Man page - asndisc(1)

Packages contains this manual

Package:  ncbi-tools-bin
apt-get install ncbi-tools-bin

Manuals in package:
• asn2ff(1)
• asn2gb(1)
• asntool(1)
• vecscreen(1)
• sortbyquote(1)
• trna2tbl(1)
• asn2xml(1)
• getpub(1)
• gil2bin(1)
• gene2xml(1)
• asn2all(1)
• checksub(1)
• subfuse(1)
• getmesh(1)
• taxblast(1)
• asn2asn(1)
• spidey(1)
• tbl2asn(1)
• asnval(1)
• asnmacro(1)
• idfetch(1)
• asndhuff(1)
• insdseqget(1)
• nps2gps(1)
• indexpub(1)
• findspl(1)
• asn2fsa(1)
• gbseqget(1)
• errhdr(1)
• asn2idx(1)
• trna2sap(1)
• cleanasn(1)
• asndisc(1)
• makeset(1)
• fa2htgs(1)
• debruijn(1)
Documentations in package:
• ncbi-tools-bin

Manual

ASNDISC

NAME
SYNOPSIS
DESCRIPTION
OPTIONS
AVAILABLE TESTS
AUTHOR
SEE ALSO

---

NAME

asndisc - check ASN.1 biological sequence records for discrepancies

SYNOPSIS

asndisc [ - ] [ -B ] [ -C N ] [ -F ] [ -I path ] [ -L str ] [ -N filename ] [ -P str ] [ -R ] [ -S ] [ -T ] [ -X tests ] [ -Z ] [ -a str ] [ -b ] [ -c ] [ -d tests ] [ -e tests ] [ -f ] [ -i filename ] [ -k ] [ -l ] [ -o filename ] [ -p path ] [ -r dir ] [ -s ext ] [ -t ] [ -u ] [ -w filename ] [ -x str ]

DESCRIPTION

asndisc is a command-line tool to check ASN.1-format biological sequence records for discrepancies.

OPTIONS

A summary of options is included below.

	-		Print usage message
	-B		Big sequence report
	-C N		Max count
	-F		Fix product name list

-I path

Path to Indexed binary ASN.1 data

-L str

Lineage to use

-N filename

File with list of product names to check

-P str

RePort type

g

			Genome
	b		Big sequence
	m		MegaReport
	t		Include Tag
	s		Tag for Superuser
	-R

Remote fetching from ID

	-S		Summary report
	-T		Use threads

-X tests

EXpand report categories (comma-delimited list of test names as listed below or ALL).

	-Z		Remote CDS Product Fetch
	-a str		ASN.1 type

a

			Any (default)
	e		seq-Entry
	b		Bioseq
	s		bioseq-Set
	m		seq-subMit
	t		baTch bioseq-set
	u		batch seq-sUbmit
	c		Catenated seq-entry
	-b

Batch file is Binary

	-c		Batch file is Compressed
	-d str		Disable tests (comma-delimited list of test names as listed below).
	-e str		Enable tests (comma-delimited list of test names as listed below).
	-f		Use Feature table output format

-i filename

Single input file (standard input by default)

	-k		Local fetching
	-l		Load components in advance

-o filename

Single output file

-p path

Path to ASN.1 files

	-r dir		Output directory
	-s ext		Output file Suffix ( .dr by default)
	-t		Big Test Set
	-u		Recurse

-w filename

Suspect product rule filename

-x str

File selection substring ( .sqn by default)

