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academic/vCAPS_coevolution: Added (Coevolution Analysis)
Signed-off-by: Dave Woodfall <dave@slackbuilds.org>
This commit is contained in:
Petar Petrov
Dave Woodfall
parent
1f0ff62f35
commit
0a28023757
7 changed files with 357 additions and 0 deletions
114
academic/vCAPS_coevolution/01_caps_verbose.patch
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114
academic/vCAPS_coevolution/01_caps_verbose.patch
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@ -0,0 +1,114 @@
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diff -pruN orig/caps.cpp new/caps.cpp
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--- orig/caps.cpp 2012-12-15 17:13:23.000000000 +0200
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+++ new/caps.cpp 2020-09-09 23:07:46.080566000 +0300
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@@ -14,7 +14,7 @@
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#include <gsl/gsl_statistics.h>
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#include<sys/time.h>
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#include<iomanip>
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-
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+#include <bits/stdc++.h>
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@@ -69,6 +69,8 @@
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const gsl_rng_type * T;
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gsl_rng *r;
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+vector<double> totaltempnew;
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+double alphathresh = 0;
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int main(int argc, char *argv[]){
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@@ -543,16 +545,27 @@ int main(int argc, char *argv[]){
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print_splash(output);
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+ OUTPUT << "\n\File1: " << files[i] << endl;
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vec1.print_to_fasta(output.c_str());
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+ OUTPUT << "\n\nFile2: " << files[j] << endl;
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vec2.print_to_fasta(output.c_str());
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int length1 = vec1.sequences[0].length();
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int length2 = vec2.sequences[0].length();
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+ OUTPUT << "\n\nLength1: " << length1 << endl;
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+ OUTPUT << "Length2: " << length2 << endl;
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if(tree_in ==0){
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tree1 = create_input_tree(vec1.names, vec1.sequences);
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tree2 = create_input_tree(vec2.names, vec2.sequences);
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+
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+ // Output the CAPS generated trees to the .out file of each pair
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+ string temptre1 = TreeTemplateTools::treeToParenthesis(*tree1, true);
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+ string temptre2 = TreeTemplateTools::treeToParenthesis(*tree2, true);
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+ OUTPUT << "\n" << endl;
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+ OUTPUT << "CAPS generated tree 1: " << temptre1 << endl;
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+ OUTPUT << "CAPS generated tree 2: " << temptre2 << endl;
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}/*else if(tree_in ==1 && variable==1){
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std::auto_ptr<DistanceMatrix> DS;
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@@ -666,6 +679,7 @@ int main(int argc, char *argv[]){
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int value = floor(((totaltemp.size())*(1-(threshval))))+1;
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threshold = totaltemp[value];
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+ totaltempnew = totaltemp;
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/*=======================================================*/
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@@ -870,6 +884,30 @@ int Chi_squared (int num_pairs, int num_
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} /* ----- end of function Chi_squared ----- */
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+/*
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+ * === FUNCTION ======================================================================
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+ * Name: find_alpha
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+ * Description: Find the index of an element in a vector totaltemp
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+ * Help from: https://www.geeksforgeeks.org/how-to-find-index-of-a-given-element-in-a-vector-in-cpp/
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+ * https://stackoverflow.com/questions/8647635/elegant-way-to-find-closest-value-in-a-vector-from-above
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+ * Author: Petar Petrov, University of Turku (Finland); pebope@utu.fi
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+ * =====================================================================================
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+ */
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+double getIndex(std::vector<double> const& v, double K)
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+{
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+ auto const it = std::lower_bound(v.begin(), v.end(), fabs(K));
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+ //auto it = std::upper_bound(v.begin(), v.end(), fabs(K));
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+
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+ if (it != v.end()) {
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+ int index = distance(v.begin(), it);
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+ alphathresh = (((int)1+(double)v.size()-(int)index)/(double)v.size());
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+ return alphathresh;
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+ //cerr << index << "\t" << alphathresh << endl;
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+ }
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+ else {
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+ cerr << "ELEMENT NOT FOUND!" << endl;
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+ }
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+}
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@@ -890,9 +928,9 @@ int print_inter(vector<double>& Correl1,
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output << endl << endl;
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output << "Coevolving Pairs of amino acid sites\n";
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- output << "=============================================================================\n";
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- output << "Col1(real)\tCol2(real)\tDmean1\t\tDmean2\t\tCorrelation\tBootstrap value\n\n";
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- output << "=============================================================================\n";
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+ output << "================================================================================================================================\n";
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+ output << "Col1(real)\tCol2(real)\tDmean1\t\tDmean2\t\tCorrelation\tBootstrap value\tP-value1\tP-value2\tMean P-value\tCorrelation1\tCorrelation2\n\n";
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+ output << "================================================================================================================================\n";
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//double mean = average_vec<double>(Correl);
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//double SD = SD_vf(Correl, mean);
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@@ -951,9 +989,11 @@ int print_inter(vector<double>& Correl1,
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// }
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+ double Alpha1 = getIndex(totaltempnew, Correl1[cor]);
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+ double Alpha2 = getIndex(totaltempnew, Correl2[cor]);
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//if(bootval>=bootcut && re1<=8 && re2<=8 ){
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if(bootval>=bootcut){
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- output << i+1 << "(" << i-gaps1+1 << ")\t\t" << j+1 << "(" << (j+1)-gaps2 << ")\t\t" << averDi << "\t\t" << averDj << "\t\t" << (Correl1[cor]+Correl2[cor])/2 << "\t" << bootval << endl;
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+ output << i+1 << "(" << i-gaps1+1 << ")\t\t" << j+1 << "(" << (j+1)-gaps2 << ")\t\t" << averDi << "\t\t" << averDj << "\t" << (Correl1[cor]+Correl2[cor])/2 << "\t" << bootval << "\t" << Alpha1 << "\t" << Alpha2 << "\t" << (Alpha1+Alpha2)/2 << "\t" << Correl1[cor] << "\t" << Correl2[cor] << endl;
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signif.push_back(((Correl1[cor]+Correl2[cor])/2));
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++pairs;
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vector<int> tem;
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38
academic/vCAPS_coevolution/02_caps_sort_input.patch
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38
academic/vCAPS_coevolution/02_caps_sort_input.patch
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@ -0,0 +1,38 @@
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diff -pruN old/caps.cpp new/caps.cpp
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--- old/caps.cpp 2022-01-20 09:30:24.409886691 +0200
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+++ new/caps.cpp 2022-01-20 09:39:10.669845265 +0200
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@@ -1,4 +1,5 @@
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#include<iostream>
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+#include <algorithm>
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#include<fstream>
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#include"BCFasta.h"
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#include"file_manip.h"
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@@ -15,7 +16,7 @@
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#include<sys/time.h>
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#include<iomanip>
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#include <bits/stdc++.h>
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-
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+#include <vector>
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#include <Seq/SequenceApplicationTools.h>
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@@ -69,6 +70,10 @@
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const gsl_rng_type * T;
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gsl_rng *r;
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+// make sure filenames are sorted!
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+// https://stackoverflow.com/a/34757557
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+bool compareFunction (std::string a, std::string b) {return a<b;}
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+
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vector<double> totaltempnew;
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double alphathresh = 0;
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int main(int argc, char *argv[]){
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@@ -189,6 +194,8 @@ int main(int argc, char *argv[]){
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vector<string> files;
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files = Folder_to_vector(mystring.c_str());
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+ // make sure filenames are sorted!
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+ std::sort(files.begin(),files.end(),compareFunction);
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Fasta_vector file;
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file.ref_num=0;
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33
academic/vCAPS_coevolution/README
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33
academic/vCAPS_coevolution/README
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vCAPS: (verbose) Coevolution Analysis using Protein Sequences
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CAPS is aimed at measuring the coevolution between amino acid sites
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belonging to the same protein (intra-molecular coevolution) or to two
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functionally or physically interacting proteins (inter-molecular
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coevolution). The Software implements an improved method to detect
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intra-molecular coevolution as published in Genetics (Fares and Travers,
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2006) and also inter-protein coevolution analysis. The improved scoring
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of amino acid sites is obtained by maximum likelihood ancestral state
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reconstruction along with simulations to assess significance.
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This is a modified version of "CAPS_coevolution", used in the AutoCoEv
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pipeline:
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https://github.com/mattilalab/autocoev
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It applies two _unofficial_ patches:
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- 01_caps_verbose: makes the program output its generated trees, as well
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as the p-value for each correlated amino acid pair
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- 02_caps_sort_input: introduce a function to sort input file names
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The produced executable is called "vCAPS" and can be installed along
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"caps" from CAPS_coevolution. Building CAPS from source requires the
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Bio++ 1.9 suite libraries, but make sure the current versions of the
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bppsuite (and its dependencies) are NOT installed at build time.
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Citing CAPS:
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CAPS: coevolution analysis using protein sequences. Fares MA, McNally D.
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Bioinformatics. 2006 Nov 15;22(22):2821-2. PMID: 17005535
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The mathematical model has been described separately:
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A novel method for detecting intramolecular coevolution: adding a
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further dimension to selective constraints analyses. Fares MA, Travers
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SA. Genetics. 2006 May;173(1):9-23. PMID: 16547113
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14
academic/vCAPS_coevolution/References
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14
academic/vCAPS_coevolution/References
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@ -0,0 +1,14 @@
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If you use CAPS in your research, please include the following citations:
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CAPS: coevolution analysis using protein sequences.
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Fares MA, McNally D.
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Bioinformatics. 2006 Nov 15;22(22):2821-2.
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PMID: 17005535
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https://www.ncbi.nlm.nih.gov/pubmed/17005535
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The mathematical model has been described separately:
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A novel method for detecting intramolecular coevolution: adding a further dimension to selective constraints analyses.
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Fares MA, Travers SA.
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Genetics. 2006 May;173(1):9-23.
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PMID: 16547113
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https://www.ncbi.nlm.nih.gov/pubmed/16547113
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19
academic/vCAPS_coevolution/slack-desc
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19
academic/vCAPS_coevolution/slack-desc
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@ -0,0 +1,19 @@
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# HOW TO EDIT THIS FILE:
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# The "handy ruler" below makes it easier to edit a package description.
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# Line up the first '|' above the ':' following the base package name, and
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# the '|' on the right side marks the last column you can put a character in.
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# You must make exactly 11 lines for the formatting to be correct. It's also
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# customary to leave one space after the ':' except on otherwise blank lines.
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|-----handy-ruler------------------------------------------------------|
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vCAPS_coevolution: vCAPS_coevolution (Coevolution Analysis using Protein Sequences)
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vCAPS_coevolution:
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vCAPS_coevolution: CAPS is aimed at measuring the coevolution between amino acid
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vCAPS_coevolution: sites belonging to the same protein (intra-molecular coevolution)
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vCAPS_coevolution: or to two functionally or physically interacting proteins (inter-
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vCAPS_coevolution: molecular coevolution). In addition, a test which assesses
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vCAPS_coevolution: whether two proteins are interacting is implemented.
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vCAPS_coevolution:
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vCAPS_coevolution: Home: http://bioinf.gen.tcd.ie/~faresm/software/software.html
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vCAPS_coevolution:
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vCAPS_coevolution:
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129
academic/vCAPS_coevolution/vCAPS_coevolution.SlackBuild
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129
academic/vCAPS_coevolution/vCAPS_coevolution.SlackBuild
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@ -0,0 +1,129 @@
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#!/bin/bash
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# Slackware build script for vCAPS_coevolution
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# Copyright 2020-2022 Petar Petrov slackalaxy@gmail.com
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# All rights reserved.
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#
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# Redistribution and use of this script, with or without modification, is
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# permitted provided that the following conditions are met:
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#
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# 1. Redistributions of this script must retain the above copyright
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# notice, this list of conditions and the following disclaimer.
