If the directory contains files that don't have spaces in them, the earlier commands will generate errors as the source and destination names for the mv command will be the same and mv generally doesn't like that.
The following can be executed in a directory that has files with and without blanks in the name. It will attempt only to move the files with blanks:
This is horrible in terms of efficiency and I would do it the way Chubler_XL suggested with an additional test:
I have a problem with the script below
#!/bin/sh
for vo in `find -maxdepth 1 -type f -regex "^\./*$"`
do
ls -l "$vo"
some other commands
done
It works fine until `find ...` returns files with spaces. I've tryed to change IFS but haven't succeed
Any solutions? (4 Replies)
I'm trying to do something like that:
for $filename in `ls -1`
do
some_command $filename
done
but it doesn't work properly for file names with spaces, for...in splits at spaces. Anyway around? (4 Replies)
Hi All,
I see similar problems in past threads but so far no answers have worked for me. I am trying to write a script which parses a txt file that contains one filename per line, then finds those files on the local disk and copies them to a specified directory.
What I have:
... (4 Replies)
Hi
I hope someone will be able to resolve this little teaser!
I am running a script
for file in `ls directory`
do
echo "$file"
...other code here....
done
this works fine unless we receive a file with a name which has a space in it
ie
"filena me"
(I know its not good... (8 Replies)
I need to loop through the files in a directory and process the files. But some of the filenames contain spaces.
Here is a little test script I've been using to experiment. (I'm not really going to call 'echo', I'm doing some other processing.) Everything I try fails. How can I do this??... (7 Replies)
I want to ftp all the sh files in the directory. Also if any of the file name
contains spaces in them, it should be converted to underscores before it is ftped. I wrote the following code below:
FILESSH=$(ls /mysh/*.sh)
--- FILESH being used here for some other task ---
echo "$FILESSH" |... (3 Replies)
Hello All,
I am trying to remove all tabspaces and all blankspaces from my file using sed & awk, but not getting proper code. Please help me out.
My file is like this (<b> means one blank space, <t> means one tab space)-
$ cat file
NARESH<b><b><b>KUMAR<t><t>PRADHAN... (3 Replies)
Hey there, this is my first post and I'll try to explain my situation as best I can.Here is a sample of the input file:
ADO Sample.h,v ADO Sample 2010-05-21 lyonsb /repository/patents/TSCommon/OpenSource/Dundass/ug6mfc/DataSources/Ado/ADO Sample
ADO SampleDoc.h,v ADO SampleDoc 2010-05-21... (3 Replies)
Hello
I've got a certain no. of files in a directory whose names I'm reading and redirecting into a temporary text file using the command below:
ls -l | grep ^- | awk '{print $9}'However, whenever the file names contain spaces the above command considers only the part of the file name up to... (5 Replies)
I'm trying to handle some files with spaces in their name using "" or \ . Like "file 1" or file\ 1.
My current confusion can be expressed by the following shell script:
#!/bin/bash
touch "file 1" "file 2"
echo -n "ls: " ; ls
echo ---
for file in "file 1" "file 2" ; do
echo $file... (9 Replies)
Discussion started by: Ralph
9 Replies
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)