Lee Bergstrand 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

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:

	#!/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

	#!/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:

	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'

	#!/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")

	#!/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

	==> 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:

	#!/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