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#
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# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED
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# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
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# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO
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# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
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# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
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# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
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# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
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# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
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# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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cd $(dirname $0) ; CWD=$(pwd)
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PRGNAM=vCAPS_coevolution
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VERSION=${VERSION:-2.0_2UN}
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BUILD=${BUILD:-1}
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TAG=${TAG:-_SBo}
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PKGTYPE=${PKGTYPE:-tgz}
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SRCNAM=caps
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SRCVER=2.0
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BINNAM=vCAPS
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if [ -z "$ARCH" ]; then
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case "$( uname -m )" in
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i?86) ARCH=i586 ;;
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arm*) ARCH=arm ;;
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*) ARCH=$( uname -m ) ;;
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esac
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fi
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if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then
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echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE"
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exit 0
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fi
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TMP=${TMP:-/tmp/SBo}
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PKG=$TMP/package-$PRGNAM
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OUTPUT=${OUTPUT:-/tmp}
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if [ "$ARCH" = "i586" ]; then
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SLKCFLAGS="-O2 -march=i586 -mtune=i686"
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LIBDIRSUFFIX=""
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elif [ "$ARCH" = "i686" ]; then
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SLKCFLAGS="-O2 -march=i686 -mtune=i686"
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LIBDIRSUFFIX=""
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elif [ "$ARCH" = "x86_64" ]; then
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SLKCFLAGS="-O2 -fPIC"
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LIBDIRSUFFIX="64"
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else
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SLKCFLAGS="-O2"
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LIBDIRSUFFIX=""
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fi
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LIBDIRPATH="-Wl,-rpath,/usr/lib${LIBDIRSUFFIX}/Bpp1.9"
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set -e
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rm -rf $PKG
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mkdir -p $TMP $PKG $OUTPUT
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cd $TMP
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rm -rf ${SRCNAM}${SRCVER}_src
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unzip $CWD/${SRCNAM}2_src.zip
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cd ${SRCNAM}${SRCVER}_src
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chown -R root:root .
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find -L . \
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\( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \
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-o -perm 511 \) -exec chmod 755 {} \; -o \
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\( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \
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-o -perm 440 -o -perm 400 \) -exec chmod 644 {} \;
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# This is needed for gcc in Slackware 14.2
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sed -i "s:CC=g++ -g:CC=g++-5 -g -std=c++11:" Makefile
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# Use our CFLAGS and the custom (legacy) lib path
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sed -i "s:CFLAGS=:CFLAGS=$SLKCFLAGS $LIBDIRPATH:" Makefile
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# Find the legacy bpp libraries
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sed -i "s:-lbpp-phyl:-L/usr/lib${LIBDIRSUFFIX}/Bpp1.9 -lbpp-phyl:g" Makefile
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sed -i "s:-lbpp-numcalc:-L/usr/lib64${LIBDIRSUFFIX}/Bpp1.9 -lbpp-numcalc:g" Makefile
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sed -i "s:-lbpp-utils:-L/usr/lib64${LIBDIRSUFFIX}/Bpp1.9 -lbpp-utils:g" Makefile
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sed -i "s:-lbpp-seq:-L/usr/lib64${LIBDIRSUFFIX}/Bpp1.9 -lbpp-seq:g" Makefile
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# Rename the produced executable
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sed -i "s:-o caps:-o $BINNAM:" Makefile
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# Use our patches
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patch -p1 -i $CWD/01_caps_verbose.patch
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patch -p1 -i $CWD/02_caps_sort_input.patch
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# we already specified g++-5 above, so no need for this
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#source /etc/profile.d/gcc5.sh
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make all
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# Install the binary produced from our patched source, as "vCAPS"
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install -D -m755 $BINNAM $PKG/usr/bin/$BINNAM
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find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \
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| cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true
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mkdir -p $PKG/usr/share/$PRGNAM
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cp -a sample structures trees TLR1.fa.out $PKG/usr/share/$PRGNAM
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mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
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cp -a \
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caps_manual.pdf \
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$PKG/usr/doc/$PRGNAM-$VERSION
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cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
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cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References
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mkdir -p $PKG/install
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cat $CWD/slack-desc > $PKG/install/slack-desc
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cd $PKG
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/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE
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10
academic/vCAPS_coevolution/vCAPS_coevolution.info
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10
academic/vCAPS_coevolution/vCAPS_coevolution.info
Normal file
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@ -0,0 +1,10 @@
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PRGNAM="vCAPS_coevolution"
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VERSION="2.0_2UN"
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HOMEPAGE="http://bioinf.gen.tcd.ie/caps/home.html"
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DOWNLOAD="https://raw.githubusercontent.com/slackalaxy/sources/main/caps2_src.zip"
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MD5SUM="0914007c32ed22a9cb8a47b55cd18a39"
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DOWNLOAD_x86_64=""
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MD5SUM_x86_64=""
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REQUIRES="bpp1.9-phyl"
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MAINTAINER="Petar Petrov"
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EMAIL="slackalaxy@gmail.com"
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