README
¶
Go (lang) genomic scripts
Quick install of goFish packages run the command:
go get -v github.com/edotau/goFish
For a full golang build, GOROOT, GOPATH, GOBIN set up:
git clone https://github.com/edotau/goFish.git; ./goFish/setup.sh
GoDocs are available: goFishDocs
Directories
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| Path | Synopsis |
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Package algorithms contains basic implementations of popular algorithms in computer science
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Package algorithms contains basic implementations of popular algorithms in computer science |
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Package api is a collection of open source golang projects repurposed or simplified into goFish functions and/or packages
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Package api is a collection of open source golang projects repurposed or simplified into goFish functions and/or packages |
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Package axt contain data structures to operate on pairwise alignment files are produced from Blastz, an alignment tool available from Webb Miller's lab at Penn State University.
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Package axt contain data structures to operate on pairwise alignment files are produced from Blastz, an alignment tool available from Webb Miller's lab at Penn State University. |
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The following code was forked and modified from grailbio.
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The following code was forked and modified from grailbio. |
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bash package implements simple bash commands that are sometimes useful when writing go scripts
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bash package implements simple bash commands that are sometimes useful when writing go scripts |
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Package bed provides an interface along with functions to compute different Browser Extinsible Data (BED) formated files.
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Package bed provides an interface along with functions to compute different Browser Extinsible Data (BED) formated files. |
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Package bigWig is used to process bigwig files which are binary compressed data to provide a visual of aligned sequencing data
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Package bigWig is used to process bigwig files which are binary compressed data to provide a visual of aligned sequencing data |
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Package chain contains data structures and functions to process genome to genome alignments pairwise alignment that allow gaps in both sequences simultaneously.
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Package chain contains data structures and functions to process genome to genome alignments pairwise alignment that allow gaps in both sequences simultaneously. |
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cmd
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alleleStats
alleleStats is a tool to investigate heterozygous snp variance and calculate fishers exact to examine the significance of the association (or contingency) between beterozygous alleles
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alleleStats is a tool to investigate heterozygous snp variance and calculate fishers exact to examine the significance of the association (or contingency) between beterozygous alleles |
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chainReader
general tool to example chain alignments between two whole genomes, find inversion, or return a simple print of all chain regions
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general tool to example chain alignments between two whole genomes, find inversion, or return a simple print of all chain regions |
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genePreDict
genePredDict is a software tool used to operate (concat, find, query or and colapse dups) on ucsc geneSeq format
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genePredDict is a software tool used to operate (concat, find, query or and colapse dups) on ucsc geneSeq format |
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geneSeQuery
geneSeQueryL processes data tables from gtf, gff3, and genePred gene feture formats, process custom data frames, and sql querys from ensembl and ucsc databases
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geneSeQueryL processes data tables from gtf, gff3, and genePred gene feture formats, process custom data frames, and sql querys from ensembl and ucsc databases |
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goIndels
goIndels - is a quick script to fild indels in sam/bam alignment
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goIndels - is a quick script to fild indels in sam/bam alignment |
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goToBed
goToBed is a simplified version of ucsc overlap section to analyze non/overlapping genomic regions in a dataset and filtering var variants of interests
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goToBed is a simplified version of ucsc overlap section to analyze non/overlapping genomic regions in a dataset and filtering var variants of interests |
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nucmerParse
nucmerParse is used parse and extra interesting genomic regions from nucmer suffix tree alignments
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nucmerParse is used parse and extra interesting genomic regions from nucmer suffix tree alignments |
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statFastQc
vimFastqc quickly access esfastq quality control metrics
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vimFastqc quickly access esfastq quality control metrics |
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templates
Package templates contain golang template scripts for quick and easy golang programing
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Package templates contain golang template scripts for quick and easy golang programing |
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vimBam
vimBam
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vimBam |
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vimUrl
vimUrl can view http url links and print data stream to stdout
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vimUrl can view http url links and print data stream to stdout |
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Package code describes biological sequence letters coded by bytes and sometimes encoded into hash int64s
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Package code describes biological sequence letters coded by bytes and sometimes encoded into hash int64s |
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Package concurrency contains functions used to build concurrent processes and/or tasks in both pipelines and workflows very much still in development
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Package concurrency contains functions used to build concurrent processes and/or tasks in both pipelines and workflows very much still in development |
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Package csv contains data structures to parse comma separated value takes and perform statical analysis
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Package csv contains data structures to parse comma separated value takes and perform statical analysis |
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dataflow package is an implementation combining workflow/tasks mananging concpets most popular in data science.
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dataflow package is an implementation combining workflow/tasks mananging concpets most popular in data science. |
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Package fasta contains data structures for processes and functions that operate on fasta files containing base sequences
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Package fasta contains data structures for processes and functions that operate on fasta files containing base sequences |
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Package fastq contains data structures and functions to process sequencing data coming off the sequencer
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Package fastq contains data structures and functions to process sequencing data coming off the sequencer |
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GeneSeq contains functions and other data structures for processing gene models and annotations from difference public data bases like ENSEMBL and UCSC Currently supports genePred and GTF formats
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GeneSeq contains functions and other data structures for processing gene models and annotations from difference public data bases like ENSEMBL and UCSC Currently supports genePred and GTF formats |
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GraphQL is a simple low-level client modified from https://github.com/machinebox/graphql
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GraphQL is a simple low-level client modified from https://github.com/machinebox/graphql |
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Package keras implements many functionalities from the popular Keras API which is a deep learning API written in Python, running on top of the machine learning platform TensorFlow.
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Package keras implements many functionalities from the popular Keras API which is a deep learning API written in Python, running on top of the machine learning platform TensorFlow. |
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Modified from https://github.com/cdipaolo/goml for the sole purpose of teaching myself how to implement machine learning models from scratch Original code and documentation can be found at: https://github.com/cdipaolo/goml
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Modified from https://github.com/cdipaolo/goml for the sole purpose of teaching myself how to implement machine learning models from scratch Original code and documentation can be found at: https://github.com/cdipaolo/goml |
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Package reference contains reference information useful for building hash lookups of genomes
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Package reference contains reference information useful for building hash lookups of genomes |
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Package simpleio contains core utils that reading in data optimized for both memory allocation, speed, and performance
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Package simpleio contains core utils that reading in data optimized for both memory allocation, speed, and performance |
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Package stats contains functions to perform statistical tests
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Package stats contains functions to perform statistical tests |
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Package vcf declares vcf struct data fields and contains methods and functions that operate on the Vcf struct
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Package vcf declares vcf struct data fields and contains methods and functions that operate on the Vcf struct |
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