ncbi-tools6 (6.1.20120620-2) doc/man/asndisc.1

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+.TH ASNDISC 1 2012-06-24 NCBI "NCBI Tools User's Manual"
+.SH NAME
+asndisc \- check ASN.1 biological sequence records for discrepancies
+.SH SYNOPSIS
+.B asndisc
+[\|\fB\-\fP\|]
+[\|\fB\-B\fP\|]
+[\|\fB\-C\fP\ \fIN\fP\|]
+[\|\fB\-F\fP\|]
+[\|\fB\-I\fP\ \fIpath\fP\|]
+[\|\fB\-L\fP\ \fIstr\fP\|]
+[\|\fB\-N\fP\ \fIfilename\fP\|]
+[\|\fB\-P\fP\ \fIstr\fP\|]
+[\|\fB\-R\fP\|]
+[\|\fB\-S\fP\|]
+[\|\fB\-T\fP\|]
+[\|\fB\-X\fP\ \fItests\fP\|]
+[\|\fB\-Z\fP\|]
+[\|\fB\-a\fP\ \fIstr\fP\|]
+[\|\fB\-b\fP\|]
+[\|\fB\-c\fP\|]
+[\|\fB\-d\fP\ \fItests\fP\|]
+[\|\fB\-e\fP\ \fItests\fP\|]
+[\|\fB\-f\fP\|]
+[\|\fB\-i\fP\ \fIfilename\fP\|]
+[\|\fB\-k\fP\|]
+[\|\fB\-l\fP\|]
+[\|\fB\-o\fP\ \fIfilename\fP\|]
+[\|\fB\-p\fP\ \fIpath\fP\|]
+[\|\fB\-r\fP\ \fIdir\fP\|]
+[\|\fB\-s\fP\ \fIext\fP\|]
+[\|\fB\-t\fP\|]
+[\|\fB\-u\fP\|]
+[\|\fB\-w\fP\ \fIfilename\fP\|]
+[\|\fB\-x\fP\ \fIstr\fP\|]
+.SH DESCRIPTION
+\fBasndisc\fP is a command-line tool to check ASN.1-format biological
+sequence records for discrepancies.
+.SH OPTIONS
+A summary of options is included below.
+.TP
+\fB\-\fP
+Print usage message
+.TP
+\fB\-B\fP
+Big sequence report
+.TP
+\fB\-C\fP\ \fIN\fP
+Max count
+.TP
+\fB\-F\fP
+Fix product name list
+.TP
+\fB\-I\fP\ \fIpath\fP
+Path to Indexed binary ASN.1 data
+.TP
+\fB\-L\fP\ \fIstr\fP
+Lineage to use
+.TP
+\fB\-N\fP\ \fIfilename\fP
+File with list of product names to check
+.TP
+\fB\-P\fP\ \fIstr\fP
+RePort type
+.RS
+.PD 0
+.IP g
+Genome
+.IP b
+Big sequence
+.IP m
+MegaReport
+.IP t
+Include Tag
+.IP s
+Tag for Superuser
+.PD
+.RE
+.TP
+\fB\-R\fP
+Remote fetching from ID
+.TP
+\fB\-S\fP
+Summary report
+.TP
+\fB\-T\fP
+Use threads
+.TP
+\fB\-X\fP\ \fItests\fP
+EXpand report categories (comma-delimited list of test names as listed
+below or ALL).
+.TP
+\fB\-Z\fP
+Remote CDS Product Fetch
+.TP
+\fB\-a\fP\ \fIstr\fP
+ASN.1 type
+.RS
+.PD 0
+.IP a
+Any (default)
+.IP e
+seq-Entry
+.IP b
+Bioseq
+.IP s
+bioseq-Set
+.IP m
+seq-subMit
+.IP t
+baTch bioseq-set
+.IP u
+batch seq-sUbmit
+.PD
+.RE
+.TP
+\fB\-b\fP
+Batch file is Binary
+.TP
+\fB\-c\fP
+Batch file is Compressed
+.TP
+\fB\-d\fP\ \fIstr\fP
+Disable tests (comma-delimited list of test names as listed below).
+.TP
+\fB\-e\fP\ \fIstr\fP
+Enable tests (comma-delimited list of test names as listed below).
+.TP
+\fB\-f\fP
+Use Feature table output format
+.TP
+\fB\-i\fP\ \fIfilename\fP
+Single input file (standard input by default)
+.TP
+\fB\-k\fP
+Local fetching
+.TP
+\fB\-l\fP
+Load components in advance
+.TP
+\fB\-o\fP\ \fIfilename\fP
+Single output file
+.TP
+\fB\-p\fP\ \fIpath\fP
+Path to ASN.1 files
+.TP
+\fB\-r\fP\ \fIdir\fP
+Output directory
+.TP
+\fB\-s\fP\ \fIext\fP
+Output file Suffix (\fB.dr\fP by default)
+.TP
+\fB\-t\fP
+Big Test Set
+.TP
+\fB\-u\fP
+Recurse
+.TP
+\fB\-w\fP\ \fIfilename\fP
+Suspect product rule filename
+.TP
+\fB\-x\fP\ \fIstr\fP
+File selection substring (\fB.sqn\fP by default)
+.SS AVAILABLE TESTS
+.P
+.ad l
+.nh
+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, 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
+.hy
+.ad b
+.SH AUTHOR
+The National Center for Biotechnology Information.
+.SH SEE ALSO
+.BR asnval (1),
+.BR cleanasn (1).