cdskit accession2fasta

cdskit accession2fasta retrieves FASTA sequences from a list of GenBank accessions through NCBI E-utilities. Put one accession on each line of the input text file.

Key options

• --accession_file PATH is required.
• --email ADDRESS identifies requests to NCBI and is recommended for production or repeated downloads.
• --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 retain whole GenBank record sequences.
• Joined CDS locations and reverse-strand orientation are honored; only the first CDS is exported, not every CDS in a genomic record.
• --seq_name_format STR selects underscore-separated metadata fields for output IDs. Enclose a field name that contains underscores in brackets, for example [molecule_type]_organism. Use --list_seq_name_keys yes to inspect available fields.
• --strict yes|no defaults to yes: missing, duplicate, or unexpected retrieved accessions stop the command before output is written. no accepts the returned records with a warning. Repeated requests and versionless accession aliases are supported. This check precedes the optional CDS extraction filter.
• --out_file - writes FASTA to standard output; this is the default.

Retrieval depends on NCBI availability. In strict mode, a retrieval mismatch returns a nonzero exit status and preserves an existing output file. Missing CDS features are still reported and omitted when --extract_cds yes is selected.

Example

Command

cdskit accession2fasta --accession_file input.txt --out_file output.fasta

input.txt

FM211860.1
FM211829.1
FM211877.1
FM211842.1
FM211850.1

output.fasta

>Orthoclada_laxa_FM211860
TCACCCATGTCCTCTACAACCTCTCCCCCGCCGAGCTGTACGAGCAGGCGATCAAGTACG
AGAAGGGGTCGTTTATCACGGCCACCGGCGCGCTGGCGACGCTGTCGGGCGCTAAGACAG
GCCGGTCGCCCAGGGACAAGCGCGTCGTCAAGGACGAGGCCGCCGCGCAGGACCTGTGGT
GGGGCAAGGGGTCGCCGAACATCGAGATGGACGAGCACACGTTCCTCACCAACAGGGAGA
GGGCAGTCGACTACCTCAACTCCCTCGACAAGGTGTTCGTGAACGACCAGTTCCTGAACT
GGGACCCGGAGAACTGCATCAAGGTCCGCATCATCTCCGCCAGGGCGTACCACTCCCCCT
TCATGCATAACATGTGCATCCGCCCCACGGAGGAAGAGCTGGAGAGCTTCGGCACGCCGG
ACTTCACCATCTACAACGCCGGGCAGTTCCCCTGCAACCGTTACACGCACTACATGACGT
CGTCGACGAGCGTAGACATCAACCTCGCTAGGAGGGAGATGGTGATCCTGGGCACGCAGT
ACGCCGGGGAGATGAAGAAGGGCCTCTTCGGCGTCATGCACTACCTCATGCCCAAGCGCG
GCATCCTCTCGCTGCACTCCGGGTGCAATATGGGCAAGGACGGTGACGTCGCCCTCTTCT
TTGGGCTCTCAGGGACCGGGAGGACGACGCTGTCAACGGACCACAATAGGCTCCTGATCG
