12-29-2011
Just i want trim the space specific columns,it not necessary to check the 4 th column is there or not.
Just trim....
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Hello Friends,
Can any one help me with this issue:
I would like to format a file:
say if I have rows like:
4512 , SMITH , I-28984 ,, 4324 , 4343
42312 , SMITH , I-2EE8984 ,, 432E4E4 , 4343
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I have a file with only one field something like this :
213.45
220.65
240.47
345.67
320.45
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Hi,
I want to trim the spaces on left side of the variable value. For eg: if it is 4 spaces followed by value, All the spaces on the left should be supressed.
Easy but want it quickly.
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Hi,
I have a requirement to remove certain spaces from a table of information, but I'm unsure where to start.
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Hi All
I've a file which is similar to the one given below
column1 coulmn2 column3 column4
A B C D
X Y
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A|B|C|D
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F||G|H
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Hi guru's,
I am trying to write a script to generate a csv file by connecting to database run a query and put the values into csv file.
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Please help.
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Hi,
I'm using awk to print columns from a tab delimited text file:
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How can I tell awk to print the whole column content as column 6?
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LEARN ABOUT DEBIAN
hmmalign
hmmalign(1) HMMER Manual hmmalign(1)
NAME
hmmalign - align sequences to a profile HMM
SYNOPSIS
hmmalign [options] <hmmfile> <seqfile>
DESCRIPTION
Perform a multiple sequence alignment of all the sequences in seqfile, by aligning them individually to the profile HMM in hmmfile.
The new alignment is output to stdout in Stockholm format.
The sequences in seqfile are aligned in unihit local alignment mode. Therefore they should already be known to contain a single domain;
they should not contain more than one domain. They may be fragments. The optimal alignment may assign some residues as nonhomologous (N
and C states), in which case these residues are still included in the resulting alignment, but shoved to the outer edges. To trim these
nonhomologous residues from the result, see the --trim option.
OPTIONS
-h Help; print a brief reminder of command line usage and all available options.
-o <f> Direct the output alignment to file <f>, rather than to stdout.
--allcol
Include columns in the output alignment for every match (consensus) state in the hmmfile, even if it means having all-gap columns.
This is useful in analysis pipelines that need to be able to maintain a predetermined profile HMM architecture (with an unchanging
number of consensus columns) through an hmmalign step.
--mapali <f>
Merge the existing alignment in file <f> into the result, where <f> is exactly the same alignment that was used to build the model
in hmmfile. This is done using a map of alignment columns to consensus profile positions that is stored in the hmmfile. The multi-
ple alignment in <f> will be exactly reproduced in its consensus columns (as defined by the profile), but the displayed alignment in
insert columns may be altered, because insertions relative to a profile are considered by convention to be unaligned data.
--trim Trim nonhomologous residues (assigned to N and C states in the optimal alignments) from the resulting multiple alignment output.
--amino
Specify that all sequences in seqfile are proteins. By default, alphabet type is autodetected from looking at the residue composi-
tion.
--dna Specify that all sequences in seqfile are DNAs.
--rna Specify that all sequences in seqfile are RNAs.
--informat <s>
Declare that the input seqfile is in format <s>. Accepted sequence file formats include FASTA, EMBL, Genbank, DDBJ, Uniprot, Stock-
holm, and SELEX. Default is to autodetect the format of the file.
--outformat <s>
Specify that the msafile is in format <s>. Currently the accepted multiple alignment sequence file formats only include Stockholm
and SELEX. Default is to autodetect the format of the file.
SEE ALSO
See hmmer(1) for a master man page with a list of all the individual man pages for programs in the HMMER package.
For complete documentation, see the user guide that came with your HMMER distribution (Userguide.pdf); or see the HMMER web page
(@HMMER_URL@).
COPYRIGHT
@HMMER_COPYRIGHT@
@HMMER_LICENSE@
For additional information on copyright and licensing, see the file called COPYRIGHT in your HMMER source distribution, or see the HMMER
web page (@HMMER_URL@).
AUTHOR
Eddy/Rivas Laboratory
Janelia Farm Research Campus
19700 Helix Drive
Ashburn VA 20147 USA
http://eddylab.org
HMMER
@HMMER_VERSION@ @HMMER_DATE@ hmmalign(1)