Merge pull request #394 from abondrn/ioToBio-genbank

multimap implemented

CHANGELOG.md

@@ -10,10 +10,19 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Added
 - Alternative start codons can now be used in the `synthesis/codon` DNA -> protein translation package (#305)
 - Added a parser and writer for the `pileup` sequence alignment format (#329)
+- Created copy methods for Feature and Location to address concerns raised by [(#342)](https://github.com/TimothyStiles/poly/issues/342)
+- Created new methods to convert polyjson -> genbank.
+- Created new `Feature.StoreSequence` method to enable [(#388)](https://github.com/TimothyStiles/poly/issues/388)
+
+### Changed
+- **Breaking**: Genbank parser uses new custom multimap for `Feature.Attributes`, which allows for duplicate keys. This changes the type of Features.Attributes from `map[string]string` to `MultiMap[string, string]`, an alias for `map[string]string` defined in `multimap.go`. [(#383)](https://github.com/TimothyStiles/poly/issues/383)
+- Improves error reporting for genbank parse errors via a new `ParseError` struct.
 
 ### Fixed
 - `fastq` parser no longer becomes de-aligned when reading (#325)
 - `fastq` now handles optionals correctly (#323)
+- Adds functional test and fix for [(#313)](https://github.com/TimothyStiles/poly/issues/313).
+- In addition to expanding the set of genbank files which can be validly parsed, the parser is more vocal when it encounters unusual syntax in the "feature" section. This "fail fast" approach is better as there were cases where inputs triggered a codepath which would neither return a valid Genbank object nor an error, and should help with debugging.
 
 ## [0.26.0] - 2023-07-22
 Oops, we weren't keeping a changelog before this tag!

CONTRIBUTING.md

@@ -93,6 +93,18 @@ In order to simplify the development experience, and environment setup, the poly
 
 Whether you're a beginner with Go or you're an experienced developer, You should see the suggestions popup automatically when you goto the *Plugins* tab in VSCode. Using these plugins can help accelerate the development experience and also allow you to work more collaboratively with other poly developers.
 
+## Local Checks
+
+Poly runs numerous CI/CD checks via Github Actions before a PR can be merged. In order to make your PR mergeable, your PR must pass all of these checks.
+
+A quick way to check your PR will pass is to run:
+
+```sh
+gofmt -s -w . && go test ./...
+```
+
+Additionally, you may want to [install](https://golangci-lint.run/usage/install/#local-installation) and run the linter.
+
 # How to report a bug
 
 ### Security disclosures

bio/example_test.go

@@ -253,7 +253,7 @@ ORIGIN
 	records, _ := parser.Parse()
 
 	fmt.Println(records[0].Features[2].Attributes["translation"])
-	// Output: MTMITPSLHACRSTLEDPRVPSSNSLAVVLQRRDWENPGVTQLNRLAAHPPFASWRNSEEARTDRPSQQLRSLNGEWRLMRYFLLTHLCGISHRIWCTLSTICSDAA
+	// Output: [MTMITPSLHACRSTLEDPRVPSSNSLAVVLQRRDWENPGVTQLNRLAAHPPFASWRNSEEARTDRPSQQLRSLNGEWRLMRYFLLTHLCGISHRIWCTLSTICSDAA]
 }
 
 func ExampleNewSlow5Parser() {

bio/fasta/fasta.go

@@ -26,15 +26,15 @@ Fasta Parser begins here
 Many thanks to Jordan Campbell (https://github.com/0x106) for building the first
 parser for Poly and thanks to Tim Stiles (https://github.com/TimothyStiles)
 for helping complete that PR. This work expands on the previous work by allowing
-for concurrent  parsing and giving Poly a specific  parser subpackage,
+for concurrent  parsing and giving Poly a specific parser subpackage,
 as well as few bug fixes.
 
 Fasta is a very simple file format for working with DNA, RNA, or protein sequences.
 It was first released in 1985 and is still widely used in bioinformatics.
 
-https://en.wikipedia.org/wiki/_format
+https://en.wikipedia.org/wiki/FASTA_format
 
-One interesting use of the concurrent  parser is working with the Uniprot
+One interesting use of the concurrent parser is working with the Uniprot
 fasta dump files, which are far too large to fit into RAM. This parser is able
 to easily handle those files by doing computation actively while the data dump
 is getting parsed.

