Programming languages

A simple GFF3 parser in Python

Problem:

You need to parse a GFF3 file containing information about sequence features. You prefer to use a minimal, depedency-free solution instead of importing the GFF3 data into a database right away. However, you need to have a standard-compatible parser

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Posted by Uli Köhler in Bioinformatics, Python

A GeneOntology OBO v1.4 parser in Python

The GeneOntology Consortium provides bulk data download for the GO terms in the OBO v1.2 format.

If you Google GO OBO parser, there is something missing. You can easily find parsers in Perl, parsers in Java, but not even BioPython has a parser in Python. The format itself, however seems like it’s tailor-made for Python’s generator concept. Only a few SLOCs are needed to get it work without storing everything in RAM.

I used this parser in a prototype project that allows to search GO interactively (it’s fast). I’m not sure when/if I’ll publish that, but here is the parser code.

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Posted by Uli Köhler in Bioinformatics, Python

A simple tool for FASTA statistics

The issue

It is surprisingly difficult to compute simple statistics of FASTA files using existing software. I recently needed to compute the nucleotide count and relative GC frequency of a single sequence in FASTA format, but unless you install dependency-heavy native software like FASTX or you develop it by yourself using BioPython or similar, there doesn’t seem to be a simple, dependency-free solution for this simple set of problem.

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Posted by Uli Köhler in Bioinformatics, Python

mmap with Boost IOStreams: A minimalist’s example

The following C++ program uses boost::iostreams to memory-map a file, read it’s content into a std::string and print it to cout.

It provides a minimal example of how to use the boost::iostreams portable mmap functionality.

//Compile like this: g++ -o mmap mmap.cpp -lboost_iostreams
#include <boost/iostreams/device/mapped_file.hpp>
#include <iostream>
#include <string>
using namespace std;
using namespace boost::iostreams;

int main(int argc, char** argv) {
   //Initialize the memory-mapped file
   mapped_file_source file(argv[1]);
   //Read the entire file into a string
   string fileContent(file.data(), file.size());
   //Print the string
   cout << fileContent;
   //Cleanup
   file.close();
}

Also see A simple mmap() readonly example

Posted by Uli Köhler in C/C++

Reading TAR files in C++

This article describes a method of  reading TAR archives (including .tar.gz and .tar.bz2) in C++ using Boost IOStreams.

You could use libtar for this, but the original version hasn’t been updated since 2003 and doesn’t provide you flexibility and insight to the internal structure of a TAR archive. Continue reading →

Posted by Uli Köhler in Algorithms, C/C++

How to compile & install libc++ on Linux

Problem:

You want to compile and install libc++ (sometimes also named libcxx), but CMake complains with this error message

CMake Error at cmake/Modules/MacroEnsureOutOfSourceBuild.cmake:7 (message):
libcxx requires an out of source build. Please create a separate</em>

build directory and run 'cmake /path/to/libcxx [options]' there.
Call Stack (most recent call first):
 CMakeLists.txt:24 (MACRO_ENSURE_OUT_OF_SOURCE_BUILD)
CMake Error at cmake/Modules/MacroEnsureOutOfSourceBuild.cmake:8 (message):
 In-source builds are not allowed.

CMake would overwrite the makefiles distributed with Compiler-RT.
 Please create a directory and run cmake from there, passing the path
 to this source directory as the last argument.
 This process created the file `CMakeCache.txt' and the directory `CMakeFiles'.
 Please delete them.
Call Stack (most recent call first):
 CMakeLists.txt:24 (MACRO_ENSURE_OUT_OF_SOURCE_BUILD)

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Posted by Uli Köhler in Build systems, C/C++, Linux

git svn: Clone latest revision only

Problem:

You want to use git-svn to clone a SVN repository, but you don’t want to clone the entire history (which can be quite slow) but only the latest revision.

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Posted by Uli Köhler in git, Shell, Subversion, Version management

Compiling LevelDB as LLVM binary on Linux

Some time ago I wrote a guide on how to compile and install LevelDB on Linux.

Recently I’m desperately trying to get into LLVM and a tutorial series on how to use LLVM with C/C++ is coming shortly.

As I’m using LevelDB in many of my projects I’d like a way of generating a LLVM IR (intermediate representation) of the LevelDB C++ source – I could link a LLVM program to the native binary, but in order to profit from LLVMs features I suppose using IRs for as many dependencies as possible is the way to go.

Generally there are two ways to go:

  1. Use the g++ LLVM backend
  2. Use clang++

I usually tend to use clang++ for LLVM tasks because even with colorgcc and some recent improvements in gcc error message generation I prefer the clang++ error messages, even if I have way more experience with gcc error messages. Additionally the g++ with LLVM backend does seem to have some bugs, including interpreting -emit-llvm as -e -m -i …, plus recent distribution versions don’t work too well with the LLVM gold plugin and it has proved difficult to tell GCC reliably that it shall use llvm-ld as linker.

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Posted by Uli Köhler in C/C++, Databases, LLVM