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

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

version: 2
jobs:
  build:

    working_directory: ~/repo

    machine: true

    steps:
        - checkout

LeeBergstrand

#!/usr/bin/env python3

"""
Created by: Lee Bergstrand

Description: Makes newer InterProScan TSV file compatible with Pygenprop.

Requirements:  None

"""

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

NC_007514.1_1800	2da1d06b2f7f511868a9c2917777ab82	498	Pfam	PF12183	Restriction endonuclease NotI	231	461	7.8E-98	T	14-05-2018	IPR022009	Restriction endonuclease, type II, NotI		
NC_007514.1_1661	c1968ae7cab9a5d53947002f3518f2c2	247	Pfam	PF02585	GlcNAc-PI de-N-acetylase	11	127	4.3E-21	T	14-05-2018	IPR003737	N-acetylglucosaminyl phosphatidylinositol deacetylase-related		Reactome: R-HSA-162710
NC_007514.1_1661	c1968ae7cab9a5d53947002f3518f2c2	247	TIGRFAM	TIGR04001	thiol_BshB1: bacillithiol biosynthesis deacetylase BshB1	8	235	1.9E-96	T	14-05-2018	IPR023842	Bacillithiol biosynthesis deacetylase, BshB1	GO:0019213|GO:0071793	
NC_007514.1_1661	c1968ae7cab9a5d53947002f3518f2c2	247	PANTHER	PTHR12993:SF21		11	232	2.8E-49	T	14-05-2018
NC_007514.1_1661	c1968ae7cab9a5d53947002f3518f2c2	247	PANTHER	PTHR12993		11	232	2.8E-49	T	14-05-2018	IPR003737	N-acetylglucosaminyl phosphatidylinositol deacetylase-related		Reactome: R-HSA-162710
NC_007514.1_1652	87cd3c15562a2ce4954e59e9d87f2ae8	404	Pfam	PF01747	ATP-sulfurylase	175	385	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:

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

==> 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 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