GCGACGACGAGCACTGCTGGAGCGACAATGGCGTCTCCAACATTGAGGGTGGTTGTTATG
CCAAGTGTATAGACCTGTCCCAGGAGAAAGAACCTGATATTTGGAACGCCATCAAGTTTG
GAACTGTGTTGGAGAACGTTGTCTTCGACGAGCATACTCGCGAAGTGGACTATGCCGATA
AATCTGTAACAGAGAACACTCGGGCTGCTTACCCGATCGAGTACATCCCCAACGCCAAGA
TACCATGCGTCGGGCCGCACCCGAAGAACGTCATCCTCTTGGCGTGTGACGCATTCGGTG
TCCTCCCGCCCGTCAGCAAGCTGAACCTGGCGCAGACCATGTACCATTTCATCAGCGGCT
ACACTGCTCTGGTTGCCGGCACGGAAGAAGGCATCAAGGAGCCACAGGCTACGTTCTCCG
CCTGCTTCGGTGCGGCTTTCATCATGCTCCACCCAACCAAGTACGCCGCCATGCTTGCCG
AGAAGATGCAGAAGTATGGCGCCACCGGGTGGCTTGTGAACACCGGCTGGTCCGGCGGCA
GGTATGGCGTGGGCAAGAGGATCCGGCTGCCCTACACCAGGAAGATCATCGACGCCATCC
ACTCCGGCGAGCTCCTCACCGCGAACTACAAGAAGACCGAGGTCTTCGGCCTGGAGATCC
CCACTGAGATCGAGGGCGTGCCGTCGGAAATCCTCGACCCCATCAACACTTGGACGGACA
AGGCGGCGTACAAGGAGACGCTCCTGAAGCTGGCTGGCCTGTTCAGGAAGAACTTCGAG
>Chasmanthium_latifolium_FM211829
TCACCCATGTCCTCTACAACCTCTCCCCGGGAGAGCTGTACGAGCAGGCGATCAAGTACG
AGAAGGGGTCGTTCATCACGTCCACCGGCGCGCTGGCGACGCTCTCCGGCGCCAAGACCG
GCCGGTCGCCCAGGGATAAGCGCGTCGTCAAGGACGAGGCCGCCGCGCAGGATCTGTGGT
GGGGCAAGGGCTCGCCGAACATCGAGATGGACGAGCACACGTTCCTCACGAACAGGGAGA
GGGCCGTCGACTACCTCAACTCCCTCGACAAGGTGTTCGTGAACGACCAGTTCCTGAACT
GGGACCCCGAGAACCGCATCAAGGTCCGCATCATCTCCGCCAGGGCGTACCACTCCCTCT
TCATGCACAACATGTGCATCCGGCCCACGGAGGAGGAGCTGGAGAGCTTCGGCACGCCGG
ACTTCACCATTTACAACGCCGGGCAGTTCCCCTGCAACCGGTACACGCACTACATGACGT
CGTCCACCAGCGTAGACATCAACCTCGCTAGGAGGGAGATGGTGATCCTGGGCACGCAGT
ACGCCGGCGAGATGAAGAAGGGCCTCTTCGGCGTCATGCACTACCTCATGCCCAAACGCC
ACATTCTCTCGCTGCACTCCGGATGCAACATGGGCAGAGACGGTGACGTCGCCCTCTTCT
TTGGGCTCTCAGGTACCAGAAAGACGACGCTGTCGACGGACCACAACCGGCTTCTGATCG
GTGACGACGAACACTGCTGGAGCGACAATGGCGTCTCCAACATCGAGGGCGGTTGCTGCG
CCAAGTGCATAGACCTCTCCCAGGAGAAAGAGCCTGATATCTGGAACGCCATCAAGTTTG
GAACTGTGCTGGAGAACGTTGTCTTCGATGAACATACTCGAGAAGTTGACTACGCTGATA
AATCTGTCACCGAGAACACTCGGGCTGCTTACCCGATCGAGTACATCCCCAACGCCAAGA
TACCCTGCGTCGGGCCGCACCCGAAGAACGTCATTCTCTTGGCCTGCGACGCATTCGGCG
TGCTCCCGCCTGTCAGCAAGCTGAACCTGGCGCAGACCATGTACCATTTCATCAGTGGCT
ACACTGCTCTGGTTGCCGGCACGGAAGACGGCATTAAGGAGCCACAGGCTACTTTCTCCG
CCTGCTTCGGCGCCGCTTTCATCATGCTCCACCCGACCAAGTACGCCGCCATGCTCGCCG
AGAAGATGCAGAAGTACGGCGCCACCGGGTGGCTTGTGAACACCGGCTGGTCCGGCGGGA
GGTACGGTGTGGGCAAGAGGATCAAGCTGCCGTACACCAGGAAGATCATCGACGCCATCC
ACTCCGGCGAGCTCCTCACCGCCAACTACAAGAAGACCGAGGTCTTCGGCCTGGAGATAC
CCACTGAGATCGACGGCGTGCCGTCGGAAATCCTCGACCCCATCAGCACCTGGACGGACA
AGGCGGCGTGCAAGGACACTCTCCTGAAGCTGGCCGGCCTGTTCAGGAAGAACTTCGAG