bio/genbank/data/NC_001141.2_redux.gb

@@ -0,0 +1,147 @@
+LOCUS       NC_001141             439888 bp    DNA     linear   CON 15-SEP-2023
+DEFINITION  Saccharomyces cerevisiae S288C chromosome IX, complete sequence.
+ACCESSION   NC_001141
+VERSION     NC_001141.2
+DBLINK      BioProject: PRJNA128
+            Assembly: GCF_000146045.2
+KEYWORDS    RefSeq.
+SOURCE      Saccharomyces cerevisiae S288C
+  ORGANISM  Saccharomyces cerevisiae S288C
+            Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina;
+            Saccharomycetes; Saccharomycetales; Saccharomycetaceae;
+            Saccharomyces.
+REFERENCE   1  (bases 1 to 439888)
+  AUTHORS   Engel,S.R., Wong,E.D., Nash,R.S., Aleksander,S., Alexander,M.,
+            Douglass,E., Karra,K., Miyasato,S.R., Simison,M., Skrzypek,M.S.,
+            Weng,S. and Cherry,J.M.
+  TITLE     New data and collaborations at the Saccharomyces Genome Database:
+            updated reference genome, alleles, and the Alliance of Genome
+            Resources
+  JOURNAL   Genetics 220 (4) (2022)
+   PUBMED   34897464
+REFERENCE   2  (bases 1 to 439888)
+  AUTHORS   Churcher,C., Bowman,S., Badcock,K., Bankier,A., Brown,D.,
+            Chillingworth,T., Connor,R., Devlin,K., Gentles,S., Hamlin,N.,
+            Harris,D., Horsnell,T., Hunt,S., Jagels,K., Jones,M., Lye,G.,
+            Moule,S., Odell,C., Pearson,D., Rajandream,M., Rice,P., Rowley,N.,
+            Skelton,J., Smith,V., Barrell,B. et al.
+  TITLE     The nucleotide sequence of Saccharomyces cerevisiae chromosome IX
+  JOURNAL   Nature 387 (6632 SUPPL), 84-87 (1997)
+   PUBMED   9169870
+REFERENCE   3  (bases 1 to 439888)
+  AUTHORS   Goffeau,A., Barrell,B.G., Bussey,H., Davis,R.W., Dujon,B.,
+            Feldmann,H., Galibert,F., Hoheisel,J.D., Jacq,C., Johnston,M.,
+            Louis,E.J., Mewes,H.W., Murakami,Y., Philippsen,P., Tettelin,H. and
+            Oliver,S.G.
+  TITLE     Life with 6000 genes
+  JOURNAL   Science 274 (5287), 546 (1996)
+   PUBMED   8849441
+REFERENCE   4  (bases 1 to 439888)
+  CONSRTM   NCBI Genome Project
+  TITLE     Direct Submission
+  JOURNAL   Submitted (14-SEP-2023) National Center for Biotechnology
+            Information, NIH, Bethesda, MD 20894, USA
+REFERENCE   5  (bases 1 to 439888)
+  CONSRTM   Saccharomyces Genome Database
+  TITLE     Direct Submission
+  JOURNAL   Submitted (04-MAY-2012) Department of Genetics, Stanford
+            University, Stanford, CA 94305-5120, USA
+  REMARK    Protein update by submitter
+REFERENCE   6  (bases 1 to 439888)
+  CONSRTM   Saccharomyces Genome Database
+  TITLE     Direct Submission
+  JOURNAL   Submitted (31-MAR-2011) Department of Genetics, Stanford
+            University, Stanford, CA 94305-5120, USA
+  REMARK    Sequence update by submitter
+REFERENCE   7  (bases 1 to 439888)
+  CONSRTM   Saccharomyces Genome Database
+  TITLE     Direct Submission
+  JOURNAL   Submitted (14-DEC-2009) Department of Genetics, Stanford
+            University, Stanford, CA 94305-5120, USA
+COMMENT     REVIEWED REFSEQ: This record has been curated by SGD. The reference
+            sequence is identical to BK006942.
+
+            On Apr 26, 2011 this sequence version replaced NC_001141.1.
+
+            ##Genome-Annotation-Data-START##
+            Annotation Provider :: SGD
+            Annotation Status   :: Full Annotation
+            Annotation Version  :: R64-4-1
+            URL                 :: http://www.yeastgenome.org/
+            ##Genome-Annotation-Data-END##
+            COMPLETENESS: full length.
+FEATURES             Location/Qualifiers
+     source          1..439888
+                     /organism="Saccharomyces cerevisiae S288C"
+                     /mol_type="genomic DNA"
+                     /strain="S288C"
+                     /db_xref="taxon:559292"
+                     /chromosome="IX"
+     telomere        complement(1..7784)
+                     /note="TEL09L; Telomeric region on the left arm of
+                     Chromosome IX; composed of an X element core sequence, X
+                     element combinatorial repeats, a long Y' element, and a