AVAILABLE TESTS

MISSING_GENES, EXTRA_GENES, MISSING_LOCUS_TAGS, DUPLICATE_LOCUS_TAGS, BAD_LOCUS_TAG_FORMAT, INCONSISTENT_LOCUS_TAG_PREFIX, NON_GENE_LOCUS_TAG, DISC_COUNT_NUCLEOTIDES, MISSING_PROTEIN_ID, INCONSISTENT_PROTEIN_ID, FEATURE_LOCATION_CONFLICT, GENE_PRODUCT_CONFLICT, DUPLICATE_GENE_LOCUS, EC_NUMBER_NOTE, PSEUDO_MISMATCH, JOINED_FEATURES, OVERLAPPING_GENES, OVERLAPPING_CDS, CONTAINED_CDS, RNA_CDS_OVERLAP, SHORT_CONTIG, INCONSISTENT_BIOSOURCE, SUSPECT_PRODUCT_NAMES, DISC_PRODUCT_NAME_TYPO, DISC_PRODUCT_NAME_QUICKFIX, INCONSISTENT_SOURCE_DEFLINE, PARTIAL_CDS_COMPLETE_SEQUENCE, EC_NUMBER_ON_UNKNOWN_PROTEIN, TAX_LOOKUP_MISSING, TAX_LOOKUP_MISMATCH, SHORT_SEQUENCES, SUSPECT_PHRASES, DISC_SUSPICIOUS_NOTE_TEXT, COUNT_TRNAS, FIND_DUP_TRNAS, FIND_BADLEN_TRNAS, FIND_STRAND_TRNAS, COUNT_RRNAS, FIND_DUP_RRNAS, RNA_NO_PRODUCT, TRANSL_NO_NOTE, NOTE_NO_TRANSL, TRANSL_TOO_LONG, CDS_TRNA_OVERLAP, COUNT_PROTEINS, DISC_FEAT_OVERLAP_SRCFEAT, MISSING_GENPRODSET_PROTEIN, DUP_GENPRODSET_PROTEIN, MISSING_GENPRODSET_TRANSCRIPT_ID, DISC_DUP_GENPRODSET_TRANSCRIPT_ID, DISC_PERCENT_N, N_RUNS, ZERO_BASECOUNT, ADJACENT_PSEUDOGENES, DISC_LONG_NO_ANNOTATION, NO_ANNOTATION, DISC_INFLUENZA_DATE_MISMATCH, DISC_SHORT_INTRON, DISC_MISSING_VIRAL_QUALS, DISC_SRC_QUAL_PROBLEM, DISC_MISSING_SRC_QUAL, DISC_DUP_SRC_QUAL, DISC_DUP_SRC_QUAL_DATA, DISC_HAPLOTYPE_MISMATCH, DISC_FEATURE_MOLTYPE_MISMATCH, DISC_CDS_WITHOUT_MRNA, DISC_EXON_INTRON_CONFLICT, DISC_FEATURE_COUNT, DISC_SPECVOUCHER_TAXNAME_MISMATCH, DISC_GENE_PARTIAL_CONFLICT, DISC_FLATFILE_FIND_ONCALLER, DISC_CDS_PRODUCT_FIND, DISC_DUP_DEFLINE, DUP_DISC_ATCC_CULTURE_CONFLICT, DISC_USA_STATE, DISC_INCONSISTENT_MOLTYPES, DISC_SUBMITBLOCK_CONFLICT, DISC_POSSIBLE_LINKER, DISC_TITLE_AUTHOR_CONFLICT, DISC_BAD_GENE_STRAND, DISC_MAP_CHROMOSOME_CONFLICT, DISC_RBS_WITHOUT_GENE, DISC_CITSUBAFFIL_CONFLICT, DISC_REQUIRED_CLONE, DISC_SOURCE_QUALS_ASNDISC, DISC_mRNA_ON_WRONG_SEQUENCE_TYPE, DISC_RETROVIRIDAE_DNA, DISC_CHECK_AUTH_CAPS, DISC_CHECK_RNA_PRODUCTS_AND_COMMENTS, DISC_MICROSATELLITE_REPEAT_TYPE, DISC_MITOCHONDRION_REQUIRED, DISC_UNPUB_PUB_WITHOUT_TITLE, DISC_QUALITY_SCORES, DISC_INTERNAL_TRANSCRIBED_SPACER_RRNA, DISC_PARTIAL_PROBLEMS, DISC_BACTERIAL_PARTIAL_NONEXTENDABLE_PROBLEMS, DISC_BACTERIAL_PARTIAL_NONEXTENDABLE_EXCEPTION, DISC_SUSPECT_RRNA_PRODUCTS, DISC_SUSPECT_MISC_FEATURES, DISC_BACTERIA_MISSING_STRAIN, DISC_MISSING_DEFLINES, DISC_MISSING_AFFIL, DISC_BACTERIA_SHOULD_NOT_HAVE_ISOLATE, DISC_BACTERIA_SHOULD_NOT_HAVE_MRNA, DISC_CDS_HAS_NEW_EXCEPTION, DISC_TRINOMIAL_SHOULD_HAVE_QUALIFIER, DISC_METAGENOMIC, DISC_METAGENOME_SOURCE, ONCALLER_GENE_MISSING, ONCALLER_SUPERFLUOUS