Test and compile

benben-miao · Apr 15, 2022 · 13d4abe · 13d4abe
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diff --git a/.gitignore b/.gitignore
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+ncbi-parser.exe
diff --git a/MK919144.1.gbk b/MK919144.1.gbk
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+LOCUS       MK919144                 567 bp    DNA     linear   VRT 10-JUL-2020
+DEFINITION  Acanthopagrus pacificus voucher SPAR040418-1 16S ribosomal RNA
+            gene, partial sequence; mitochondrial.
+ACCESSION   MK919144
+VERSION     MK919144.1
+KEYWORDS    .
+SOURCE      mitochondrion Acanthopagrus pacificus (Pacific sunbream)
+  ORGANISM  Acanthopagrus pacificus
+            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
+            Actinopterygii; Neopterygii; Teleostei; Neoteleostei;
+            Acanthomorphata; Eupercaria; Spariformes; Sparidae; Acanthopagrus.
+REFERENCE   1  (bases 1 to 567)
+  AUTHORS   Hasan,M.E., Durand,J.-D. and Iwatsuki,Y.
+  TITLE     Acanthopagrus datnia (Hamilton, 1822), a senior synonym
+            of#Acanthopagrus longispinnis (Valenciennes, 1830) (Perciformes:
+            Sparidae)
+  JOURNAL   Zootaxa 4750 (2), 151-181 (2020)
+REFERENCE   2  (bases 1 to 567)
+  AUTHORS   Hassan,M.E., Durand,J.-D. and Iwatsuki,Y.
+  TITLE     Direct Submission
+  JOURNAL   Submitted (10-MAY-2019) Ocean, IRD, MARBEC cc093 Bat 24 Place E.
+            Bataillon, Montpellier, Herault 34095, France
+FEATURES             Location/Qualifiers
+     source          1..567
+                     /organism="Acanthopagrus pacificus"
+                     /organelle="mitochondrion"
+                     /mol_type="genomic DNA"
+                     /specimen_voucher="SPAR040418-1"
+                     /db_xref="BOLD:SPARM032-19.16S"
+                     /db_xref="taxon:1129777"
+                     /country="Viet Nam: Ba Ria-Vung Tau, V##ng T##u (fish
+                     market in Ho Chi Minh, D2)"
+                     /collection_date="04-Apr-2018"
+                     /collected_by="Jean-Dominique Durand"
+                     /identified_by="Jean-Dominique Durand"
+     rRNA            <1..>567
+                     /product="16S ribosomal RNA"
+ORIGIN      
+        1 aagaggtccc gcctgccctg tgactatatg ttcaacggcc gcggtatttt gaccgtgcga
+       61 aggtagcgta atcacttgtc ttttaaatga agacctgtat gaatggcacc acgagggctt
+      121 aactgtctcc ctctcccagt caatgaaatt gattcccccg tgcagaagcg gggataaaag
+      181 cataagacga gaagacccta tggagcttaa gacgccagga cagctcatgt taaacactcc
+      241 aaaataaagg aaataaactg attgaaaccc tgtcctagtg tctttggttg gggcgaccac
+      301 ggggaaaaat ctaaccccca tgtggaatag gaatactatt ttcccatacc caagagttcc
+      361 cgctctaata aacagaactt ctgaccaaaa tggatccggc aatgccgatc aacggaccga
+      421 gttaccctag ggataacagc gcaatcctct taaagagtcc ctatcgacaa gggggtttac
+      481 gacctcgatg ttggatcagg acatcctaat ggtgcagccg ctattaaggg ttcgtttgtt
+      541 caacgattaa agtcctacgt gatctga
+//
+
diff --git a/MK919144.1.seq b/MK919144.1.seq
@@ -0,0 +1 @@
+AAGAGGTCCCGCCTGCCCTGTGACTATATGTTCAACGGCCGCGGTATTTTGACCGTGCGAAGGTAGCGTAATCACTTGTCTTTTAAATGAAGACCTGTATGAATGGCACCACGAGGGCTTAACTGTCTCCCTCTCCCAGTCAATGAAATTGATTCCCCCGTGCAGAAGCGGGGATAAAAGCATAAGACGAGAAGACCCTATGGAGCTTAAGACGCCAGGACAGCTCATGTTAAACACTCCAAAATAAAGGAAATAAACTGATTGAAACCCTGTCCTAGTGTCTTTGGTTGGGGCGACCACGGGGAAAAATCTAACCCCCATGTGGAATAGGAATACTATTTTCCCATACCCAAGAGTTCCCGCTCTAATAAACAGAACTTCTGACCAAAATGGATCCGGCAATGCCGATCAACGGACCGAGTTACCCTAGGGATAACAGCGCAATCCTCTTAAAGAGTCCCTATCGACAAGGGGGTTTACGACCTCGATGTTGGATCAGGACATCCTAATGGTGCAGCCGCTATTAAGGGTTCGTTTGTTCAACGATTAAAGTCCTACGTGATCTGA
diff --git a/README.md b/README.md
@@ -0,0 +1,115 @@
+### NCBI-Parser
+Search any term from all NCBI databases to obtain matched entries, and download all NCBI GenBank format files and sequences corresponding to accessory number in genbank directory, finally  export all Species Latin names, Accessory Number, Sequence Length, Division, Collection Country, Collection Date, Collected Worker, Identified Worker, and Reference information, etc. of the search records as tabular files.
