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
hhmake
HHMAKE(1) User Commands HHMAKE(1)NAME
hhmake - build an HMM from an input alignment or convert between HMMER format and HHsearch format
SYNOPSIS
hhmake -i file [options]
DESCRIPTION
HHmake version 2.0.15 (June 2012) Build an HMM from an input alignment in A2M, A3M, or FASTA format, or convert between HMMER format (.hmm)
and HHsearch format (.hhm). 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). (C) Johannes Soeding, Michael Remmert, Andreas Biegert, Andreas Hauser
-i <file>
query alignment (A2M, A3M, or FASTA), or query HMM
Output options:
-o <file>
HMM file to be written to (default=<infile.hhm>)
-a <file>
HMM file to be appended to
-v <int>
verbose mode: 0:no screen output 1:only warings 2: verbose
-seq <int>
max. number of query/template sequences displayed (def=10) Beware of overflows! All these sequences are stored in memory.
-cons make consensus sequence master sequence of query MSA
-name <name>
use this name for HMM (default: use name of first sequence)
Filter query multiple sequence alignment
-id [0,100] maximum pairwise sequence identity (%) (def=90)
-diff [0,inf[
filter MSA by selecting most diverse set of sequences, keeping at least this many seqs in each MSA block of length 50 (def=100)
-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)
-neff [1,inf]
target diversity of alignment (default=off)
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
Pseudocount (pc) options:
-pcm 0-2 position dependence of pc admixture 'tau' (pc mode, default=0)
0: no pseudo counts:
tau = 0
1: constant
tau = a
2: diversity-dependent: tau = a/(1 + ((Neff[i]-1)/b)^c) (Neff[i]: number of effective seqs in local MSA around column i) 3: constant
diversity pseudocounts
-pca [0,1] overall pseudocount admixture (def=1.0)
-pcb [1,inf[ Neff threshold value for -pcm 2 (def=1.5)
-pcc [0,3] extinction exponent c for -pcm 2 (def=1.0)
-pre_pca [0,1]
PREFILTER pseudocount admixture (def=0.8)
-pre_pcb [1,inf[ PREFILTER threshold for Neff (def=1.8)
Context-specific pseudo-counts:
-nocontxt
use substitution-matrix instead of context-specific pseudocounts
-contxt <file> context file for computing context-specific pseudocounts (default=debian/tmp/usr/share/hhsuite/data/context_data.lib)
-cslib
<file> column state file for fast database prefiltering (default=debian/tmp/usr/share/hhsuite/data/cs219.lib)
Example: hhmake -i test.a3m
hhmake 2.0.15 June 2012 HHMAKE(1)