>Thysanolaena_latifolia_FM211877
TCACCCATGTCCTCTACAACCTCTCCCCGGCTGAGCTGTACGAGCAGGCGATCAAATACG
AGAAGGGGTCGTTCATCACGTCCACCGGCGCGCTGGCGACGCTGTCCGGCGCCAAGACCG
GCCGGTCGCCCAGGGACAAGCGCGTCGTCAAGGACGAGGCTGCCGCGCAGGAGCTGTGGT
GGGGCAAGGGCTCGCCCAACATCGAGATGGACGAGCACACGTTCCTGACCAACAGGGAGA
GGGCCGTCGACTACCTCAACTCCCTGGACAAGGTGTTCGTGAACGACCAGTTCCTCAACT
GGGATCCGGAGAACCGCATCAAGGTCCGCATCATCTCCGCCAGGGCGTACCACTCCCTCT
TCATGCATAACATGTGCATCCGTCCCACGGAGGAGGAGCTGGAGAGTTTCGGCACGCCGG
ACTTCACCATTTACAACGCCGGGCAGTTTCCCTGTAACCGTTACACGCACTACATGACGT
CGTCCACGAGCGTAGACATCAACCTCGCTAGGAGGGAGATGGTGATCCTGGGCACGCAGT
ACGCCGGGGAGATGAAGAAGGGCCTCTTCGGCGTCATGCACTACCTCATGCCCAAACGCC
ACATCCTCTCCCTGCACTCCGGCTCCAATATGGGCAAGGACGGTGACGTCGCCCTCTTCT
TCGGTCTCTCAGGTACCGGAAAGACCACGCTGTCGACGGATCACAATAGGCTCCTGATCG
GCGACGACGAGCACTGCTGGAGCGACACTGGCGTCTCCAACATTGAGGGCGGTTGTTATG
CCAAGTGCATAGACCTGTCTCGAGAGAAAGAACCTGATATTTGGAACGCCATCAAGTTTG
GAACTGTGCTGGAGAACGTCGTCTTCGATGAGCATACTCGAGAAGTTGACTATTCTGATA
AATCTGTCACCGAGAACACCCGAGCTGCTTACCCCATCGAGTACATCCCTAACGCCAAGA
TCCCGTGCGTCGGGCCGCACCCGAAGAACGTCATCCTCTTGGCGTGCGACGCGTTCGGCG
TGCTCCCGCCTGTCAGCAAGCTCAACCTGGCGCAGACCATGTACCATTTCATCAGCGGCT
ACACTGCTCTGGTTGCCGGCACGGAAGACGGCATCAAGGAGCCACAGGCTACGTTCTCCG
CCTGTTTCGGCGCAGCTTTCATCATGCTCCATCCGACCAAGTACGCCGCCATGCTCGCCG
AGAAGATGCAGAAGTATGGAGCCACCGGGTGGCTTGTGAACACCGGTTGGTCCGGTGGAA
GGTACGGTGTGGGCAAGAGGATCAGGCTGCCATACACCAGGAAGATCATCGACTCCATCC
ACTCCGGCGAGCTCCTCACCGCCAACTACAAGAAGACCGAGGTCTTTGGCCTGGAGATCC
CCACTAAGGTCGACGGCGTGCCGTCGGAAATCCTCGACCCCATCAACACCTGGACGGACA
AGGCCGCGTACAAGGAAACGCTGCTGAAGCTGGCCGGCCCGTTCAGGAACAACTTCGAG
>Echinolaena_inflexa_FM211842
TCACCCATGTCCTCTACAACCTCTCGCCTGCTGAGCTGTACGAGCAGGCGATCAAGTACG
AGAAGGGGTCGTTCATCACGTCCAACGGCGCGCTGGCCACGCTGTCCGGCGCCAAGACCG
GGCGGTCGCCCAGGGACAAGCGCGTCGTCAAGGACGAGGCCGCGGCGCAGGAGCTGTGGT
GGGGCAAGGGCTCGCCGAACATCGAGATGGACGAGCACACGTTCCTGACCAACAGGGAGA
GGGCAGTGGACTACCTCAACTCCCTCGACAAGGTGTTCGTGAACGACCAGTTCCTCAACT
GGGACCCGGAGAACCGCATCAAAGTCCGCATCATCTCCGCCAGGGCGTACCACTCCCTCT
TCATGCACAACATGTGCATCCGCCCCACGGACGAGGAGCTGGAGAGCTTCGGCACGCCGG
ACTTCACCATTTACAACGCGGGGCAGTTCCCGTGCAACCGTTACACGCACTACATGACGT
CGTCGACGAGCGTAGACATCAACCTCGCTAGGAGGGAGATGGTGATCCTGGGCACGCAGT
ACGCCGGCGAGATGAAGAAGGGGCTCTTCGGCGTCATGCACTACCTCATGCCCAAGCGCG
GCATCCTCTCGCTGCACTCCGGCTGCAATATGGGCAAGGACGGTGACGTCGCCCTCTTCT
TTGGCCTCTCAGGTACCGGGAAGACGACGCTGTCGACAGATCATAACAGGCTTCTGATCG
GTGACGATGAGCACTGCTGGAGCGACAACGGCGTGTCCAACATTGAGGGCGGCTGCTACG
