| import inspect | |
| def render(string,variables=None): | |
| """Wrapper method for String Template: | |
| name="Jeff" | |
| render("Hello, $name") | |
| >>Hello, Jeff | |
| """ | |
| t = Template(string) | |
| if not variables: |
| #get sequences by regex match from a fasta file | |
| from argparse import ArgumentParser | |
| import re | |
| parser = ArgumentParser(description="grep for fasta IDs") | |
| group = parser.add_mutually_exclusive_group() | |
| group.add_argument("--query_string","-q") | |
| group.add_argument("--query_file","-f") |
| #include "mkl.h" | |
| #include <math.h> | |
| #include <float.h> | |
| #include <stdio.h> | |
| /* Auxiliary routine: printing a matrix */ | |
| void print_matrix(float * matrix, int nrow, int ncol) { | |
| for (int i = 0; i < nrow; i++) { | |
| for (int j = 0; j < ncol; j++) { | |
| printf("%.*e\t",FLT_DIG, matrix[i * ncol + j]); |
| #include "mkl.h" | |
| #include <math.h> | |
| #include <float.h> | |
| #include <ctime> | |
| #include <stdio.h> | |
| /* Auxiliary routine: printing a matrix */ | |
| void print_matrix(double * matrix, int nrow, int ncol) { | |
| for (int i = 0; i < nrow; i++) { | |
| for (int j = 0; j < ncol; j++) { |
| #this is a simple way to plot a matrix from a txt file | |
| mat_data_frame=read.table("data.txt",header=F) | |
| #rev is there to start plotting M(0,0) in the upper left corner | |
| #col=rainbow(10) uses the rainbow color palette. You can find other ones here: | |
| #http://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/palettes.html | |
| image(as.matrix(rev(mat_data_frame)),col=rainbow(10)) |
| #Get repo list, filter git urls | |
| GITHUB_NAME=octocat | |
| curl https://api.github.com/users/$GITHUB_NAME/repos > github_response | |
| for repo in `cat github_response | jq -r '.[] | .git_url'`; do; | |
| git clone $repo; | |
| done |
| # Use dots (.) instead of ($) | |
| R_ify <- function(expr) eval(parse(text= | |
| gsub("\\.","$",substitute(expr)))) | |
| R_ify(mtcars.mpg) |
| template <typename T> | |
| ostream &operator<<(ostream &os, const vector<T> &v) { | |
| os << "["; | |
| typename vector<T>::const_iterator it; | |
| for (it = v.begin(); it != v.end() - 1; ++it) { | |
| os << *it << ", "; | |
| } | |
| os << *(it) << "]"; | |
| return os; | |
| } |
| #include <vector> | |
| #include <numeric> | |
| #include <random> | |
| using namespace std; | |
| template <typename T> | |
| T sum(vector<T> v) { | |
| return accumulate(v.begin(), v.end(), 0.0); | |
| } |
For a given KEGG pathway, we want to get a list of all the genes. Ensembl IDs are convenient here.
KEGG provides a REST API for some tasks, but is far from complete. For example, it is possible to map from KEGG to NCBI IDs, but not to Ensembl IDs.
The implementation peforms the following steps:
