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asndisc - Online in the Cloud

Run asndisc in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command asndisc that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

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

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