+                     short terminal stretch of telomeric repeats"
+                     /db_xref="SGD:S000028896"
+     gene            complement(<483..>6147)
+                     /locus_tag="YIL177C"
+                     /db_xref="GeneID:854630"
+     mRNA            complement(join(<483..4598,4987..>6147))
+                     /locus_tag="YIL177C"
+                     /product="Y' element ATP-dependent helicase"
+                     /transcript_id="NM_001179522.1"
+                     /db_xref="GeneID:854630"
+     CDS             complement(join(483..4598,4987..6147))
+                     /locus_tag="YIL177C"
+                     /EC_number="3.6.4.12"
+                     /note="Putative Y' element ATP-dependent helicase"
+                     /codon_start=1
+                     /product="Y' element ATP-dependent helicase"
+                     /protein_id="NP_012092.1"
+                     /db_xref="GeneID:854630"
+                     /db_xref="SGD:S000001439"
+                     /translation="MKVSDRRKFEKANFDEFESALNNKNDLVHCPSITLFESIPTEVR
+                     SFYEDEKSGLIKVVKFRTGAMDRKRSFEKVVISVMVGKNVKKFLTFVEDEPDFQGGPI
+                     PSKYLIPKKINLMVYTLFQVHTLKFNRKDYDTLSLFYLNRGYYNELSFRVLERCHEIA
+                     SARPNDSSTMRTFTDFVSGAPIVRSLQKSTIRKYGYNLAPYMFLLLHVDELSIFSAYQ
+                     ASLPGEKKVDTERLKRDLCPRKPIEIKYFSQICNDMMNKKDRLGDILHIILRACALNF
+                     GAGPRGGAGDEEDRSITNEEPIIPSVDEHGLKVCKLRSPNTPRRLRKTLDAVKALLVS
+                     SCACTARDLDIFDDNNGVAMWKWIKILYHEVAQETTLKDSYRITLVPSSDGISLLAFA
+                     GPQRNVYVDDTTRRIQLYTDYNKNGSSEPRLKTLDGLTSDYVFYFVTVLRQMQICALG
+                     NSYDAFNHDPWMDVVGFEDPNQVTNRDISRIVLYSYMFLNTAKGCLVEYATFRQYMRE
+                     LPKNAPQKLNFREMRQGLIALGRHCVGSRFETDLYESATSELMANHSVQTGRNIYGVD
+                     SFSLTSVSGTTATLLQERASERWIQWLGLESDYHCSFSSTRNAEDVVAGEAASSNHHQ
+                     KISRVTRKRPREPKSTNDILVAGQKLFGSSFEFRDLHQLRLCYEIYMADTPSVAVQAP
+                     PGYGKTELFHLPLIALASKGDVEYVSFLFVPYTVLLANCMIRLGRCGCLNVAPVRNFI
+                     EEGYDGVTDLYVGIYDDLASTNFTDRIAAWENIVECTFRTNNVKLGYLIVDEFHNFET
+                     EVYRQSQFGGITNLDFDAFEKAIFLSGTAPEAVADAALQRIGLTGLAKKSMDINELKR
+                     SEDLSRGLSSYPTRMFNLIKEKSEVPLGHVHKIRKKVESQPEEALKLLLALFESEPES
+                     KAIVVASTTNEVEELACSWRKYFRVVWIHGKLGAAEKVSRTKEFVTDGSMQVLIGTKL
+                     VTEGIDIKQLMMVIMLDNRLNIIELIQGVGRLRDGGLCYLLSRKNSWAARNRKGELPP
+                     IKEGCITEQVREFYGLESKKGKKGQHVGCCGSRTDLSADTVELIERMDRLAEKQATAS
+                     MSIVALPSSFQESNSSDRYRKYCSSDEDSNTCIHGSANASTNASTNAITTASTNVRTN
+                     ATTNASTNATTNASTNASTNATTNASTNATTNSSTNATTTASTNVRTSATTTASINVR
+                     TSATTTESTNSSTNATTTESTNSSTNATTTESTNSNTSATTTASINVRTSATTTESTN
+                     SSTSATTTASINVRTSATTTKSINSSTNATTTESTNSNTNATTTESTNSSTNATTTES
+                     TNSSTNATTTESTNSNTSAATTESTNSNTSATTTESTNASAKEDANKDGNAEDNRFHP
+                     VTDINKESYKRKGSQMVLLERKKLKAQFPNTSENMNVLQFLGFRSDEIKHLFLYGIDI
+                     YFCPEGVFTQYGLCKGCQKMFELCVCWAGQKVSYRRIAWEALAVERMLRNDEEYKEYL
+                     EDIEPYHGDPVGYLKYFSVKRREIYSQIQRNYAWYLAITRRRETISVLDSTRGKQGSQ
+                     VFRMSGRQIKELYFKVWSNLRESKTEVLQYFLNWDEKKCQEEWEAKDDTVVVEALEKG
+                     GVFQRLRSMTSAGLQGPQYVKLQFSRHHRQLRSRYELSLGMHLRDQIALGVTPSKVPH
+                     WTAFLSMLIGLFYNKTFRQKLEYLLEQISEVWLLPHWLDLANVEVLAADDTRVPLYML
+                     MVAVHKELDSDDVPDGRFDILLCRDSSREVGE"
+     rep_origin      7470..8793
+                     /note="ARS902; Putative replication origin; identified in
+                     multiple array studies, not yet confirmed by plasmid-based
+                     assay"
+                     /db_xref="SGD:S000130156"
+     mRNA            join(<155222,155311..>155765)
+                     /gene="COX5B"
+                     /locus_tag="YIL111W"
+                     /product="cytochrome c oxidase subunit Vb"
+                     /transcript_id="NM_001179459.1"
+                     /db_xref="GeneID:854695"
+CONTIG      join(BK006942.2:1..439888)
+//
+