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Table of contents

1. Introduction
2. Bioinformatic Scripts
   1. countCharAlign.py
   2. getPositionsChar.py
   3. convert_Single_Line.sh
3. Microfluidics
   1. micGrowthSim.py
   2. detectAndCropCircle.py

Introduction

Intro text

Bioinformatic Scripts

countCharAlign.py

Introduction: Counts a given special character (-c argument) per position in a single line fasta formatted alignment file.

Link: Here

Usage: python countCharAlign.py -i inputFasta -o output -c '.'

getPositionsChar.py

Introduction: Finds the flanking position where the given special character stops (and sequence begins) end ends (and sequence stops). Outputs a tab delimited file with the sequence header, start position of sequence, end position of sequence.

Link: Here

Usage: python getPositionChar.py -i inputFasta -o output -c '.'

convert_Single_Line.sh

Introduction: Converts from a multi-lined fasta format to a single-lined fasta format.

Link: Here

Microfludics

micGrowthSim.py

Introduction: A simulation for to find out probabilities that we will detect microbial species based on their relative abundance in the sample of origin.

Link: Here

Usage: python micGrowthSim.py

detectAndCropCircle.py

Introduction: A program that detects circles in an image, crops the sub-image, and writes it to file.

Link: Here

Usage: python detectAndCropCircle.py -i inputImageDirectory -o outputDirectory