CTAAGTGCATAGACCTGTCCCAGGAGAAAGAGCCTGATATTTGGAACGCCATCAAGTTTG
GAACTGTGCTGGAGAACGTCGTCTTCGACGAGCATACTCGTGAGGTTGACTACGCCGACA
AATCTGTCACCGAGAACACCCGCGCCGCCTACCCGATCGAGTACATCCCGAACGCCAAGA
TACCCTGCGTCGGGCCACACCCCAAGAACGTCATCCTCCTGGCGTGCGACGCCTTCGGCG
TCCTCCCGCCGGTCAGCAAGCTCAACCTGGCGCAGACCATGTACCACTTCATCAGCGGCT
ACACCGCCCTGGTCGCCGGCACGGAGGACGGCATCAAGGAGCCGCAGGCCACCTTCTCCG
CCTGCTTCGGCGCGGCCTTCATCATGCTCCACCCGACCAAGTACGCCGCCATGCTCGCCG
AGAAGATGCAGAAGTATGGCGCCACCGGGTGGCTTGTCAACACCGGCTGGTCCGGCGGCA
GGTACGGCGTGGGCAAGAGGATCAGGCTGCCCTACACCAGGAAGATCATCGACGCCATCC
ACTCCGGCGAGCTCCTCACCGCCAACTACCAGAAGACGGAGGTGTTCGGCCTGGAGATCC
CCACCAAGATCGACGGCGTGCCGTCGGAAATCCTCGACCCCATCAACACCTGGACGGACA
AGGCCGCGTACAAGGAGACGCTCCTGAAGCTTGCCGGGCTCTTCAAGAAGAACTTCGAG
>Ichnanthus_vicinus_FM211850
TCACCCATGTCCTCTACAACCTATCGCCTGCTGAGCTGTACGAGCAGTCGATCAAGTACG
AGAAGGGTTCGTTCATCACGTCCACCGGCGCGCTGGCCACGCTGTCGGGCGCCAAGACCG
GGCGGTCGCCCAGGGACAAGCGCGTCGTCAAGGACGAGGCCGCGGCGCAGGAGCTGTGGT
GGGGCAAGGGCTCGCCGAACATCGAGATGGACGAGCACACGTTCCTGACCAACAGGGAAA
GGGCCGTGGACTACCTCAACTCGCTGGACAAGGTGTTCGTGAACGACCAGTTCCTCAACT
GGGACCCGGAGAACCGCATCAAGGTCCGCATCATCTCCGCCAGGGCGTACCACTCCCCCT
TCATGCACAACATGTGCATCCGCCCCACGGACGAGGAGCTGGAGCGTTTCGGCACGCCGG
ACTTCACCATTTACAACGCCGGGCAGTTCCCCTGTAACCGTTACACGCACTACATGACGT
CGTCCACCAGCGTAGACATCAACCTCGCTAGGAGGGAGATGGTGATCCTGGGCACGCAGT
ACGCCGGCGAGATGAAGAAGGGGCTCTTCGGCGTCATGCACTACCTCATGCCCAGGCGCG
GCATCCTCTCGCTCCACTCCGGATGCAATATGGGCAAGGACGGTGACGTCGCCCTCTTCT
TTGGCCTCTCAGGTACCGGGAAGACGACGCTGTCGACAGATCATAACAGGCTTCTGATTG
GTGACGATGAGCACTGCTGGAGCGACAATGGCGTCTCCAACATCGAGGGCGGCTGCTATG
CCAAATGCATAGACCTGTCCCAGGAAAAAGAGCCTGATATTTGGAATGCCATCAAGTTTG
GGACTGTGCTAGAGAACGTCGTCTTCGATGAGCATACTCGCGAGGTTGACTACGTCGACA
AATCTGTCACCGAGAACACTCGGGCCGCCTACCCGATCGAGTACATCCCCAACGCCAAGA
TCCCCTGCGTCGGCCCACACCCCAAGAACGTCATCCTCCTGGCTTGCGACGCCTTCGGCG
TGCTCCCGCCGGTCAGCAAGCTGAACCTGGCGCAGACCATGTACCACTTCATCAGTGGCT
ACACTGCCCTGGTGGCCGGCACGGAGGACGGCATCAAGGAGCCGCAGGCCACCTTCTCGG
CCTGCTTCGGCGCGGCCTTCATCATGCTCCACCCCACCAAGTATGCCGCCATGCTCGCTG
AGAAGATGCAGAAGTATGGCGCCACCGGGTGGCTTGTCAACACCGGCTGGTCCGGCGGCA
GGTACGGCGTGGGCAAGAGGATCAGGCTGCCCTACACCAGGAAGATCATCGACGCCATCC
ACTCCGGCGACCTCCTCAACGCCGAGTACCAGAAGACGGAGGTGTTCGGCCTGGAGATCC
CCACCAAGCTCGACGGCGTGCCGTCAGAAATCCTCGACCCCATCAACACCTGGACGGACA
AGGCCGCGTACAAGGAGACGCTCCTGAAGCTCGCCGGGCTCTTCAAGAAGAACTTCGAG

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.