annotate test-data/OUT_concat/MutCount_concat_log.output @ 0:acc3674e515b draft default tip

planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty

 ------ Occurences and frequencies of codons, amino-acids, amino-acids types -------

The script counts the number of codons, amino acids, and types of amino acids in sequences,
as well as the mutation bias from one item to another between 2 sequences.

Counting are then compared to empirical p-values, obtained from bootstrapped sequences obtained from a subset of sequences.
In the output files, the pvalues indicate the position of the observed data in a distribution of empirical countings obtained from
a resample of the data. Values above 0.95 indicate a significantly higher counting, values under 0.05 a significantly lower counting.
    Sequences file : concatenation.fasta
    Species retained for countings : Ps,Pp,Pu,Ac,Ap,Pf,Pg,Ph,Pi

Processing : reading input file, opening output files, building dictionaries.
    Warning : countings might be biased and show high differences between species because of high variations of the indels proportions among sequences.
    Frequences are more representative.

    Indels percent :
    Ps : 0.174520069808 %
    Pp : 1.78883071553 %
    Pu : 21.8586387435 %
    Ac : 9.90401396161 %
    Ap : 8.98778359511 %
    Pf : 15.7504363002 %
    Pg : 4.31937172775 %
    Ph : 5.55555555556 %
    Pi : 8.11518324607 %

Processing : resampling ...
    Parameters : 200 iterations, 200 codon per resampled sequence, species used : Ps,Pp,Pu,Pf

    10%
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    90%
    100%
    Done.

Processing : countings....

Countings on Ps
Countings on Pp
Countings transitions between Ps and Pp
Countings on Pu
Countings transitions between Ps and Pu
Countings on Ac
Countings transitions between Ps and Ac
Countings on Ap
Countings transitions between Ps and Ap
Countings on Pf
Countings transitions between Ps and Pf
Countings on Pg
Countings transitions between Ps and Pg
Countings on Ph
Countings transitions between Ps and Ph
Countings on Pi
Countings transitions between Ps and Pi
Countings transitions between Pp and Pu
Countings transitions between Pp and Ac
Countings transitions between Pp and Ap
Countings transitions between Pp and Pf
Countings transitions between Pp and Pg
Countings transitions between Pp and Ph
Countings transitions between Pp and Pi
Countings transitions between Pu and Ac
Countings transitions between Pu and Ap
Countings transitions between Pu and Pf
Countings transitions between Pu and Pg
Countings transitions between Pu and Ph
Countings transitions between Pu and Pi
Countings transitions between Ac and Ap
Countings transitions between Ac and Pf
Countings transitions between Ac and Pg
Countings transitions between Ac and Ph
Countings transitions between Ac and Pi
Countings transitions between Ap and Pf
Countings transitions between Ap and Pg
Countings transitions between Ap and Ph
Countings transitions between Ap and Pi
Countings transitions between Pf and Pg
Countings transitions between Pf and Ph
Countings transitions between Pf and Pi
Countings transitions between Pg and Ph
Countings transitions between Pg and Pi
Countings transitions between Ph and Pi

    Done.

Processing : creating dataframes ...
Writing dataframes to output files ...

Done.