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Full Discussion: rename a file to include the ip address
Top Forums UNIX for Dummies Questions & Answers rename a file to include the ip address Post 302095910 by MrMac on Sunday 12th of November 2006 07:29:43 AM
Old 11-12-2006
thanks guys, great help - edited the example and when it runs I get "no closing quote" - any ideas what that could be..

this is what I am running:

Code:
#!/bin/ksh

hostFile='GLOBAL_hostFile.txt'
myUser='****'
myPasswd='*********'

GLOBAL_BACKUP='full_export.dmp'

while read host
do
ftp -n  <<EOF
   open ${host}
   user ${myUser} ${myPasswd}
   cd /global/prd/cycle/export
   get ${GLOBAL_BACKUP} ${GLOBAL_BACKUP}_${host}
EOF
done < "${hostFile}"

apologies......
Last edited by MrMac; 11-13-2006 at 07:55 AM..
 

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LEARN ABOUT DEBIAN

bp_classify_hits_kingdom

BP_CLASSIFY_HITS_KINGDOM(1p)				User Contributed Perl Documentation			      BP_CLASSIFY_HITS_KINGDOM(1p)

NAME

       classify_hits_kingdom - classify BLAST hits by taxonomic kingdom

   USAGE
       classify_hits_kingdom [-i tab_file] [-i second_BLAST_file] [-e evalue_cutoff]
			     [-t dir_where_TAXONOMY_files_are] [-g gi2taxid]
			     [-z PATH_TO_zcat] [-v]

   DESCRIPTION
       Will print out the taxonomic distribution (at the kingdom level) for a set of hits against the NR database.  This script assumes you've
       done a search against the protein database, you'll have to make minor changes in the gi_taxid part to point to the gi_taxid_nuc.dump file.

       This expects BLAST files in tabbed -m9 or -m8 format.  Output with -m 8 or use blast2table.pl to convert (or fastam9_to_table.PLS if using
       FASTA).

	 Input values:
	  -t/--taxonomy  directory where the taxonomy .dmp files are (from NCBI)
	  -g/--gi	 Location of gi_taxid_prot.dmp (or gi_taxid_nucl.dmp if
			 the search was against a NT db)
	  -i/--in	 The name of the tab delimited -m8/-m9 output files to
			 process.

	   -e/--evalue	 Provide an E-value cutoff for hits to be considered
	   -z/--zcat	 Path to the 'zcat' executable, can also be 'gunzip -c'
			 if no zcat on your system.
	  Flags
	   -v/--verbose  To turn on verbose messages
	   -h/--help	 Display this helpful information

       This is intended to be useful starting script, but users may want to customize the output and parameters.  Note that I am summarizing the
       kingdoms here and Eukaryota not falling into Metazoa, Viridiplantae, or Fungi gets grouped into the general superkingdom Eukaryota. for
       simplicity.  There are comments in the code directing you to where changes can be made if you wanted to display hits by phylum for example.
       Note that you must wipe out the cache file 'gi2class' that is craeed in your directory after making these changes.

   AUTHOR
       Jason Stajich jason_at_bioperl_dot_org

perl v5.14.2							    2012-03-02					      BP_CLASSIFY_HITS_KINGDOM(1p)
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