Hi guys,
Please guide me if you have a solution to this problem. I have tried paste -s but it's not giving the desired output.
I have a file with the following content-
A123 box1
B345 bat2
C431 my_id
A123 service
C431 box1
A123 my_id
I need two different outputs-
OUTPUT1
A123... (6 Replies)
Hi,
I need to join two files based on first column of both files.If first column of first file matches with the first column of second file, then the lines should be merged together and go for next line to check. It is something like:
File one:
110001 abc efd
110002 fgh dfg
110003 ... (10 Replies)
Hi,
I have file1.txt and file2.txt and would like to create file3.txt based on one column in UNIX
Eg:
file1.txt
17328756,0000786623.pdf,0000786623
20115537,0000793892.pdf,0000793892
file2.txt
12521_74_4.zip,0000786623.pdf
12521_15_5.zip,0000793892.pdf
Desired Output
... (5 Replies)
Hi ,
I have few files which contains user name and data transfer rate in MBs and this data is collected for year and for each month report is saved in 12 different files I have to merge all the files to prepare the final report
Files are as below
Similarly I have 10 more files ... (5 Replies)
Hi Friends,
I have a file
file1.txt
1|ABC|3|jul|dhj
2|NHU|4|kil|eu
3|hjd|34|hfd|43
file2.txt
1||3|KING|dhj
2|NHU||k|
3|hjd|34|hd|43
i want to merge file1.txt file2.txt based on the column null values in file2.txif there are any nulls in column values , (5 Replies)
Hi,
Please excuse me , i have searched unix forum, i am unable to find what i expect ,
my query is , i have 2 files of same structure and having 1 similar field/column , i need to merge 2 tables/files based on the one matched field/column (that is field 1),
file 1:... (5 Replies)
Discussion started by: karthikram
5 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)