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

       -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, 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

AUTHOR

       The National Center for Biotechnology Information.

SEE ALSO

       asnval(1), cleanasn(1).