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| author | abims-sbr |
|---|---|
| date | Fri, 01 Feb 2019 10:28:50 -0500 |
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------ 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% 20% 30% 40% 50% 60% 70% 80% 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.