brantfaircloth

#!/usr/bin/env python
# encoding: utf-8
"""
bed_from_genbank.py

grab the gene records from a genbank file (edit for other record types).

- requires:  biopython

"""

jeetsukumaran

#! /usr/bin/env python

##############################################################################
# Following functions have been taken from the DendroPy library from:
##
##  DendroPy Phylogenetic Computing Library.
##
##  Copyright 2010 Jeet Sukumaran and Mark T. Holder.
##  All rights reserved.
##

nickloman

rsync -av rsync://ftp.ncbi.nlm.nih.gov/genomes/Bacteria --include "*/" --include "Bacteria/Escherichia*/*.fna" --exclude=* .

# bonus script - concatenate chromosomes and plasmids into single fasta file, make sure the files don't already exist

find . -mindepth 1 -type d | xargs -L 1 -I '{}' find {} -name "*.fna" | while read i ; do cat "$i" >> `dirname "$i"`.fasta ; done

davidshinn

#!/usr/bin/env python
"""
simple example script for running and testing notebook resulting in a new workbook.

Usage: `ipnbdoctest.py foo.ipynb foo_new.ipynb`

Each cell is submitted to the kernel, and the outputs are compared with those stored in the notebook.
"""

import io

rchikhi

#!/usr/bin/env python
doc = """
Quickly estimates insert sizes of read datasets, given some sequence(s) they can be mapped to.
Author: Rayan Chikhi         

short usage: <reference> <*.fastq> 

example: 
         estimate-insert-sizes contigs.fa readsA_1.fq readsA_2.fq readsB_1.fq readsB_2.fq

code-of-kpp

import numbers

import six

import numpy
import matplotlib.collections
from matplotlib import pyplot

# using example from
# http://nbviewer.ipython.org/github/dpsanders/matplotlib-examples/blob/master/colorline.ipynb