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
pynast
VERSION:(1) User Commands VERSION:(1)NAME
PyNAST - alignment of short DNA sequences
SYNOPSIS
pynast [options] {-i input_fp -t template_fp}
DESCRIPTION
[] indicates optional input (order unimportant) {} indicates required input (order unimportant)
Example usage:
pynast -i my_input.fasta -t my_template.fasta
OPTIONS --version
show program's version number and exit
-h, --help
show this help message and exit
-t TEMPLATE_FP, --template_fp=TEMPLATE_FP
path to template alignment file [REQUIRED]
-i INPUT_FP, --input_fp=INPUT_FP
path to input fasta file [REQUIRED]
-v, --verbose
Print status and other information during execution [default: False]
-p MIN_PCT_ID, --min_pct_id=MIN_PCT_ID
minimum percent sequence identity to consider a sequence a match [default: 75.0]
-l MIN_LEN, --min_len=MIN_LEN
minimum sequence length to include in NAST alignment [default: 1000]
-m PAIRWISE_ALIGNMENT_METHOD, --pairwise_alignment_method=PAIRWISE_ALIGNMENT_METHOD
method for performing pairwise alignment [default: uclust]
-a FASTA_OUT_FP, --fasta_out_fp=FASTA_OUT_FP
path to store resulting alignment file [default: derived from input filepath]
-g LOG_FP, --log_fp=LOG_FP
path to store log file [default: derived from input filepath]
-f FAILURE_FP, --failure_fp=FAILURE_FP
path to store file of seqs which fail to align [default: derived from input filepath]
-e MAX_E_VALUE, --max_e_value=MAX_E_VALUE
Depreciated. Will be removed in PyNAST 1.2
-d BLAST_DB, --blast_db=BLAST_DB
Depreciated. Will be removed in PyNAST 1.2
SEE ALSO
http://pynast.sourceforge.net
Version: pynast 1.1 August 2011 VERSION:(1)