cdskit parsegb

cdskit parsegb converts a GenBank-formatted file to FASTA and constructs sequence IDs from record metadata.

Key options

• --extract_cds yes|no extracts the first CDS feature from each record (yes by default). Records without a CDS are reported and omitted. Use no to export whole record sequences.
• --seq_name_format STR selects underscore-separated metadata fields for output IDs. The default is organism_accessions. Enclose a field name that contains underscores in brackets, for example [molecule_type]_organism.
• --list_seq_name_keys yes prints the available annotation keys and values to standard error before conversion.
• --in_seq_format must be genbank or gb; genbank is the default.

CDS extraction follows joined locations and reverse-strand orientation. If writing GenBank with --out_seq_format genbank, the retained CDS location and translation exceptions are rebased to the extracted sequence. Other genomic features and reference locations are not carried over with stale coordinates.

Example

Command

cdskit parsegb --seq_file input.gb --out_file output.fasta

input.gb

LOCUS       NM_001080339             906 bp    mRNA    linear   MAM 11-OCT-2020
DEFINITION  Bos taurus lysozyme (renal amyloidosis) (LYZ1), mRNA.
ACCESSION   NM_001080339 XM_001249625
VERSION     NM_001080339.1
KEYWORDS    RefSeq.
SOURCE      Bos taurus (cattle)
  ORGANISM  Bos taurus
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Laurasiatheria; Artiodactyla; Ruminantia;
            Pecora; Bovidae; Bovinae; Bos.
REFERENCE   1  (bases 1 to 906)
  AUTHORS   Nonaka Y, Akieda D, Aizawa T, Watanabe N, Kamiya M, Kumaki Y,
            Mizuguchi M, Kikukawa T, Demura M and Kawano K.
  TITLE     X-ray crystallography and structural stability of digestive
            lysozyme from cow stomach
  JOURNAL   FEBS J 276 (8), 2192-2200 (2009)
   PUBMED   19348005
  REMARK    GeneRIF: In this investigation, we obtained the crystallographic
            structure of recombinant bovine stomach lysozyme 2 (BSL2).
REFERENCE   2  (bases 1 to 906)
  AUTHORS   Irwin DM, White RT and Wilson AC.
  TITLE     Characterization of the cow stomach lysozyme genes: repetitive DNA
            and concerted evolution
  JOURNAL   J Mol Evol 37 (4), 355-366 (1993)
   PUBMED   8308905
REFERENCE   3  (bases 1 to 906)
  AUTHORS   Irwin DM and Wilson AC.
  TITLE     Multiple cDNA sequences and the evolution of bovine stomach
            lysozyme
  JOURNAL   J Biol Chem 264 (19), 11387-11393 (1989)
   PUBMED   2738070
COMMENT     PROVISIONAL REFSEQ: This record has not yet been subject to final
            NCBI review. The reference sequence was derived from M26245.1.
            On Jan 16, 2007 this sequence version replaced XM_001249625.1.

