This is one of the standard library utilities that is not given the attention it deserves. cgitb gives you detailed information about an error, and I ...
Every time I write something in python, I like to make it possible to people to get informative message when they fail to run a tool because they are ...
This code doesn't work looks like some issue in defining the list in KEYS.Although all the values are mentioned properly still while executing the sys ...
This is an example where we can use ruffus proxy logging to share the log between different tasks. Of course we can use the traditional logging stuff ...
This is a quick way of displaying the git log as a nice tree on the browser.I will be cloning the google genomics repo on github as an exampleLogin to ...
This is a small tool I added lately on github. I had to monitor some disk usage for our group members on our servers so I had to develop a small cron ...
A function to shuffle multiple NumPy arrays in unison. One typical use case could be the shuffling of training data and the corresponding class labels ...
This is a small function that I am using in one of my pipelines that send information about the size of a specific file, It is fun to use and may be u ...
I just struggled a little bit of converting ~10 Gb sized CSVs to SQLite databases for more effective processing because of memory issues :PI came up w ...
A customer in a store is purchasing five items. Design a program that asks for theprice of each item, and then displays the subtotal of the sale, the ...
I came across this nice package python-progressbar and I am sharing one of the examples they provide. It is a nice way of keeping your package users a ...
I am heavily into sports predictions these days where I collect raw data from various different sources. One of the challenges is to merge the informa ...
The shell commands like `find` inlinux/unix environments are quite powerful and useful. However, often I want to get a bunch of file paths as an itera ...
I found this package useful in case we want to display nice tables as output in some python programs, so I tried it and decided to add it to CodersCro ...
this is one of the snippets I have configured with my Sublime Editor, I like to have some snippets and code like that to play with the data or if I ha ...
I am a novice programmer. I made this script to search for DNA Fur-binding sequences (ATTATTANTAATAAT or TAATAATNATTATTA), allowing for up to 2 mismat ...
There is a lot of tools out there, very useful for command line usage, and very widely used in Bioinformatics, which rapidly turns out to be annoying ...
Hi, I'm trying to generalize my program for a planetary orbit to more planets, so I wrote a Planet class.I know it works because it prints the positio ...
This is a Bayesian classifier that handles conditional dependence by splitting the feature space into pairs and approximating the cummulative probabil ...
I came across this package lately and I decided to test it since I was always looking at an ORM like system but with no database layer related to it, ...
This is a quite usual task we always run through, we have a target (region) list with location and we want to get the coverage from a bam file on thes ...
The code here tries to open a fasta file including mature miRNA sequences and read them for counting their 3mer contents. Here the purpose is to show ...
In this code I am parsing a fastq file and I am extracting all sequences length to an array, that I feed to numpy and then got the average sequence le ...
I am working on a pipeline with Ruffus and I have a lot of Tasks that depends on other Tasks using the @follows decorator. It happens that when testin ...
One of the usual tasks when it comes to examine an alignment file is to check the number of reads that successfully mapped to the reference genome and ...
Django middleware that can turn any url of your application into its own profile, either as text output or as binary output that can later be analysed ...
I came through this approach to intersect dataframes in R, I am sure there is a lot of other way of doing this but this solved my problem today :), if ...
I am developing a pipeline, and the program is outputting a lot of information in stderr that I didnt want to store in log file, I just need one or tw ...
I have a large tabular blast file that I am trying to filter.I would like to print the first instance of a match, and the any reflections of a match.F ...
I added Ruffus as a runnable instalnce at CodersCrowd in order to showcase all good things that can be built with this library, and also to solve prob ...
Today I wanted to monitor a code block in python and I was interested in knowing basic information on elapsed time per function. A lot of solutions ex ...
I am using the default color palette from ggplot2 and would like to be abe to extract the colors mapped to my variablemy function is like follows :p = ...
Hi,This is a particular question. As you all know we are making it possible to run codes @CodersCrowd, what a lot of members suggested is that most co ...
Here is an example of something I wanted to be implemented directly in intersectBed that can sometimes be useful. It would be great to adda flavor of ...
Another implementation of SW algorithm. This example can be used and embedded into a code that relies on SW for local alignment, I find it handy for e ...
Here is something I do frequently, I just thought it might be useful to share. Sometimes I do create dataframe and do some graphic output using ggplot ...
A lot of big streaming companies like Spotify, Pandora, etc are more and more pushing towards a better and more stable frameworks and the best thing t ...
Hello all,I am using a pachage from Bioconductor TEQC, and when I load my reads as a bam file, the object created (class RangedData) looks like thisRa ...
As any process that you would run on python, I used to use subprocess on my python codes to run bedtools utilities such as intersectBed, until I met p ...
As I am sure many of you, I use extensively join, sort and grep programs in the shell.However, although very fast, these programs do have some limitat ...
Here is an implementation (one of many on the web), of the local and global alignment in python. I am creating this code with errors introduced intent ...
Today I used ShortRead R package when I was checking a series of fastq files after finding out that I had an alignment showing huge coverage at some p ...
A script for gene set enrichment over KEGG, the perl script serves as automation for the analysis of several gene set files inside a directory, the R ...
The python script rpkmforgenes.py is written for calculating gene expression for RNA-Seq data. It was used for a study published in PLoS Computational ...
A basic example script using the Biomart Rubygem to retrieve genomic co-ordinates based on a text list of reference transcript ids. Used to construct ...
I am trying to extract flanking regions of a list of SNPs, I implemented my code in R using Bioconductor and even though the process seems straightfor ...
CIGAR strings are a mandatory field in the Sequence Alignment/Mapping (SAM) specification. This field describes the relationship between the alignment ...
This is a part 3/3 of "one-line series". One-line commands with perl, awk or sed are very useful in bioinformatics for data/files manipulation. There ...
This is a part 2/3 of "one-line series". One-line commands with perl, awk or sed are very useful in bioinformatics for data/files manipulation. There ...
This is a part 1/3 of "one-line series". One-line commands with perl, awk or sed are very useful in bioinformatics for data/files manipulation. There ...
This is an interesting implementation for RNA-seq analysis in python developed by Hanfei Sun. You can find the source code and the documentation https ...
This script calls the program bigWigSummary to extract enrichment from a bunch of bigWig files (they can be a lot of ChIP-seq experiments for example) ...
Obtaining the actual sequence making up a gene from NCBI is simple using a browser, but not so much when wanting to do it in batch. This script obtain ...
A sample script using the ETE package to detect shift in internal nodes where a significant change in enrichment values (could be anything) happens ...
A typical task in bioinformatics analysis is the usage of online tools. Regardless of the task to be done, there is a general approach to display resu ...
Analyze human Genome in R. Read more here http://www.biocodershub.net/community/analyzing-human-genome-r-scripts/ and here http://userwww.service.emor ...
Homemade Genbank report parser using regular expressions. Once desired data is captured, it can be printed in any format.WI Bioinformatics course - Fe ...
Correlation is one of the most used tasks in computational biology, while using packages like R is very simple, sometimes we need to do it on the fly ...