+
+### Usage
+```bash
+ncbi-parser.exe --help
+Usage: ncbi-parser.exe [OPTIONS]
+
+  Description: Search any term from all NCBI databases to obtain matched
+  entries, and download all NCBI GenBank format files and sequences
+  corresponding to accessory number in genbank directory, finally export all
+  Species Latin names, Accessory Number, Sequence Length, Division, Collection
+  Country, Collection Date, Collected Worker, Identified Worker, and Reference
+  information, etc. of the search records as tabular files.
+
+  1. Get options and parameters help:
+
+  ncbi-parser --help
+
+  2. Example (simple information). Users only need to input the search term,
+  and the default search is in NCBI nucleotide database:
+
+  ncbi-parser --term "Acanthopagrus 16S" --output results.xls
+
+  3. Example (complete information). Specify the NCBI database type, input the
+  search term, specify the number of records to download and extract, and
+  suggest setting a larger parameter max_record:
+
+  ncbi-parser --db_type nucleotide --term "Acanthopagrus 16S" --max_record 500
+  --res_type gb --output results.xls
+
+Options:
+  --db_type TEXT     Please input NCBI database type, default: "nucleotide",
+                     including: [pubmed, protein, nuccore, ipg, nucleotide,
+                     structure, genome, annotinfo, assembly, bioproject,
+                     biosample, blastdbinfo, books, cdd, clinvar, gap,
+                     gapplus, grasp, dbvar, gene, gds, geoprofiles,
+                     homologene, medgen, mesh, ncbisearch, nlmcatalog, omim,
+                     orgtrack, pmc, popset, proteinclusters, pcassay, protfam,
+                     pccompound, pcsubstance, seqannot, snp, sra, taxonomy,
+                     biocollections, gtr]  [required]
+  --term TEXT        Please input search term content, default: "Acanthopagrus
+                     16S"  [required]
+  --max_record TEXT  Please input max record number, default: "100", up to:
+                     10000  [required]
+  --res_type TEXT    Please input result type, default: "gb", including:
+                     ["gb", "fasta", "gbwithparts", "gbcoll"]
+  --output TEXT      Please input output full name (path + name + extension).
+                     default="results.xls"
+  --help             Show this message and exit.
+```
+
+### NCBI GenBank format
+```shell
+LOCUS       LC649152                1081 bp    DNA     linear   VRT 03-SEP-2021
+DEFINITION  Acanthopagrus bifasciatus Kuroshio Biological Research Foundation
+            KBF-I 361 mitochondrial genes for 12S rRNA, tRNA-Val, 16S rRNA,
+            partial and complete sequence.
+ACCESSION   LC649152
+VERSION     LC649152.1
+KEYWORDS    .
+SOURCE      mitochondrion Acanthopagrus bifasciatus (twobar seabream)
+  ORGANISM  Acanthopagrus bifasciatus
+            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
+            Actinopterygii; Neopterygii; Teleostei; Neoteleostei;
+            Acanthomorphata; Eupercaria; Spariformes; Sparidae; Acanthopagrus.
