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

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planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
author abims-sbr
date Fri, 01 Feb 2019 10:28:50 -0500
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1
2 ------ Occurences and frequencies of codons, amino-acids, amino-acids types -------
3
4 The script counts the number of codons, amino acids, and types of amino acids in sequences,
5 as well as the mutation bias from one item to another between 2 sequences.
6
7 Counting are then compared to empirical p-values, obtained from bootstrapped sequences obtained from a subset of sequences.
8 In the output files, the pvalues indicate the position of the observed data in a distribution of empirical countings obtained from
9 a resample of the data. Values above 0.95 indicate a significantly higher counting, values under 0.05 a significantly lower counting.
10 Sequences file : concatenation.fasta
11 Species retained for countings : Ps,Pp,Pu,Ac,Ap,Pf,Pg,Ph,Pi
12
13 Processing : reading input file, opening output files, building dictionaries.
14 Warning : countings might be biased and show high differences between species because of high variations of the indels proportions among sequences.
15 Frequences are more representative.
16
17 Indels percent :
18 Ps : 0.174520069808 %
19 Pp : 1.78883071553 %
20 Pu : 21.8586387435 %
21 Ac : 9.90401396161 %
22 Ap : 8.98778359511 %
23 Pf : 15.7504363002 %
24 Pg : 4.31937172775 %
25 Ph : 5.55555555556 %
26 Pi : 8.11518324607 %
27
28 Processing : resampling ...
29 Parameters : 200 iterations, 200 codon per resampled sequence, species used : Ps,Pp,Pu,Pf
30
31 10%
32 20%
33 30%
34 40%
35 50%
36 60%
37 70%
38 80%
39 90%
40 100%
41 Done.
42
43 Processing : countings....
44
45 Countings on Ps
46 Countings on Pp
47 Countings transitions between Ps and Pp
48 Countings on Pu
49 Countings transitions between Ps and Pu
50 Countings on Ac
51 Countings transitions between Ps and Ac
52 Countings on Ap
53 Countings transitions between Ps and Ap
54 Countings on Pf
55 Countings transitions between Ps and Pf
56 Countings on Pg
57 Countings transitions between Ps and Pg
58 Countings on Ph
59 Countings transitions between Ps and Ph
60 Countings on Pi
61 Countings transitions between Ps and Pi
62 Countings transitions between Pp and Pu
63 Countings transitions between Pp and Ac
64 Countings transitions between Pp and Ap
65 Countings transitions between Pp and Pf
66 Countings transitions between Pp and Pg
67 Countings transitions between Pp and Ph
68 Countings transitions between Pp and Pi
69 Countings transitions between Pu and Ac
70 Countings transitions between Pu and Ap
71 Countings transitions between Pu and Pf
72 Countings transitions between Pu and Pg
73 Countings transitions between Pu and Ph
74 Countings transitions between Pu and Pi
75 Countings transitions between Ac and Ap
76 Countings transitions between Ac and Pf
77 Countings transitions between Ac and Pg
78 Countings transitions between Ac and Ph
79 Countings transitions between Ac and Pi
80 Countings transitions between Ap and Pf
81 Countings transitions between Ap and Pg
82 Countings transitions between Ap and Ph
83 Countings transitions between Ap and Pi
84 Countings transitions between Pf and Pg
85 Countings transitions between Pf and Ph
86 Countings transitions between Pf and Pi
87 Countings transitions between Pg and Ph
88 Countings transitions between Pg and Pi
89 Countings transitions between Ph and Pi
90
91 Done.
92
93 Processing : creating dataframes ...
94 Writing dataframes to output files ...
95
96 Done.