            ##Evidence-Data-START##
            Transcript exon combination :: M26245.1, CK975923.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN03145435, SAMN03145498
                                           [ECO:0000348]
            ##Evidence-Data-END##
FEATURES             Location/Qualifiers
     source          1..906
                     /organism="Bos taurus"
                     /mol_type="mRNA"
                     /db_xref="taxon:9913"
                     /chromosome="5"
                     /map="5"
     gene            1..906
                     /gene="LYZ1"
                     /gene_synonym="LYSOZYME; LYZ"
                     /note="lysozyme (renal amyloidosis)"
                     /db_xref="BGD:BT11901"
                     /db_xref="GeneID:781349"
     exon            1..158
                     /gene="LYZ1"
                     /gene_synonym="LYSOZYME; LYZ"
                     /inference="alignment:Splign:2.1.0"
     CDS             23..466
                     /gene="LYZ1"
                     /gene_synonym="LYSOZYME; LYZ"
                     /EC_number="3.2.1.17"
                     /note="1,4-beta-N-acetylmuramidase C; lysozyme C-1"
                     /codon_start=1
                     /product="lysozyme C-1 precursor"
                     /protein_id="NP_001073808.1"
                     /db_xref="BGD:BT11901"
                     /db_xref="GeneID:781349"
                     /translation="MKALIILGFLFLSVAVQGKVFERCELARTLKKLGLDGYKGVSLA
                     NWLCLTKWESSYNTKATNYNPGSESTDYGIFQINSKWWCNDGKTPNAVDGCHVSCSEL
                     MENEIAKAVACAKQIVSEQGITAWVAWKSHCRDHDVSSYVEGCTL"
     sig_peptide     23..76
                     /gene="LYZ1"
                     /gene_synonym="LYSOZYME; LYZ"
                     /inference="COORDINATES: ab initio prediction:SignalP:4.0"
     mat_peptide     77..463
                     /gene="LYZ1"
                     /gene_synonym="LYSOZYME; LYZ"
                     /product="lysozyme C-1"
     exon            159..323
                     /gene="LYZ1"
                     /gene_synonym="LYSOZYME; LYZ"
                     /inference="alignment:Splign:2.1.0"
     exon            324..399
                     /gene="LYZ1"
                     /gene_synonym="LYSOZYME; LYZ"
                     /inference="alignment:Splign:2.1.0"
     exon            400..906
                     /gene="LYZ1"
                     /gene_synonym="LYSOZYME; LYZ"
                     /inference="alignment:Splign:2.1.0"
ORIGIN
        1 gacatttgac ttctcagtca acatgaaggc tctcattatt ctggggtttc tcttcctttc
       61 tgttgctgtc cagggcaagg tctttgagag atgtgagctt gccagaactc tgaagaaact
      121 tggactggat ggctataagg gagtcagtct ggcaaactgg ctgtgtttga ccaaatggga
      181 aagcagttat aacacaaaag ctacaaacta caatcctggc agtgaaagca ctgattatgg
      241 gatatttcag atcaacagca aatggtggtg taatgatggc aaaaccccca acgcagttga
      301 cggctgtcat gtatcctgca gcgaattaat ggaaaatgag atcgcgaaag ctgtagcgtg
      361 tgccaagcag attgtcagtg agcaaggcat tacagcatgg gtggcatgga aaagtcactg
      421 tcgagaccat gacgtcagca gttatgttga gggttgcacg ctgtaactgt ggagttatca
      481 ttcttcagct cattttgtct ctttttcacg ttaaggaagt aatagttgaa tgaaagctta
      541 taccaccatt ccttcaagca aacaatggtt ttacagaagc aggagcatat ggtcttctaa
      601 gaagcttaat gtttatctaa tgtgttaatt atttgacact aggcctataa tatttttcag
      661 tttgctagta aaactaatgc tggtgaatat ttgtctaaat tcttaattat ctaatatatc
      721 tccagtatat tcagttctta attaaagcaa gaacatttat gcaccttgct gatcatgaag
      781 gaatataaag agggattaga tgaactgttg ctttttctta atttcattag cattatgaca
      841 aattcagaga cagatgagtc tgcaactatt gaaattaatt gctggttaac cacagatatg
      901 aaatga
//

LOCUS       NM_001285711             447 bp    mRNA    linear   MAM 30-JUN-2020
DEFINITION  Capra hircus serum lysozyme (S-LZ), mRNA.
ACCESSION   NM_001285711 XM_005680194
VERSION     NM_001285711.1
KEYWORDS    RefSeq.
SOURCE      Capra hircus (goat)
  ORGANISM  Capra hircus
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Laurasiatheria; Artiodactyla; Ruminantia;
            Pecora; Bovidae; Caprinae; Capra.
COMMENT     PROVISIONAL REFSEQ: This record has not yet been subject to final
            NCBI review. The reference sequence was derived from GQ903681.1.
            On Oct 22, 2013 this sequence version replaced XM_005680194.1.