+REFERENCE   1
+  AUTHORS   Sado,T., Fukuchi,T. and Miya,M.
+  TITLE     Reference data for MiFish metabarcoding analysis
+  JOURNAL   Unpublished
+REFERENCE   2  (bases 1 to 1081)
+  AUTHORS   Sado,T., Fukuchi,T. and Miya,M.
+  TITLE     Direct Submission
+  JOURNAL   Submitted (27-AUG-2021) Contact:Tetsuya Sado Natural History Museum
+            & Institute, Chiba; 955-2 Aoba-cho, Chuo-ku, Chiba, Chiba 260-8682,
+            Japan URL :http://www2.chiba-muse.or.jp/NATURAL/
+FEATURES             Location/Qualifiers
+     source          1..1081
+                     /organism="Acanthopagrus bifasciatus"
+                     /organelle="mitochondrion"
+                     /mol_type="genomic DNA"
+                     /specimen_voucher="Kuroshio Biological Research Foundation
+                     KBF-I 361"
+                     /db_xref="taxon:767411"
+                     /PCR_primers="fwd_name: L-708-12S, fwd_seq:
+                     ttayacatgcaagtatccgc, rev_name: H-1784-16SG, rev_seq:
+                     ttcagctttcccttgcggtac"
+     rRNA            <1..894
+                     /product="12S ribosomal RNA"
+     tRNA            895..967
+                     /product="tRNA-Val"
+     rRNA            968..>1081
+                     /product="16S ribosomal RNA"
+ORIGIN      
+        1 acccccgtga aaatgcccta cagttccccg cccggaaaca aggagccggt atcaggcaca
+       61 ttcaatttag cccacgacac cttgctcagc cacaccctca agggtactca gcagtgataa
+      121 accttgacac ataagtgaaa acttgaatca gttaaagcta agtagggccg gtaaaactcg
+      181 tgccagccac cgcggttata cgagaggccc aagttgttag aaatcggcgt aaagggtggt
+      241 taagaataag attaaaatta aagccgaaca tctttagtag ctgttatacg ctttcaaaga
+      301 caagaagccc aactgcgaaa gtagctttat attttctgaa cccacgaaag ctaaggtaca
+      361 aactgggatt agatacccca ctatgcttag ccgtaaacat cgacagttta ttacattttc
+      421 tgtccgcctg ggtactacaa gcattagctc aaaacccaaa ggacttggcg gtgctttaga
+      481 cccacctaga ggagcctgtt ctagaaccga tattccccgt tcaacctcac ctctccttgc
+      541 ctctcagcct atataccgcc gtcgttcagc ttaccctgtg aagggcaaaa agtaagcaaa
+      601 attggcactg cccagtacgt caggtcgagg tgtagtcaat ggagtgggaa gaaatgggct
+      661 acattccctt gtcttcaggg aactacgaat ggtgcactga aaatgtgtgc ctgaaggagg
+      721 atttagcagt aagtagtaat ttagaatatt ctactgaagc cggctcttaa gcgcgcacac
+      781 accgcccgtc actctccccg agactttaaa ttcacattaa ctaaaatatt aaatatcata
+      841 gaggggaggc aagtcgtaac atggtaagtg taccggaagg tgtacttgga aaaccagcgc
+      901 atagctaaac tagataaagc acctccctta cactgagaag atattcgtgc aaatcgaatt
+      961 gccctgagcc tatcagctag ccctctaaca aaaaacaaca cacccccatc aattaacccc
+     1021 caatgcactt acattaaatt aaacaaatca tttttccacc caagtatggg cgacagaaaa
+     1081 g
+//
+```
diff --git a/einfo.dtd b/einfo.dtd
@@ -0,0 +1,75 @@
+<!--    
+                This is the Current DTD for Entrez eInfo
+$Id: einfo.dtd 577924 2019-01-09 22:59:07Z fialkov $
+need xml2json.xsl
+-->
+<!-- ================================================================= -->
+
+<!--~~ !dtd
+~~json 
+    <json type='einfo' version='0.3'>
+      <config lcnames='true'/>
+    </json>
+~~-->
+
+<!ELEMENT	DbName		(#PCDATA)>	<!-- \S+ -->
+<!ELEMENT	Name		(#PCDATA)>	<!-- .+ -->
+<!ELEMENT	FullName	(#PCDATA)>	<!-- .+ -->
+<!ELEMENT	Description	(#PCDATA)>	<!-- .+ -->
+<!ELEMENT	DbBuild		(#PCDATA)>      <!-- .+ -->
+<!ELEMENT	TermCount	(#PCDATA)>	<!-- \d+ -->
+<!ELEMENT	Menu		(#PCDATA)>	<!-- .+ -->
+<!ELEMENT	DbTo		(#PCDATA)>	<!-- \S+ -->
+<!ELEMENT	MenuName	(#PCDATA)>	<!-- .+ -->
+<!ELEMENT	Count		(#PCDATA)>	<!-- \d+ -->
+<!ELEMENT	LastUpdate	(#PCDATA)>	<!-- \d+ -->
+
+<!ELEMENT	ERROR		(#PCDATA)>	<!-- .+ -->
+<!ELEMENT	Warning		(#PCDATA)>  <!-- .+ -->
+
+<!ELEMENT	IsDate		(#PCDATA)>	<!-- (Y|N) -->
+<!ELEMENT	IsNumerical	(#PCDATA)>	<!-- (Y|N) -->
+<!ELEMENT	SingleToken	(#PCDATA)>	<!-- (Y|N) -->
+<!ELEMENT	Hierarchy	(#PCDATA)>	<!-- (Y|N) -->
+<!ELEMENT	IsHidden	(#PCDATA)>	<!-- (Y|N) -->
+<!ELEMENT       IsRangable      (#PCDATA)>      <!-- (Y|N) -->
+<!ELEMENT       IsTruncatable   (#PCDATA)>      <!-- (Y|N) -->
+
+
+<!ELEMENT	DbList		(DbName+)>
+
+<!ELEMENT	Field		(Name,
+                FullName,
+				Description,
+				TermCount,
+				IsDate,
+				IsNumerical,
+				SingleToken,
+				Hierarchy,
+                                IsHidden,
+                                IsRangable?,
+                IsTruncatable?)>
+
+<!ELEMENT	Link		(Name,Menu,Description,DbTo)>
+
+
+<!ELEMENT	LinkList	(Link*)>
+<!ELEMENT	FieldList	(Field*)>
+
+<!ELEMENT	DbInfo		(DbName,
+				MenuName,
+				Description,
+				DbBuild?,
+				Warning?,
+				Count?,
+				LastUpdate?,
+				FieldList?,
+				LinkList?)>
+<!--~~ <eInfoResult>
+~~ json
+  <object>
+      <member select='DbList'/>
+      <array key='dbinfo' select='DbInfo|ERROR'/>
+  </object>
+~~-->				
+<!ELEMENT  eInfoResult     (DbList|(DbInfo|ERROR)+)>
diff --git a/esearch.dtd b/esearch.dtd
@@ -0,0 +1,103 @@
+<!--
+                This is the Current DTD for Entrez eSearch
+$Id: eSearch_020511.dtd 85163 2006-06-28 17:35:21Z olegh $
+-->
+<!-- ================================================================= -->
+
+<!--~~ !dtd
+~~json 
+    <json type='esearch' version='0.3'>
+      <config lcnames='true'/>
+    </json>
+~~-->
+
+<!ELEMENT       eSearchResult  (
+                                 (
+                                   (
+                                     Count,
+                                     ( RetMax,
+                                       RetStart,
+                                       QueryKey?,
+                                       WebEnv?,
+                                       IdList,
+                                       TranslationSet,
+                                       TranslationStack?,
+                                       QueryTranslation
+                                      )?
+                                   ) | ERROR
+                                 ),
+                                 ErrorList?,
+                                 WarningList?