_GENE, DISC_SHORT_RRNA, ONCALLER_CHECK_AUTHORITY, ONCALLER_CONSORTIUM, ONCALLER_STRAIN_CULTURE_COLLECTION_MISMATCH, ONCALLER_MULTISRC, ONCALLER_MULTIPLE_CULTURE_COLLECTION, DISC_SEGSETS_PRESENT, DISC_NONWGS_SETS_PRESENT, DISC_FEATURE_LIST, DISC_CATEGORY_HEADER, DISC_MISMATCHED_COMMENTS, DISC_STRAIN_TAXNAME_MISMATCH, DISC_HUMAN_HOST, DISC_BAD_BACTERIAL_GENE_NAME, TEST_BAD_GENE_NAME, ONCALLER_ORDERED_LOCATION, ONCALLER_COMMENT_PRESENT, ONCALLER_DEFLINE_ON_SET, ONCALLER_HIV_RNA_INCONSISTENT, SHORT_PROT_SEQUENCES, TEST_EXON_ON_MRNA, TEST_HAS_PROJECT_ID, ONCALLER_HAS_STANDARD_NAME, ONCALLER_MISSING_STRUCTURED_COMMENTS, DISC_REQUIRED_STRAIN, MISSING_GENOMEASSEMBLY_COMMENTS, DISC_BACTERIAL_TAX_STRAIN_MISMATCH, TEST_CDS_HAS_CDD_XREF, TEST_UNUSUAL_NT, TEST_LOW_QUALITY_REGION, TEST_ORGANELLE_NOT_GENOMIC, TEST_UNWANTED_SPACER, TEST_ORGANELLE_PRODUCTS, TEST_SP_NOT_UNCULTURED, TEST_BAD_MRNA_QUAL, TEST_UNNECESSARY_ENVIRONMENTAL, TEST_UNNECESSARY_VIRUS_GENE, TEST_UNWANTED_SET_WRAPPER, TEST_MISSING_PRIMER, TEST_UNUSUAL_MISC_RNA, TEST_AMPLIFIED_PRIMERS_NO_ENVIRONMENTAL_SAMPLE, TEST_DUP_GENES_OPPOSITE_STRANDS, TEST_SMALL_GENOME_SET_PROBLEM, TEST_OVERLAPPING_RRNAS, TEST_MRNA_SEQUENCE_MINUS_STRAND_FEATURES, TEST_TAXNAME_NOT_IN_DEFLINE, TEST_COUNT_UNVERIFIED, SHOW_TRANSL_EXCEPT, SHOW_HYPOTHETICAL_CDS_HAVING_GENE_NAME, TEST_DEFLINE_PRESENT, TEST_MRNA_OVERLAPPING_PSEUDO_GENE, FIND_OVERLAPPED_GENES, DISC_BIOMATERIAL_TAXNAME_MISMATCH, DISC_CULTURE_TAXNAME_MISMATCH, DISC_CHECK_AUTH_NAME, NON_RETROVIRIDAE_PROVIRAL, RNA_PROVIRAL, SHORT_SEQUENCES_200, DISC_10_PERCENTN, N_RUNS_14, MOLTYPE_NOT_MRNA, TECHNIQUE_NOT_TSA, MISSING_STRUCTURED_COMMENT, MISSING_PROJECT, MULTIPLE_CDS_ON_MRNA, DUP_DISC_CBS_CULTURE_CONFLICT, DIVISION_CODE_CONFLICTS, RRNA_NAME_CONFLICTS, EUKARYOTE_SHOULD_HAVE_MRNA, MRNA_SHOULD_HAVE_PROTEIN_TRANSCRIPT_IDS, ONCALLER_COUNTRY_COLON, ONCALLER_BIOPROJECT_ID, ONCALLER_STRAIN_TAXNAME_CONFLICT, ONCALLER_MORE_NAMES_COLLECTED_BY, ONCALLER_MORE_OR_SPEC_NAMES_IDENTIFIED_BY, ONCALLER_SUSPECTED_ORG_IDENTIFIED, ONCALLER_SUSPECTED_ORG_COLLECTED, ONCALLER_SWITCH_STRUCTURED_COMMENT_PREFIX, DISC_CITSUB_AFFIL_DUP_TEXT, ONCALLER_DUPLICATE_PRIMER_SET, END_COLON_IN_COUNTRY, DISC_PROTEIN_NAMES, DISC_TITLE_ENDS_WITH_SEQUENCE, DISC_INCONSISTENT_STRUCTURED_COMMENTS, DISC_INCONSISTENT_DBLINK, DISC_INCONSISTENT_MOLINFO_TECH, DISC_GAPS, DISC_BAD_BGPIPE_QUALS, TEST_SHORT_LNCRNA, TEST_TERMINAL_NS, TEST_ALIGNMENT_HAS_SCORE, UNCULTURED_NOTES_ONCALLER, SEQ_ID_PHRASES, NO_PRODUCT_STRING

AUTHOR

The National Center for Biotechnology Information.

SEE ALSO

asnval (1), cleanasn (1).

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