ASNDISC(1)

🦋 ASNDISC — check those ASN.1 bio-sequence records for drama (discrepancies) 💅

okay bestie, welcome to asndisc(1) from the NCBI Tools User's Manual — it's a command-line tool and it's lowkey iconic.

✨ NAME ✨

asndisc — check ASN.1 biological sequence records for discrepancies. that's the whole job. it looks at your records and goes "hmm, girl, something's off here." 🔍

🌸 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 that checks ASN.1-format biological sequence records for discrepancies. it is literally the friend who reads your essay and circles the weird bits. no cap. ✨

🎀 OPTIONS 🎀

here's the summary of options, bestie — yes, all of them, we're not skipping a single one, that would be not the vibe. 🫶

• - — print the usage message. the lonely little dash that just wants to tell you how things work.
• -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 the 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 🧵 (yes queen, parallel)
• -X tests — EXpand report categories. it takes a comma-delimited list of test names as listed below, or ALL. 🌈
• -Z — Remote CDS Product Fetch 🛰️
• -a str — ASN.1 type
  • a — Any (this is the default, bestie)
  • 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 🔥

okay so this is the part where I hold up the whole entire list like a trophy, because every single one of these test names matters and we are NOT dropping any of them, periodt. 💅

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

that's the full roster, bestie. every. single. one. use them with -X, -d, and -e (they're comma-delimited, and -X also takes ALL). ✨

👑 AUTHOR 👑

The National Center for Biotechnology Information. slay. 💜

🌈 SEE ALSO 🌈

asnval(1), cleanasn(1). go give them a look too, they're the friend group. 🦋

and that's a wrap, bestie — this page is from the NCBI Tools User's Manual, source/version vibes from the National Center for Biotechnology Information, dated 2016-09-01. ASNDISC(1) forever. periodt. 💅🎀