+                               )>
+
+
+<!ELEMENT       Count             (#PCDATA)>  <!-- \d+ -->
+<!ELEMENT       RetMax            (#PCDATA)>  <!-- \d+ -->
+<!ELEMENT       RetStart          (#PCDATA)>  <!-- \d+ -->
+<!ELEMENT       Id                (#PCDATA)>  <!-- \d+ -->
+
+<!ELEMENT       From              (#PCDATA)>  <!-- .+ -->
+<!ELEMENT       To                (#PCDATA)>  <!-- .+ -->
+<!ELEMENT       Term              (#PCDATA)>  <!-- .+ -->
+
+<!ELEMENT       Field             (#PCDATA)>  <!-- .+ -->
+
+<!ELEMENT       QueryKey          (#PCDATA)>  <!-- \d+ -->
+<!ELEMENT       WebEnv            (#PCDATA)>  <!-- \S+ -->
+
+<!ELEMENT       Explode           (#PCDATA)>  <!-- (Y|N) -->
+<!ELEMENT       OP                (#PCDATA)>  <!-- (AND|OR|NOT|RANGE|GROUP) -->
+<!ELEMENT       IdList            (Id*)>
+
+<!ELEMENT       Translation       (From, To)>
+<!ELEMENT       TranslationSet    (Translation*)>
+
+<!ELEMENT       TermSet           (Term, Field, Count, Explode)>
+
+<!--~~ <TranslationStack>
+~~ json <array/>
+~~-->
+<!ELEMENT       TranslationStack  ((TermSet|OP)*)>
+
+<!-- Error message tags  -->
+<!--~~ <ERROR>
+~~ json <json key="ERROR"/>
+~~-->
+<!ELEMENT        ERROR                  (#PCDATA)>  <!-- .+ -->
+
+<!ELEMENT        OutputMessage          (#PCDATA)>  <!-- .+ -->
+
+<!ELEMENT        QuotedPhraseNotFound   (#PCDATA)>  <!-- .+ -->
+
+<!ELEMENT        PhraseIgnored          (#PCDATA)>  <!-- .+ -->
+
+<!ELEMENT        FieldNotFound          (#PCDATA)>  <!-- .+ -->
+
+<!ELEMENT        PhraseNotFound         (#PCDATA)>  <!-- .+ -->
+
+
+<!ELEMENT        QueryTranslation       (#PCDATA)>  <!-- .+ -->
+
+<!--~~ <ErrorList>
+~~ json
+  <object>
+    <array key="phrasesnotfound" select='PhraseNotFound'/>
+    <array key="fieldsnotfound" select='FieldsNotFound'/>
+  </object>
+~~-->
+<!ELEMENT        ErrorList      (PhraseNotFound*,FieldNotFound*)>
+
+<!--~~ <WarningList>
+~~ json
+  <object>
+    <array key="phrasesignored" select='PhraseIgnored'/>
+    <array key="quotedphrasesnotfound" select='QuotedPhraseNotFound'/>
+    <array key="outputmessages" select='OutputMessage'/>
+  </object>
+~~-->
+<!ELEMENT        WarningList    ( PhraseIgnored*,
+                                  QuotedPhraseNotFound*,
+                                  OutputMessage* )>
+
+
+
diff --git a/favicon.ico b/favicon.ico
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		AAGAGGTCCCGCCTGCCCTGTGACTATATGTTCAACGGCCGCGGTATTTTGACCGTGCGAAGGTAGCGTAATCACTTGTCTTTTAAATGAAGACCTGTATGAATGGCACCACGAGGGCTTAACTGTCTCCCTCTCCCAGTCAATGAAATTGATTCCCCCGTGCAGAAGCGGGGATAAAAGCATAAGACGAGAAGACCCTATGGAGCTTAAGACGCCAGGACAGCTCATGTTAAACACTCCAAAATAAAGGAAATAAACTGATTGAAACCCTGTCCTAGTGTCTTTGGTTGGGGCGACCACGGGGAAAAATCTAACCCCCATGTGGAATAGGAATACTATTTTCCCATACCCAAGAGTTCCCGCTCTAATAAACAGAACTTCTGACCAAAATGGATCCGGCAATGCCGATCAACGGACCGAGTTACCCTAGGGATAACAGCGCAATCCTCTTAAAGAGTCCCTATCGACAAGGGGGTTTACGACCTCGATGTTGGATCAGGACATCCTAATGGTGCAGCCGCTATTAAGGGTTCGTTTGTTCAACGATTAAAGTCCTACGTGATCTGA