LeeBergstrand

#!/usr/bin/env python 
# Created by: Lee Bergstrand 
# Descript: A simple script that modifies the elements inside a column of a CSV by
#           using a regular expression to find and replace charaters in those elements.
#
# Usage: CSVmod.py <input.csv> <output.csv> <columnNumber> <regex> <replace>
# Example: CSVmod.py myInput.csv myOutput.csv 6 ^[\t]+|[\t]$ replacement
#----------------------------------------------------------------------------------------

import csv

LeeBergstrand

#!/usr/bin/env python 
# Created by: Lee Bergstrand 
# Descript: Converts multiline FASTAs to single line FASTAs
#  
# Usage: FastaMLtoSL.py <sequences.faa> 
# Example: FastaMLtoSL.py mySeqs.faa 
#----------------------------------------------------------------------------------------
#===========================================================================================================
#Imports:
	

LeeBergstrand

.idea

LeeBergstrand

dbCAN Hmmscan Parser Issue

I was recently reverse engineering dbCAN's shell/perl script (hmmscan-parser.sh) for parsing HMMER's hmmscan human readable text results. Unfortunately, while figuring out how this script works I found an error.

#####Orignal Script:

	#!/usr/bin/env sh
	# Yanbin Yin
	# 08/18/2011

LeeBergstrand

require 'formula'

class Pypy < Formula
  homepage 'http://pypy.org/'
  url 'https://bitbucket.org/pypy/pypy/downloads/pypy-2.3-linux64.tar.bz2'
  version '2.3.0'
  sha1 '5bf5e2b2d9a002a9d81830dfffe5fa68959a8f40'

  resource 'setuptools' do
    url 'https://pypi.python.org/packages/source/s/setuptools/setuptools-3.6.tar.gz'

LeeBergstrand

#!/usr/bin/env python 
# Why you should think about hidden escape characters in your code...
# Only some editors show hidden characters.

Blam = 	":" 			
print repr(Blam)
Blam =	":" 			
print repr(Blam)

print repr("WAT")

LeeBergstrand

#!/usr/bin/env python 
# Created by: Lee Bergstrand
# Modified by: Matt McInnes
# License: MIT
# Descript: Trims FASTAs from the assembler SPAdes by coverage to remove low coverage contigs.
# ----------------------------------------------------------------------------------------
# ===========================================================================================================
# Imports:

import argparse

LeeBergstrand

==> Downloading https://downloads.sourceforge.net/project/boost/boost/1.58.0/boost_1_58_0.tar.bz2
Already downloaded: /home/lee2/.cache/Homebrew/boost-1.58.0.tar.bz2
==> Verifying boost-1.58.0.tar.bz2 checksum
tar xf /home/lee2/.cache/Homebrew/boost-1.58.0.tar.bz2
==> ./bootstrap.sh --prefix=/home/lee2/.linuxbrew/Cellar/boost/1.58.0 --libdir=/home/lee2/.linuxbrew/Cellar/boost/1.58.0/lib --without-icu --without-libraries=python,mpi
Building Boost.Build engine with toolset gcc... tools/build/src/engine/bin.linuxx86_64/b2
Unicode/ICU support for Boost.Regex?... disabled.
Generating Boost.Build configuration in project-config.jam...

Bootstrapping is done. To build, run:

LeeBergstrand

#!/usr/bin/env bash

if [ $# -eq 0 ] 
then
	echo "No arguments supplied..."
	echo "Please provide a minimum number of seqs per file."
	exit 1 
fi

MIN_LENGTH=$1

LeeBergstrand

Take this part of the config for example:

      - restore_cache:
          keys:
          - v1-dependencies-{{ checksum "requirements.txt" }}
          - v1-dependencies-
          
      - save_cache:
          key: v1-dependencies-{{ checksum "requirements.txt" }}
 paths: