Hi all
I have more than 1000 files in a folder and when ever i use a "compress" or "zcat" command it give error
/bin/zcat: Arg list too long. .
any solution for this :o (3 Replies)
say i have these many file in a directory named exam.
1)/exam/newfolder/link.txt.
2)/exam/newfolder1/
and i create a tar say exam.tar
well the problem is,
when i read the tar file i dont find any metadata about the directories,as you cannot create a tar containig empty directories.
on the... (2 Replies)
Hi
I am trying to extract a <filename>.tar.Z on a SLES machine using zcat.
The command I am using is
zcat <filename>.tar.Z | tar xf -
When I use the above I get the following message
tar: Read 7168 bytes from -
I think the message is benign because I see that my files where... (2 Replies)
Friends,
I need help with the following in UNIX.
Merge all csv files in one folder considering only 1 header row and ignoring header of all other files.
FYI - All files are in same format and contains same headers.
Thank you (4 Replies)
I created a backup script that emails all the admins when the backup is complete and attaches a log file of what what backed up. On occasion, something happens in which the backups stop working, I started "grep"ing around /var/log/syslog and I usually find the smoking gun. My goal is to zcat... (8 Replies)
Hi,
just i would like to know, how will be the response if you try to read a 40GB compressed file using zcat.
a)Uncompress the 40GB file and have it in the disk. use cat to view the steps.
b)Use zcat directly to view the compressed file?
What are the steps being occurred in step (b)?
Where... (3 Replies)
I have a tar file which i want to read and check some specific fields basis on which i want to get output.
Code
zcat samplefile.tar.gz | awk 'FNR==1 {++counter}
counter ==2 {BB=1;next}
substr($0,26,2) =="01") {next}
(substr($0,28,12) ~ "^") {next}
(substr($0,184,3) in BB) {next}
1
'... (7 Replies)
I have recently built a new server and patched Soalris 10 up tp latest bundle etc...
When I run a decompress using the format zcat fred.Z |tar -xvf - it runs at a very slow rate.
A similiar server which is less powerful runs over twice as quick.
Is there any work arounds to configure decompress... (4 Replies)
I've been struggling with this one for quite a while and cannot seem to find a solution for this find/replace scenario. Perhaps I'm getting rusty.
I have a file that contains a number of metrics (exactly 3 fields per line) from a few appliances that are collected in parallel. To identify the... (3 Replies)
Discussion started by: verdepollo
3 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)