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Tutorials (#184)
* Added example_test for genbank and gff * Added SIMPLE tutorials and notes for each parser. * Revamped seqhash docs and added simple tutorial * moved example seqhash to example_test - does this make it runnable? Co-authored-by: Timothy Stiles <[email protected]>
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‎io/fasta/example_test.go‎

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package fasta_test
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import (
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"fmt"
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"github.com/TimothyStiles/poly/io/fasta"
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)
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// This example shows how to open a file with the fasta parser. The sequences
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// within that file can then be analyzed further with different software.
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func Example_basic() {
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fastas := fasta.Read("data/base.fasta")
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fmt.Println(fastas[1].Sequence)
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// Output: ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK*
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}

‎io/fasta/fasta.go‎

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/*
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Package fasta contains fasta parsers and writers.
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Fasta is a flat text file format developed in 1985 to store nucleotide and
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amino acid sequences. It is extremely simple and well supported across many
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languages. However, this simplicity means that annotation of genetic objects
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is not supported.
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This package provides a parser and writer for working with Fasta formatted
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genetic sequences.
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*/
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package fasta
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import (
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/******************************************************************************
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Apr 25, 2021
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Parser begins here
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Fasta Parser begins here
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Many thanks to Jordan Campbell (https://github.com/0x106) for building the first
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parser for Poly and thanks to Tim Stiles (https://github.com/TimothyStiles)
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for helping complete that PR. This work expands on the previous work by allowing
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for concurrent parsing and giving Poly a specific parser subpackage,
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as well as few bug fixes.
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is a very simple file format for working with DNA, RNA, or protein sequences.
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Fasta is a very simple file format for working with DNA, RNA, or protein sequences.
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It was first released in 1985 and is still widely used in bioinformatics.
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https://en.wikipedia.org/wiki/_format
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One interesting use of the concurrent parser is working with the Uniprot
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dump files, which are far too large to fit into RAM. This parser is able
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fasta dump files, which are far too large to fit into RAM. This parser is able
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to easily handle those files by doing computation actively while the data dump
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is getting parsed.
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‎io/genbank/example_test.go‎

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package genbank_test
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import (
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"fmt"
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"github.com/TimothyStiles/poly/io/genbank"
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)
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// This example shows how to open a genbank file and search for a gene given
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// its name. After finding it, notes about the particular gene are read.
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func Example_basic() {
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sequence := genbank.Read("../../data/puc19.gbk")
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for _, feature := range sequence.Features {
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if feature.Attributes["gene"] == "bla" {
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fmt.Println(feature.Attributes["note"])
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}
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}
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// Output: confers resistance to ampicillin, carbenicillin, andrelated antibiotics
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}

‎io/genbank/genbank.go‎

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/*
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Package genbank provides genbank parsers and writers.
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GenBank is a flat text file format developed in the 1980s to annotate genetic
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sequences, and has since become the standard for sharing annotated genetic
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sequences.
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This package provides a parser and writer to convert between the GenBank file
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format and the more general poly.Sequence struct.
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*/
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package genbank
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import (

‎io/gff/example_test.go‎

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package gff_test
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import (
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"fmt"
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"github.com/TimothyStiles/poly/io/gff"
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)
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// This example shows how to open a gff file and search for a gene given its
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// locus tag. We then display the EC number of that particular gene.
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func Example_basic() {
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sequence := gff.Read("../../data/ecoli-mg1655-short.gff")
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for _, feature := range sequence.Features {
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if feature.Attributes["locus_tag"] == "b0003" {
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fmt.Println(feature.Attributes["EC_number"])
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}
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}
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// Output: 2.7.1.39
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}

‎io/gff/gff.go‎

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/*
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Package gff provides gff parsers and writers.
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GFF stands for "general feature format". It is an alternative to GenBank for
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storing data about genomic sequences. While not often used in synthetic biology
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research, it is more commonly used in bioinformatics for digesting features of
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genomic sequences.
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This package provides a parser and writer to convert between the gff file
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format and the more general poly.Sequence struct.
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*/
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package gff
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import (

‎io/rebase/example_test.go‎

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package rebase_test
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import (
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"fmt"
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"github.com/TimothyStiles/poly/io/rebase"
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)
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// This example reads rebase into an enzymeMap and returns the AarI recognition
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// sequence.
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func Example_basic() {
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enzymeMap, _ := rebase.Read("data/rebase_test.txt")
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fmt.Println(enzymeMap["AarI"].RecognitionSequence)
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// Output: CACCTGC(4/8)
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}

‎io/rebase/rebase.go‎

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package rebase
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/*
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Package rebase contains a rebase parser for rebase data dump #31.
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import (
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"encoding/json"
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"io/ioutil"
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"strings"
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)
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/******************************************************************************
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Apr 25, 2021
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REBASE Parser #31 here.
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In order to effectively simulate cloning reactions, we need to know how each
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restriction enzyme in the reaction functions. This data can be derived, in
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bulk, from the REBASE database.
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REBASE is an amazing resource run by New England Biolabs listing essentially
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every known restriction enzyme. In particular, this parser parses the REBASE
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The actual data dump itself is linked here and updated once a month:
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http://rebase.neb.com/rebase/link_withrefm
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In ./data/rebase_test.txt we have the first 1002 lines of link_withrefm from
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Apr 25, 2021. From this file, we will extract lists of restriction enzymes,
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which can be used for simulation of restriction enzyme cutting and for cloning.
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The header of this file gives a wonderful explanation of its structure. Here is the
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header with the commercial suppliers format and an example enzyme.
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Cheers,
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Keoni Gandall
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```
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REBASE version 104 withrefm.104
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<8>Tagami, H., Tayama, K., Tohyama, T., Fukaya, M., Okumura, H., Kawamura, Y., Horinouchi, S., Beppu, T., (1988) FEMS Microbiol. Lett., vol. 56, pp. 161-166.
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```
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******************************************************************************/
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*/
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package rebase
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import (
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"encoding/json"
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"io/ioutil"
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"strings"
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)
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// Enzyme represents a single enzyme within the Rebase database
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type Enzyme struct {

‎io/uniprot/example_test.go‎

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package uniprot_test
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import (
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"fmt"
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"github.com/TimothyStiles/poly/io/uniprot"
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)
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// This example shows how to open a uniprot data dump file and read the results
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// into a list. Directly using the channel without converting to an array
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// should be used for the Trembl data dump
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func Example_basic() {
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entries, _, _ := uniprot.Read("data/uniprot_sprot_mini.xml.gz")
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var entry uniprot.Entry
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for singleEntry := range entries {
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entry = singleEntry
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}
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fmt.Println(entry.Accession[0])
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// Output: O55723
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}

‎io/uniprot/uniprot.go‎

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/*
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Package uniprot provides an XML parser for Uniprot data dumps.
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Uniprot is comprehensive, high-quality and freely accessible resource of protein
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sequence and functional information. It is the best(1) protein database out there.
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Uniprot database dumps are available as gzipped FASTA files or gzipped XML files.
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The XML files have significantly more information than the FASTA files, and this
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parser specifically works on the gzipped XML files from Uniprot.
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Uniprot provides an XML schema of their data dumps(3), which is useful for
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autogeneration of Golang structs. xsdgen was used to automatically generate
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xml.go from uniprot.xsd.
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Each protein in Uniprot is known as an "Entry" (as defined in xml.go).
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The function Parse stream-reads Uniprot into an Entry channel, from which you
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can use the entries however you want. Read simplifies reading gzipped files
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from a disk into an Entry channel.
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*/
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package uniprot
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import (

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