user manual Net.pl


Introduction
============

Net.pl performs internet-related task, it especially offers specific
download facilities.


Net.pl -get
===========

Download internet document via its URI


COMMAND LINE SYNTAX
 Net.pl -get [options] <URI> > <docout>

arguments:
 URI            uniform resource locator (URI) of internet document
 docout         output destination, default STDOUT

options:
 -fofn=S        supply command argument (URI) in a file.
                The entries of the file will be appended to the argument list.


EXAMPLES

 Net.pl -get [...] > doc.html

   Download HTML document [...] to file doc.html.


Net.pl -NcbiSeq
===============

Batch sequence download via NCBI Entrez web interface, for a list of accession
numbers.


COMMAND LINE SYNTAX
 Net.pl -NcbiSeq [options] <AccNo1> [<AccNo2> ...] > <seqout>

arguments:
 AccNo          sequence accession number
 seqout         output destination, default STDOUT

options:
 -fofn=S        supply list of command arguments (accession numbers) in a file.
                The entries of the file will be appended to the argument list.
                Multiple -fofn switch statements are allowed.
 -OutFmt=S      select output file format, case-insensitive specifiers:
                  asn         ASN.1 text format
                  fasta       fastA format (default)
                  GenBank     GenBank format
                  gi          GI number


EXAMPLES

 Net.pl -NcbiSeq AC104982 > sequence.fa

   Download sequence AC104982 to file sequence.fa, save it in fasta format.

 Net.pl -NcbiSeq -OutFmt=asn AC104982 > sequence.asn

   Download sequence AC104982 to file sequence.asn, save it in ASN.1 format.


xdget - alternative to Net.pl -NcbiSeq
======================================

Internet sequence download is time-inefficient and susceptible to network
errors. Therefore, it is preferable to retrieve sequences from local databases,
if possible. A rather universal data source are BLAST databases. WashU-BLAST
provides a utility program to extract certain sequence entries from a BLAST
database. It is required, however, to create an index for a BLAST database
that is intended to be used for sequence retrieval.


COMMAND LINE SYNTAX
 xdformat [-p|-n] -X <BLAST-DB>
 xdget [-p|-n] [options] <BLAST-DB> <AccNo1> [<AccNo2> ...] > <seqout>

arguments:
 BLAST-DB       WashU BLAST database, XDF version 2.0 or higher
 AccNo          sequence accession number

options:
 -n             database contains nucleotide sequences
 -p             database contains peptide sequences

 -f             command line arguments are names of files containing identifiers
 -o S           output destination, default STDOUT

 [... and many more, cf. output of `xdget -h']


ENVIRONMENT VARIABLES

 $BLASTDB       default location (directory) of BLAST databases


EXAMPLES

 xdformat -n -X $BLASTDB/gb_primate

   Index (or re-index) sequence identifiers in existing XDF database.

 xdget -n $BLASTDB/gb_primate AC104982 > sequence.fa

   Retrieve sequence AC104982, save it to file sequence.fa, in fasta format.
