Need help to understand this small script Post: 302898658

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LEARN ABOUT DEBIAN

efetch

EFETCH(1)						      General Commands Manual							 EFETCH(1)

NAME

       efetch - retrieve entries from sequence databases.

SYNOPSIS

       efetch -options [database:]<query>

DESCRIPTION

       In  the	late  90s efetch was a very popular tool to extremely quickly retrieve entries from the most common public bioinformatics sequence
       and motif databases.

DATABASES

       SWissprot/SP, PIR, WOrmpep/WP, EMbl, GEnbank/GB, ProDom, ProSite

OPTIONS
:
       -a	     Search with Accession number

       -f	     Fasta format output

       -q	     Sequence only output (one line)

       -s <#>	     Start at position #

       -e <#>	     Stop at position #

       -o	     More options and info...

       -D <dir> Specify database directory

       -H Display index header data

       -p Display entrynames in search path

       -r Print sequence in 'raw' format

       -m Fetch from mixed mini database

       -M Mini format output

       -b Do NOT reverse the order of bytes (SunOS, IRIX do reverse, Alpha not)

       -d <dbfile> Specify database file (avoid this)

       -i <idxfile> Specify index file (avoid this)

       -l <divfile> Specify division lookup table (avoid this)

       -B <database> Specify database (archaic)

       -A Only return entryname for accession number

       -n <name> Give the sequence this name

       -x Don't require query to match entry's name exactly (avoid)

       -w For Wormpep: also fetch cross-referenced SwissProt entry

       -h shows this help text

ENVIRONMENT

       SWDIR	  = SwissProt  directory - database and EMBL index files PIRDIR     = PIR	 -- " -- WORMDIR    = Wormpep	 -- "  --  EMBLDIR
       =  EMBL	      --  " -- GBDIR	  = Genbank    -- " -- PRODOMDIR  = ProDom     -- " -- PROSITEDIR = ProSite    -- " -- DBDIR	  = User's
       own -- " -- (fasta format)

       SEQDB  database file (default SwissProt)

	      SEQDBIDX index file DIVTABL  division lookup table

	      Ex. setenv DBDIR /pubseq/seqlibs/embl/

	      Note that Prodom family consensus seqs can be fetched by PD:_#

AUTHOR

       Erik Sonnhammer (esr@sanger.ac.uk)

								     July 2010								 EFETCH(1)