Hi,
I'm not very familiar with unix shell. I want to replace the combination of two carriage returns and one newline with one carriage return and one newline. I think the best way to do this is to use sed. I tried something like this:
sed -e "s#\#\#g" file.txt
but it doesn't work.
Thanx... (2 Replies)
I am trying to use sed to replace specific characters at a specific position in the file with a different value... can this be done?
Example:
File:
A0199999123
A0199999124
A0199999125
Need to replace 99999 in positions 3-7 with 88888.
Any help is appreciated. (5 Replies)
Greetings.
I don't have experience programing scripts. I need to insert a string in a specific position of another string on another file (last.cfg), for example:
File last.cfg before using script:
login_interval=1800
lcs.machinename=client04
File last.cfg after using script:... (4 Replies)
I want to remove text from nth position to nth position couple of times in same line
my line is
"hello is there anyone can help me with this question"
I need like this
ello is there anyone can help me with question
'h' is removed and 'this' removed from the line. I want to do this... (5 Replies)
I woud like to substitue a string on a specific position for specific lines
I've got a file and I would like to change a specific string from "TOCHANGE" to "ABCABCAB"
For every line (except 1,2, 3 and the last one) , I need to check between the 9th and the 16th digits.
For the 3rd line, I... (7 Replies)
Hi,
I have file with lines key=val.
For ex(conf.file):-
c=3
ef=78
b=40
ca=40
I want to remove the line with c=3, when I execute the below command it's removing both lines i.e c=3 and ca=40. Could you please correct my command.
/usr/xpg4/bin/awk -v key=c 'match($0,key)... (3 Replies)
I have a file that I need to parse using a script. The dates in the file are displayed in the format:
Mar 2, 2011 9:09:31 PM
I have tried using the date command %e and %l but it pads an extra space for the day and hour if they are single digits.
So this I used a normal date command:
... (6 Replies)
Hi Gurus,
Apologies as I feel like this must be answered already on here somewhere but I just can't find it. I find many people looking to remove all \n and \r (CR and LF) or one or the other but the only times I've found someone trying to remove them only when both are together they've found... (7 Replies)
Hi,
I have a fixed width file.
The way this file works is say for example there are 30 columns in it each with different sizes say 10,5,2, etc...
If data in a field is less than the field size the rest of it is loaded with spaces.
I would like an awk command to that would replace
I have... (8 Replies)
Hi,
I have a file like this (about 8 columns in total, this being the 2nd column)
gi_49482297_ref_YP_039521.1_
gi_49482297_ref_YP_039521.1_
gi_49482315_ref_YP_039539.1_
gi_49482315_ref_YP_039539.1_I want to remove the _ at the end of the line.
And at later stages I would want to replace the... (5 Replies)
Discussion started by: Syeda Sumayya
5 Replies
LEARN ABOUT DEBIAN
hhconsensus
HHCONSENSUS(1) User Commands HHCONSENSUS(1)NAME
hhconsensus - calculate the consensus sequence for an A3M/FASTA input file
SYNOPSIS
hhconsensus -i <file> [options]
DESCRIPTION
HHconsensus version 2.0.15 (June 2012) Calculate the consensus sequence for an A3M/FASTA input file. (C) Johannes Soeding, Michael Rem-
mert, Andreas Biegert, Andreas Hauser Remmert M, Biegert A, Hauser A, and Soding J. HHblits: Lightning-fast iterative protein sequence
searching by HMM-HMM alignment. Nat. Methods 9:173-175 (2011).
-i <file>
query alignment (A2M, A3M, or FASTA), or query HMM
Output options:
-s <file>
append consensus sequence in FASTA (default=<infile.seq>)
-o <file>
write alignment with consensus sequence in A3M
-oa3m <file>
same
-oa2m <file>
write alignment with consensus sequence in A2M
-ofas <file>
write alignment with consensus sequence in FASTA
-v <int>
verbose mode: 0:no screen output 1:only warings 2: verbose
Filter input alignment (options can be combined):
-id [0,100] maximum pairwise sequence identity (%) (def=100)
-diff [0,inf[ filter most diverse set of sequences, keeping at least this
many sequences in each block of >50 columns (def=0)
-cov [0,100] minimum coverage with query (%) (def=0)
-qid [0,100] minimum sequence identity with query (%) (def=0)
-qsc [0,100] minimum score per column with query (def=-20.0)
Input alignment format:
-M a2m use A2M/A3M (default): upper case = Match; lower case = Insert; '-' = Delete; '.' = gaps aligned to inserts (may be omitted)
-M first
use FASTA: columns with residue in 1st sequence are match states
-M [0,100]
use FASTA: columns with fewer than X% gaps are match states
Other options:
-addss add predicted secondary structure information from PSIPRED
Example: hhconsensus -i stdin -s stdout
hhconsensus 2.0.15 June 2012 HHCONSENSUS(1)