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GENBANK FLATFILE GENERATOR
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A new flatfile generator has been written to replace the old asn2ff code.
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It is provided both as a stand-alone application, asn2gb, and as C
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functions in the NCBI software toolkit. There are several function
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parameters, with equivalent command-line arguments, that control the
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behavior of the new flatfile generator and customize its performance.
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SeqEntryToGnbk takes a SeqEntryPtr or SeqLocPtr and calls asn2gnbk_setup,
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asn2gnbk_format, and asn2gnbk_cleanup, which are available from a private
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header. It returns FALSE if there was a problem generating the flatfile.
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BioseqToGnbk is simply a convenience function that takes a BioseqPtr, looks
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up the parent SeqEntryPtr, and then calls SeqEntryToGnbk. To use these
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functions, #include <asn2gnbk.h>.
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NLM_EXTERN Boolean SeqEntryToGnbk (
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NLM_EXTERN Boolean BioseqToGnbk (
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In the asn2gb application, format, mode, style, flags, locks, and custom
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parameters are specified by the -f, -m, -s, -g, -h and -u arguments,
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FORMATS include GENBANK_FMT, EMBL_FMT, GENPEPT_FMT, and FTABLE_FMT (Sequin's
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5-column parsable feature table). If the sep passed to SeqEntryToGnbk points
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to a Bioseq-set, the function processes all Bioseqs of the appropriate
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molecule type (nucleotide or protein) for the specified format.
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MODES are RELEASE_MODE, ENTREZ_MODE (release mode strictness except that it
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allows local IDs and does not require a valid CDS /protein_id accession),
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SEQUIN_MODE, and DUMP_MODE. RefSeq records can have otherwise illegal
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qualifiers (e.g., /transcript_id) and db_xrefs show up in release mode.
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Entrez mode should be used for web display, and can show new elements that
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haven't yet finished their 4-month quarantine period.
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STYLES are NORMAL_STYLE, SEGMENT_STYLE, MASTER_STYLE, and CONTIG_STYLE.
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Segment style is the traditional representation of segmented sequences,
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while contig style displays a CONTIG line with a join of accessions instead
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of a sequence. Normal style automatically chooses between segment and contig
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style, depending upon the kind of data. (Near segmented records will be done
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in segment style. Far segmented sequences or deltas with no literals will be
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done as if you chose contig style.) Master style shows features mapped to
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the segmented Bioseq's coordinates.
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FLAGS are bit flags controlling appearance or behavior, and are ORed together.
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One 2-bit flag tells asn2gnbk to create HTML with web links, flatfile in XML
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form, or flatfile in ASN.1 form. These settings are mutually exclusive. The
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setup for creating HTML links is within SeqEntryToGnbk itself.
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#define CREATE_HTML_FLATFILE 1
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#define CREATE_XML_GBSEQ_FILE 2
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#define CREATE_ASN_GBSEQ_FILE 3
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Others control feature display behavior in contig style, whether it was
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explicitly chosen or was called when a far segmented or far delta record was
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processed in normal style.
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#define SHOW_CONTIG_FEATURES 4
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#define SHOW_CONTIG_SOURCES 8
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Another set controls translation of CDS features with far products.
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#define SHOW_FAR_TRANSLATION 16
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#define TRANSLATE_IF_NO_PRODUCT 32
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#define ALWAYS_TRANSLATE_CDS 64
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Another 2-bit flag controls where to get features when using far segmented
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parts or far component delta Bioseqs.
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#define ONLY_NEAR_FEATURES 128
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#define FAR_FEATURES_SUPPRESS 256
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#define NEAR_FEATURES_SUPPRESS 384
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Other flags allow customization of reports from genomic product sets.
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#define COPY_GPS_CDS_UP 512
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#define COPY_GPS_GENE_DOWN 1024
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The CONTIG block can be shown along with the sequence block in master or
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segment style, when appropriate.
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#define SHOW_CONTIG_AND_SEQ 2048
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Still others are expected to be rarely used, or are for testing new features.
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#define DDBJ_VARIANT_FORMAT 4096
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#define USE_OLD_SOURCE_ORG 8192
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GBSeq XML has been replaced by INSDSeq XML. The CREATE_XML_GBSEQ_FILE flag
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will actually produce INSDSeq. The original GBSeq can be generated during
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the transition period by adding the following flag.
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#define PRODUCE_OLD_GBSEQ 16384
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LOCKS are bits for controlling program performance, and are also ORed together.
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One flag set is for locking far segmented or delta components, far feature
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location Bioseqs, or far feature product Bioseqs in advance. This prevents
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the object manager from uncaching components at an inopportune time, causing
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unnecessary thrashing. Far component Bioseqs are needed for displaying the
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#define LOCK_FAR_COMPONENTS 2
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#define LOCK_FAR_LOCATIONS 4
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#define LOCK_FAR_PRODUCTS 8
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Another set attempts to do bulk accession to gi lookups in advance, which is
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possible if PubSeqFetchEnable was called by the application. Remote fetching
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in asn2gb uses this new access mechanism. Far component IDs are needed for
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the CONTIG line, far location IDs for feature location joins, and far product
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IDs for the /protein_id and /transcript_id accessions.
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#define LOOKUP_FAR_COMPONENTS 16
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#define LOOKUP_FAR_LOCATIONS 32
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#define LOOKUP_FAR_PRODUCTS 64
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#define LOOKUP_FAR_HISTORY 128
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To use PubSeqFetchEnable, the application should #include <pmfapi.h>.
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CUSTOM are bit flags suppressing specific features, and are also ORed
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One set suppresses all import features, or all that don't have specific
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custom bits of their own.
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#define HIDE_IMP_FEATS 1
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#define HIDE_REM_IMP_FEATS 2
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Another set suppresses common individual import feature types.
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#define HIDE_SNP_FEATS 4
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#define HIDE_EXON_FEATS 8
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#define HIDE_INTRON_FEATS 16
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#define HIDE_MISC_FEATS 32
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Additional bits hide CDD regions, or all features on the CDS product.
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#define HIDE_CDD_FEATS 64
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#define HIDE_CDS_PROD_FEATS 128
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mRNAs and peptide features can show /transcription or /peptide sequence.
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#define SHOW_TRANCRIPTION 256
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#define SHOW_PEPTIDE 512
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GeneRIF references in RefSeq records can also be specifically hidden, non-
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GeneRIF records can be hidden, or only the most recent 10 GeneRIFs can be
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#define HIDE_GENE_RIFS 1024
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#define ONLY_GENE_RIFS 2048
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#define LATEST_GENE_RIFS 3072
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Protein feature tables and References in feature tables can also be shown.
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#define SHOW_PROT_FTABLE 4096
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#define SHOW_FTABLE_REFS 8192
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EXTRA is an opaque pointer used for preparing internal NCBI indices. Most
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programs will pass NULL for this parameter.
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ASN2GB STANDALONE APPLICATION
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An asn2gb executable is now available on all platforms, and is packaged
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with the Sequin archive. The most commonly used arguments are shown below.
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-f Format (b GenBank, e EMBL, p GenPept, t Feature Table, x INSDSet)
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-m Mode (r Release, e Entrez, s Sequin, d Dump)
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-s Style (n Normal, s Segment, m Master, c Contig)
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-g Bit Flags (1 HTML, 2 XML, 4 ContigFeats, 8 ContigSrcs, 16 FarTransl)
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-h Lock/Lookup Flags (8 LockProd, 16 LookupComp, 64 LookupProd)
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-u Custom Flags (2 HideMostImpFeats, 4 HideSnpFeats)
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-a ASN.1 Type (a Any, e Seq-entry, b Bioseq, s Bioseq-set, m Seq-submit)
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Batch processing of Bioseq-set ASN.1 release files is also supported.
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-t Batch (1 Report, 2 Sequin/Release)
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-b Bioseq-set is Binary [T/F]
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-c Bioseq-set is Compressed [T/F]
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-p Propagate Top Descriptors [T/F]
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Remote fetching allows gi to accession lookups and fetching of far components.
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-r Remote Fetching [T/F]
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doc/asn2gb.txt
