I am trying to setup to automatically import a series of mysql database files. I am doing manually now and its a royal pain.
All the sql files are sequentially numbered in a format of 4 numbers underscore text with spaces replaced by underscores.
example:
There are 3 databases each setup... (1 Reply)
Hello all
I have data like below where the column with values (PRI, SEC ) is the char field and the rest are Numeric Fields.
200707,9580,58,7,2,1,PRI,1,1,137,205594,0,5,10,-45.51,-45.51
200707,9580,58,7,2,1,SEC,1,1,137,205594,0,5,10,-45.51,45.51... (1 Reply)
HI everyone,
I am trying to use the unix sort command to get a list of numbers sorted in ascending order but having trouble in getting it to work.
An example of this issue would be when i am trying to sort the following three
number each on a different line "1" , "2" and "116" the sort command... (3 Replies)
Hi,
I am unable to sort data on the first field
$cat t
Jim,212121,Seattle
Bill,404404,Seattle
Steve,246810,Nevada
Scott,212277,LosAngeles
Jim,212121,Ohio
sort -t"," -k1,2 t
Bill,404404,Seattle
Jim,212121,Ohio
Jim,212121,Seattle
Scott,212277,LosAngeles
Steve,246810,Nevada (7 Replies)
dear all,
i have .dat files named as:
34.dat
2.dat
16.dat
107.dat
i would like to sort them by their filenames as:
2.dat
16.dat
34.dat
107.dat
i have tried numerous combinations of sort and ls command (in vain) to obtain :
107.dat
16.dat
2.dat
34.dat (1 Reply)
Hi
I am using this
cat substitutionFeats.txt | gawk '{$0=gensub(/\t/,"blabla",1);print}' | gawk '{print length, $0}' | sort -n | sort -r
and the "sort -n" command doesn't work as expected: it leads to a wrong ordering:
64 Adjustable cuffs
64 Abrasion-
64 Abrasion pas
647 Sanitized 647... (4 Replies)
I have ran into a heavy case of PEBCAK*) and could need some advice on what i do wrong:
OS is Linux (kernel 2.6.35), sort --version reports "8.5" from 2010, shell is ksh.
Originally i had a file with with the following structure:
hdisk1 yyy
hdisk2 yyy
hdisk3 yyy
hdisk4 yyy
hdisk5 yyy... (2 Replies)
From googling and reading man pages I figured out this sorts the first column by numeric values.
sort -g -k 1,1
Why does the -n option not work? The man pages were a bit confusing.
And what if I want to sort the second column numerically? I haven't been able to figure that out. The file... (7 Replies)
Discussion started by: cokedude
7 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)