nps2gps(1) [debian man page]

NPS2GPS(1)						      General Commands Manual							NPS2GPS(1)

NAME

       nps2gps - convert nucleotide-protein sets to ASN.1 genomic product sets

SYNOPSIS

       nps2gps [-] [-D] [-F] [-G str] [-L] [-N] [-P] [-Q] [-R] [-T] [-U] [-f str] [-i filename] [-o filename] [-p path] [-r path] [-x str]

DESCRIPTION

       nps2gps converts NCBI Bioseq-sets from simple nucleotide-protein sets to full genomic product sets complete with mRNA transcripts, which it
       outputs as text ASN.1.

OPTIONS

       A summary of options is included below.

       -      Print usage message

       -D     RefSeq mRNA Titles

       -F     Map by Feature ID

       -G str General ID database name

       -L     Lock components in advance

       -N     Promote Non-coding RNAs

       -P     mRNA ID from Protein

       -Q     Special mRNA titles

       -R     Enable Remote fetching from ID

       -T     Map by Transcript ID

       -U     Remove Unnecessary gene cross-references

       -f str Substring filter

       -i filename
	      Single input file (default = stdin)

       -o filename
	      Single output file (default = stdout)

       -p path
	      Path to files for batch conversion

       -r path
	      Path for results of batch conversion

       -x str File selection suffix for batch conversion (default = .ent)

AUTHOR

       The National Center for Biotechnology Information.

SEE ALSO

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

NCBI Tools User's Manual					    2012-06-24								NPS2GPS(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)