            ##Evidence-Data-START##
            Transcript exon combination :: GQ889414.1, GQ903681.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN05462052, SAMN05462053
                                           [ECO:0000348]
            ##Evidence-Data-END##
FEATURES             Location/Qualifiers
     source          1..447
                     /organism="Capra hircus"
                     /mol_type="mRNA"
                     /db_xref="taxon:9925"
                     /chromosome="5"
                     /map="5"
     gene            1..447
                     /gene="S-LZ"
                     /gene_synonym="lysozyme; LYZ; S-LYZ; TGTLyz"
                     /note="serum lysozyme"
                     /db_xref="GeneID:100860864"
     CDS             1..447
                     /gene="S-LZ"
                     /gene_synonym="lysozyme; LYZ; S-LYZ; TGTLyz"
                     /codon_start=1
                     /product="serum lysozyme precursor"
                     /protein_id="NP_001272640.1"
                     /db_xref="GeneID:100860864"
                     /translation="MKALIILGLLLLSVAVQGKVFERCELARTLKRFGMDGFRGISLA
                     NWMCLARWESSYNTQATNYNSGDRSTDYGIFQINSHWWCNDGKTPGAVNACHIPCSAL
                     LQDDITQAVACAKRVVSDPQGIRAWVAWRSHCQNQDLTSYIQGCGV"
     sig_peptide     1..54
                     /gene="S-LZ"
                     /gene_synonym="lysozyme; LYZ; S-LYZ; TGTLyz"
                     /inference="COORDINATES: ab initio prediction:SignalP:4.0"
     exon            1..136
                     /gene="S-LZ"
                     /gene_synonym="lysozyme; LYZ; S-LYZ; TGTLyz"
                     /inference="alignment:Splign:2.0.8"
     exon            137..301
                     /gene="S-LZ"
                     /gene_synonym="lysozyme; LYZ; S-LYZ; TGTLyz"
                     /inference="alignment:Splign:2.0.8"
     exon            302..380
                     /gene="S-LZ"
                     /gene_synonym="lysozyme; LYZ; S-LYZ; TGTLyz"
                     /inference="alignment:Splign:2.0.8"
     exon            381..447
                     /gene="S-LZ"
                     /gene_synonym="lysozyme; LYZ; S-LYZ; TGTLyz"
                     /inference="alignment:Splign:2.0.8"
ORIGIN
        1 atgaaggctc tcattattct ggggcttctc ctcctttcgg tcgctgtcca aggcaaggtc
       61 tttgagagat gtgagcttgc cagaactctg aaaagatttg gaatggatgg ctttagggga
      121 atcagcctgg caaactggat gtgtttggcc agatgggaaa gcagttataa cacacaagct
      181 acaaactaca atagtggaga cagaagcact gattatggga tatttcaaat caatagccac
      241 tggtggtgta atgatggcaa aaccccagga gcagttaatg cctgtcacat accctgcagc
      301 gctttgctgc aagatgacat cactcaagct gtagcatgtg caaagagggt tgtcagtgat
      361 ccacaaggca ttagagcatg ggtggcatgg agaagtcatt gtcaaaacca agatctcacc
      421 agttacattc agggttgtgg agtgtaa
//

output.fasta

>Bos_taurus_NM_001080339
ATGAAGGCTCTCATTATTCTGGGGTTTCTCTTCCTTTCTGTTGCTGTCCAGGGCAAGGTC
TTTGAGAGATGTGAGCTTGCCAGAACTCTGAAGAAACTTGGACTGGATGGCTATAAGGGA
GTCAGTCTGGCAAACTGGCTGTGTTTGACCAAATGGGAAAGCAGTTATAACACAAAAGCT
ACAAACTACAATCCTGGCAGTGAAAGCACTGATTATGGGATATTTCAGATCAACAGCAAA
TGGTGGTGTAATGATGGCAAAACCCCCAACGCAGTTGACGGCTGTCATGTATCCTGCAGC
GAATTAATGGAAAATGAGATCGCGAAAGCTGTAGCGTGTGCCAAGCAGATTGTCAGTGAG
CAAGGCATTACAGCATGGGTGGCATGGAAAAGTCACTGTCGAGACCATGACGTCAGCAGT
TATGTTGAGGGTTGCACGCTGTAA
>Capra_hircus_NM_001285711
ATGAAGGCTCTCATTATTCTGGGGCTTCTCCTCCTTTCGGTCGCTGTCCAAGGCAAGGTC
TTTGAGAGATGTGAGCTTGCCAGAACTCTGAAAAGATTTGGAATGGATGGCTTTAGGGGA
ATCAGCCTGGCAAACTGGATGTGTTTGGCCAGATGGGAAAGCAGTTATAACACACAAGCT
ACAAACTACAATAGTGGAGACAGAAGCACTGATTATGGGATATTTCAAATCAATAGCCAC
TGGTGGTGTAATGATGGCAAAACCCCAGGAGCAGTTAATGCCTGTCACATACCCTGCAGC
GCTTTGCTGCAAGATGACATCACTCAAGCTGTAGCATGTGCAAAGAGGGTTGTCAGTGAT
CCACAAGGCATTAGAGCATGGGTGGCATGGAGAAGTCATTGTCAAAACCAAGATCTCACC
AGTTACATTCAGGGTTGTGGAGTGTAA

References

Cite the method or resource actually used and report the CDSKIT version and options.

• Sayers EW et al. (2025). GenBank 2025 update. Nucleic Acids Research 53:D56–D61. Paper — Data resource; also record the accession.version identifiers and retrieval date of the sequences used.
• Cock PJA et al. (2009). Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 25:1422–1423. Paper — Sequence parsing, feature extraction and genetic-code infrastructure used by CDSKIT.