asndisc - check ASN.1 biological sequence records for discrepancies
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]
asndisc is a command-line tool to check ASN.1-format biological sequence
records for discrepancies.
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)
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
The National Center for Biotechnology Information.
asnval(1),
cleanasn(1).