Mercurial > repos > erinija > dnp_correlation_between_profiles
comparison dnp-fourier-transform.sh @ 0:b45de206654d draft default tip
"planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
author | erinija |
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date | Fri, 01 May 2020 12:08:23 +0000 |
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-1:000000000000 | 0:b45de206654d |
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1 #!/bin/sh | |
2 | |
3 if test "$#" -ne 5; then | |
4 | |
5 echo "" | |
6 echo " CALL " | |
7 echo " sh dnp-fourier-transform.sh difreq.profiles.tabular difreq.periodogram.tabular normalization winsize trim" | |
8 echo "" | |
9 echo " INPUT " | |
10 echo " difreq.profiles.tabular - dinucleotide frequency profiles-patterns" | |
11 echo " normalization - type of normalization, suggested is quadratic =2" | |
12 echo " winsize - size of averaging window, suggested optimal value =3" | |
13 echo " trim - how many noisy points to remove from both ends of the profile suggested =4" | |
14 echo "" | |
15 echo " OUTPUT " | |
16 echo " difreq.periodogram.tabular - periodogram " | |
17 echo "" | |
18 echo " DESCRIPRION" | |
19 echo " This is a shell wrapper of the call to dnp-fourier which computes a periodogram " | |
20 echo " of a series given as a numerical column and has parameters:" | |
21 echo " dnp-fourier -f input -o output -n {normalization 0|1|2} -l length_of_smoothing_window -t {type_of_output 1|2|3}" | |
22 echo "" | |
23 echo " The parameters control a type of normalization and output:" | |
24 echo " Normalization" | |
25 echo " 0 base normalization subtracts mean" | |
26 echo " 1 linear normalization removes linear trand " | |
27 echo " 2 quadratic normalization removes quadratic trend" | |
28 echo " Output type" | |
29 echo " 1 normalization outputs normalized original series" | |
30 echo " 2 smoothing outputs smoothed original series" | |
31 echo " 3 Fourier transform outputs periofogram" | |
32 echo "" | |
33 echo " Fourier transform has to be applied on symmetrized, nonsmoothed data, since it performs" | |
34 echo " smoothing internally. Dinucleotide frequency profiles usually have a quadratic gradient," | |
35 echo " therefore a quadratic normalization is used by default. Fourier transform is applied to every " | |
36 echo " column of the input table. In the output the first column contains period as a number of base pairs." | |
37 echo "" | |
38 echo " Example of input table" | |
39 echo " pos AA AC AG AT CA CC CG CT GA GC GG GT TA TC TG TT WW SS RR YY" | |
40 echo " -73 0.05664 0.0657 0.06966 0.03644 0.08026 0.09484 0.0362 0.09086 0.07084 0.04032 0.07318 0.06466 0.03862 0.06838 0.05722 0.05602 0.18772 0.24454 0.27032 0.3101" | |
41 echo " -72 0.0668 0.06476 0.0753 0.04282 0.07022 0.08034 0.03534 0.081 0.07222 0.03512 0.06774 0.0598 0.03934 0.07496 0.06628 0.06784 0.2168 0.21854 0.28206 0.30414" | |
42 echo " -71 0.063 0.0621 0.07668 0.04316 0.06926 0.07264 0.03316 0.07992 0.07546 0.03498 0.07306 0.06406 0.04182 0.07374 0.06874 0.06812 0.2161 0.21384 0.2882 0.29442" | |
43 echo " -70 0.0624 0.0643 0.07214 0.04424 0.0642 0.06998 0.03472 0.07718 0.0723 0.03982 0.07472 0.06818 0.04282 0.07674 0.06864 0.06754 0.217 0.21924 0.28156 0.29144" | |
44 echo " -69 0.0622 0.06456 0.074 0.0426 0.0661 0.07114 0.03414 0.08016 0.0703 0.03786 0.07118 0.06754 0.0421 0.07712 0.06988 0.06904 0.21594 0.21432 0.27768 0.29746" | |
45 echo " ..." | |
46 echo "" | |
47 echo " Example of output" | |
48 echo " period AA AC AG ..." | |
49 echo " 2.100000 0.055962 0.061351 0.059462 ..." | |
50 echo " 2.200000 0.031410 0.027762 0.030298 ..." | |
51 echo " ..." | |
52 echo "" | |
53 echo " REQUIREMENT" | |
54 echo " dnp-fourier installed" | |
55 echo " conda install -c bioconda dnp-fourier" | |
56 echo "" | |
57 | |
58 exit 1 | |
59 fi | |
60 | |
61 # column comes with the header which we have to remove | |
62 input=$1 | |
63 output=$2 | |
64 | |
65 #normalization=2 | |
66 normalization=$3 | |
67 | |
68 #smoothingw=3 | |
69 smoothingw=$4 | |
70 | |
71 #trim=2 | |
72 trim=$5 | |
73 trim1=$((trim+1)) | |
74 outputtype=3 | |
75 | |
76 call=dnp-fourier | |
77 | |
78 dinucleotides=`head -n1 ${input} | sed 's/pos//'` | |
79 | |
80 for di in ${dinucleotides} | |
81 do | |
82 # column number of dinucleotide | |
83 i1=`awk -v name=$di '{ for (i=1; i<=NF; i++) if($i==name) print i; exit}' ${input}` | |
84 awk -v k=${i1} '{print $k}' $input | grep -v ${di} | tail -n +${trim1} | head -n -${trim}| cat -n > temp.${di} | |
85 | |
86 # Submit the call and parameters | |
87 ${call} -f temp.${di} -o ft_output.${di} -n ${normalization} -l ${smoothingw} -t ${outputtype} | |
88 | |
89 echo "period" > period | |
90 awk '{print $1}' ft_output.${di} >> period | |
91 | |
92 echo ${di} > ft.${di} | |
93 awk '{print $2}' ft_output.${di} >> ft.${di} | |
94 | |
95 done | |
96 paste period ft.* > ${output} | |
97 | |
98 rm temp.* ft.* period ft_output.* |