADTYVFVGTSRYSKKFKPEIAIRPKVRDQEGRMNYYWTLVEPGDKITFEATGNLVVPRYAFAMERNAGS

GFIISDTPVHDCNTTCQTPKGAINTSLPFQNIHPITIGKCPKYVKSTKLRLATGLRNVPSIQSRGLFGAI

AGFIEGGWTGMVDGWYGYHHQNEQGSGYAADLKSTQNAIDKITNKVNSVIEKMNTQFTAVGKEFNHLEKR

IENLNKKVDDGFLDIWTYNAELLVLLENERTLDYHDSNVKNLYEKVRNQLKNNAKEIGNGCFEFYHKCDN

TCMESVKNGTYDYPKYSEEAKLNREEIDGVKLESTRIYQILAIYSTVASSLVLVVSLGAISFWMCSNGSL

QCRICI

------------8<--------------------------------------------------------

Output

------

The output is the Rohlin matrix. The matrix is symmetric with zeros

on the diagonal, therefore only the up-diagonal elements are printed.

This is the output of the above example:

[5.545177444479549,8.841014310483871]

[3.295836866004322]

Where the first element of the first list corresponds to the element M[1,2]

in the matrix, the second element of the first list corresponds to M[1,3] and

the first element of the second list corresponds to M[2,3].

Usage

-----

The following command calculates the Rohlin matrix for the set of sequences

listed on the "FASTA.fa" file, with s=10 as maximum difference between labels.

$ ./flubud --s=10 --fasta="FASTA.fa" > out &

Observations

------------

1) There is no percentage indicator for the actual job to be done,

so for who of you that are impatient it is suggested to use the standard unix

commands "grep" and "wc": first, find the total number of sequences in your file

FASTA.fa with

$ grep ">" FASTA.fa | wc

(the first number is the number of sequences), then do

$ wc out

and you will see the first number growing to the number of sequences.

2) The measure used in the calculation of entropy is not normalized to

one. It is instead normalized to the length of the sequences. However, the

normalization to one is restored simply by dividing the matrix (the output)

by the length of the sequences.

To do

-----

- let the user to define the measure to be used in the calculation of entropy.

- introduce the reduction process for arbitrary partitions.