cat certain files in directories to files named after the dir?
Hi all,
I have a directory with many subdirectories each named like so: KOG0001, KOG0002, ...KOG9999.
Each of these subdirectories contain a variable number two kinds of files (nuc and prot) named like so: Capitella_sp_nuc_hits.fasta (nuc) and Capitella_sp_prot_hits.fasta (prot). The Capitella_sp part represents the name of the species and varies from file to file.
I'm trying to write a script that will go through each subdirectory and concatenate the contents of all the _prot_hits.fasta files into one file in the main directory named like KOG0001.fasta, KOG0002.fasta, and so on. I think I have it figured out except how to reference the source files that I want. Can anyone help me out?
i have data files in different directories like /jadat
/cadat etcc... i have list of this directories in a file files.
content of files:
ja
ca
directories:
/jadat
/cadat
file in each of these directories
natt_trans_like.dat
i need to loop though each directory for a... (1 Reply)
Hello!!
I have directories from 2008, with files in them. I want to create a script that will find the directoried from 2008 (example directory:
drwxr-xr-x 2 isplan users 1024 Nov 21 2008 FILES_112108), delete the files within those directories and then delete the directories... (3 Replies)
I want to move the files in a dir to different dirs based on their file names.
Ex: i have 4 different files with name -
CTS_NONE_10476031_MRL_PFT20081215a.txt
CTS_NONE_10633009_MRL_PFT20091020a.txt
CTS_NONE_10345673_MRL_PFT20081215a.txt
CTS_NONE_10872456_MRL_PFT20091020a.txt
and the 1st... (2 Replies)
I want to move the files in a dir to different dirs based on their file names.
Ex: i have 4 different files with name -
CTS_NONE_10476031_MRL_PFT20081215a.txt
CTS_NONE_10633009_MRL_PFT20091020a.txt
CTS_NONE_10345673_MRL_PFT20081215a.txt
CTS_NONE_10872456_MRL_PFT20091020a.txt
and the 1st... (4 Replies)
Hi
I am looking for the correct syntax to find all files in the current directory without listing sub-directoris. I was using the following command, but it still returns subdirectoris and files inside them:
$ ls -laR | grep -v ^./
Any idea? Thanks
PS I am in ksh88 (4 Replies)
Hi,
Here is what i'm trying to do,
-Check in two directories for a user inputed filename
-Then cat all the version found of the file to the current screen
I am a total nembie to programming, here what i have done so far....
#!/bin/bash
#Check in /home/loonatic and /var/named/master... (2 Replies)
I am very new to unix as well as shell scripting.
I have to write a script for the following requirement. In have to list all the files in directory and its sub directories along with file path and size of the file
Please help me in this regard and many thanks in advance. (3 Replies)
Dear Members,
I have a list of xml files like
abc.xml.table
prq.xml.table
...
..
.
in a txt file.
Now I have to search the file(s) in all directories and sub-directories and print the full path of file in a output txt file.
Please help me with the script or command to do so.
... (11 Replies)
I have searched this quite a long time but couldn't find the right method for me to use. I need to assign read write permission to the user for specific directories and it's sub directories and files. I do not want to use ACL. I do not want to assign user the same group of that directories too.... (0 Replies)
Discussion started by: blinkingdan
0 Replies
LEARN ABOUT DEBIAN
ampliconnoise
AMPLICONNOISE(1) AmpliconNoise Documentation AMPLICONNOISE(1)NAME
AmpliconNoise - remove noise from high throughput nucleotide sequence data
VERSION
This documentation refers to version 1.22
SYNOPSIS
See /usr/share/doc/ampliconnoise/Doc.pdf.gz for details of how to run.
DESCRIPTION
The following tools are included. Most of them have an MPI equivalent, for example SeqNoise has an equivalent SeqNoiseM which can be used
with mpirun.
FastaUnique - dereplicates fasta file
-in string input file name
Options:
FCluster
-in string distance input file name
-out string output file stub
Options:
-r resolution
-a average linkage
-w use weights
-i read identifiers
-s scale dist.
NDist - pairwise Needleman-Wunsch sequence distance matrix from a fasta file
-in string fata file name
Options:
-i output identifiers
Perseus - slays monsters
-sin string seq file name
Options:
-tin string reference sequence file
-a output alignments
-d use imbalance
-rin string lookup file name
PyroDist - pairwise distance matrix from flowgrams
-in string flow file name
-out stub out file stub
Options:
-ni no index in dat file
-rin string lookup file name
PyroNoise - clusters flowgrams without alignments
-din string flow file name
-out string cluster input file name
-lin string list file
Options:
-v verbose
-c double initial cut-off
-ni no index in dat file
-s double precision
-rin file lookup file name
SeqDist - pairwise distance matrix from a fasta file
-in string fasta file name
Options:
-i output identifiers
-rin string lookup file name
SeqNoise - clusters sequences
-in string sequence file name
-din string distance matrix file name
-out string cluster input file name
-lin string list file
Options:
-min mapping file
-v verbose
-c double initial cut-off
-s double precision
-rin string lookup file name
SplitClusterEven
-din string dat filename
-min string map filename
-tin string tree filename
-s split size
-m min size
AUTHOR
All software by Chris Quince (quince@civil.gla.ac.uk) This manpage by Tim Booth (tbooth@ceh.ac.uk)
LICENCE AND COPYRIGHT
Copyright (c) 2009 (quince@civil.gla.ac.uk). All rights reserved.
Released under the Lesser GPL.
Permission is granted for anyone to copy, use, or modify these programs and documents for purposes of research or education, provided this
copyright notice is retained, and note is made of any changes that have been made.
perl v5.12.4 2011-04-28 AMPLICONNOISE(1)