errhdr(1) [debian man page]

ERRHDR(1)						     NCBI Tools User's Manual							 ERRHDR(1)

NAME

       errhdr - produce a C header file from a set of messages

SYNOPSIS

       errhdr [-2] [-s] msgfile [hdrfile]

DESCRIPTION

       errhdr  reads  a  file describing error codes and corresponding messages and produces a C header file, either on standard output or in hdr-
       file.

       The input file has a simple text-based format; one file (errmsg/valid.msg in the source tree) starts

       MODULE valid
       $$ SEQ_INST, 1
       $^   ExtNotAllowed, 1
       # This is a comment
       A Bioseq "extension" is used for special classes of Bioseq. This class of
       Bioseq should not have one but it does. This is probably a software error.

       $^   ExtBadOrMissing, 2
       This class of Bioseq requires an "extension" but it is missing or of the
       wrong type. This is probably a software error.

       (Detailed descriptions are optional, and no "end" lines of any sort are necessary.)

OPTIONS

       A summary of options is included below.

       -2     Code, subcode tuples

       -s     Short subcode defines

AUTHOR

       The National Center for Biotechnology Information.

NCBI
								    2001-10-05								 ERRHDR(1)

ASN2FSA(1)						     NCBI Tools User's Manual							ASN2FSA(1)

NAME

       asn2fsa - convert biological sequence data from ASN.1 to FASTA

SYNOPSIS

       asn2fsa [-] [-A acc] [-D] [-E] [-H] [-L filename] [-T] [-a type] [-b] [-c] [-d path] [-e N] [-f path] [-g] [-h filename] [-i filename] [-k]
       [-l] [-m] [-o filename] [-p path] [-q filename] [-r] [-s] [-u] [-v filename] [-x str] [-z]

DESCRIPTION

       asn2fsa converts biological sequence data from ASN.1 to FASTA.

OPTIONS

       A summary of options is included below.

       -      Print usage message

       -A acc Accession to fetch

       -D     Use Dash for Gap

       -E     Extended Seq-ids

       -H     HTML spans

       -L filename
	      Log file

       -T     Use Threads

       -a type
	      Input ASN.1 type:
	      a      Automatic (default)
	      z      Any
	      e      Seq-entry
	      b      Bioseq
	      s      Bioseq-set
	      m      Seq-submit
	      t      batch processing (suitable for official releases; autodetects specific type)

       -b     Bioseq-set is Binary

       -c     Bioseq-set is Compressed

       -d path
	      Path to ReadDB Database

       -e N   Line length (70 by default; may range from 10 to 120)

       -f path
	      Path to indexed FASTA data

       -g     Expand delta gaps into Ns

       -h filename
	      Far component cache output file name

       -i filename
	      Single input file (standard input by default)

       -k     Local fetching

       -l     Lock components in advance

       -m     Master style for near segmented sequences

       -o filename
	      Nucleotide Output file name

       -p path
	      Path to ASN.1 Files

       -q filename
	      Quality score output file name

       -r     Remote fetching from NCBI

       -s     Far genomic contig for quality scores

       -u     Recurse

       -v filename
	      Protein output file name

       -x str File selection substring (.ent by default) [String]

       -z     Print quality score gap as -1

AUTHOR

       The National Center for Biotechnology Information.

SEE ALSO

       asn2all(1), asn2asn(1), asn2ff(1), asn2gb(1), asn2xml(1), asndhuff(1).

NCBI
								    2011-09-02								ASN2FSA(1)