10-17-2009
hi
I am still getting a blank document. hmm
10 More Discussions You Might Find Interesting
1. Shell Programming and Scripting
It can't be that hard, but I just can't figure it out:
I have file like:
File Sub-brick M_1 S_1 M_2 S_2 M_4 S_4 ...
xxx 1 214 731 228 621 132 578 ...
and would like to get 0 0 where M_3 S_3 is missing
xxx 1 214 731 228 621 0 0 132 578 ...
I wrote following script, but can't figure out... (3 Replies)
Discussion started by: avvk
3 Replies
2. UNIX for Dummies Questions & Answers
I have a text file that looks like the following:
rs529715 CFD
rs1550758 CIDEB
Magmas
rs12542019 CPNE1
RBM12
rs10515181 CPNE1
RBM12
rs4411112 CPT1A
Some rows have 1 column, whereas some have 2. The ones that have 2 columns have one column (1st column) that start with rs.
I need to... (6 Replies)
Discussion started by: evelibertine
6 Replies
3. UNIX for Dummies Questions & Answers
Hi,
I have a file with fixed number of columns (total 58 columns) delimeted by pipe (|). Due to a bug in the application the export file does not come with fixed number of columns. The missing data columns are being replaced by blank in the output file. In one line I can have 25 columns (33... (1 Reply)
Discussion started by: yale_work
1 Replies
4. UNIX for Dummies Questions & Answers
I have a text file that looks like the following:
5.644 39.2% 0.00 0.50 rs1695626 4 -0.003 0.21% 0.03 0.73
rs1763326 3 -0.001 0.03% 0.00 0.89
5.645 39.2% 0.00 0.50 rs770721 2 -0.002 0.07% 0.01 0.84... (7 Replies)
Discussion started by: evelibertine
7 Replies
5. UNIX for Dummies Questions & Answers
Hello all,
I have a file which is tab separated like that:
PHE_205_A TIP_127_W ARG_150_B
MET_1150_A TIP_12_W VAL_11_B
GLU_60_A TIP_130_W ARG_143_B
LEU_1033_A TIP_203_W ARG_14_B
SER_1092_A TIP_203_W
THR_1090_A TIP_203_W
SER_1092_A TIP_25_W ... (6 Replies)
Discussion started by: TheTransporter
6 Replies
6. UNIX for Dummies Questions & Answers
I have a text file which includes empty columns with missing values. I want to fill the empty columns with the character "X". How do I go about doing that? Thanks! (1 Reply)
Discussion started by: evelibertine
1 Replies
7. UNIX for Dummies Questions & Answers
Hi,
I have to text files that I want to merge by the first column. The values in the first column pretty much match for the first part. However there are some values that are present in column 1 and not present in column 2 or vice versa. For such values I would like to substitute X for the... (9 Replies)
Discussion started by: evelibertine
9 Replies
8. UNIX for Dummies Questions & Answers
Hi,
I have a text file where some of the values in columns are missing:
Input:
QhFudW3dKSYL2NTQUA 1 11133999-11134048
uhIp9KxB6USIy16CEY 1 11126760-11126774
11126775-11126805
11128065-11128068
6epeZ6CTNW4Au8uXys 1 24480823-24480872
Tp3nvutucBZ13CjuXc 1 155204870-155204891... (3 Replies)
Discussion started by: evelibertine
3 Replies
9. Shell Programming and Scripting
I am learning AWK by trying out examples whenever I need a specific conversion. I would like to edit the 'before.txt' so that all the missing data points between 140-150 are added and shown as 0.
before.txt
145 2
148 13
149 17
to below,
140 0
141 0
142 0
143 0
144 0
145 2
146 0... (5 Replies)
Discussion started by: numareica
5 Replies
10. Shell Programming and Scripting
I am using awk to match columns and output based on those matches. For some reason it is not printing matching columns, am I missing something?
Operating system - windows with cygwin.
Command that I am using:
sed 's/]*,]*/,/g' $tempdir/file1 > $tempdir/file1.$$ && awk -F, 'FNR==NR{f2=$2... (7 Replies)
Discussion started by: dis0wned
7 Replies
LEARN ABOUT DEBIAN
hmmfetch
hmmfetch(1) HMMER Manual hmmfetch(1)
NAME
hmmfetch - retrieve profile HMM(s) from a file
SYNOPSIS
hmmfetch [options] <hmmfile> <key>
(retrieves HMM named <key>)
hmmfetch -f [options] <hmmfile> <keyfile>
(retrieves all HMMs listed in <keyfile>)
hmmfetch --index [options] <hmmfile>
(indexes <hmmfile> for fetching)
DESCRIPTION
Quickly retrieves one or more profile HMMs from an <hmmfile> (a large Pfam database, for example).
The <hmmfile> must be indexed first, using hmmfetch --index. The index is a binary file named <hmmfile>.ssi.
The default mode is to retrieve a single profile by name or accession, called the <key>. For example:
% hmmfetch Pfam-A.hmm Caudal_act
% hmmfetch Pfam-A.hmm PF00045
With the -f option, a <keyfile> containing a list of one or more keys is read instead. The first whitespace-delimited field on each non-
blank non-comment line of the <keyfile> is used as a <key>, and any remaining data on the line is ignored; this allows a variety of white-
space delimited datafiles to be used as <keyfile>s. The <keyfile> argument can be a '-' (dash) character, in which case the keyfile is
read from standard input; this allows unix ninjas to construct sophisticated invocations using pipes.
By default, the HMM is printed to standard output in HMMER3 format.
OPTIONS
-h Help; print a brief reminder of command line usage and all available options.
-f The second commandline argument is a <keyfile> instead of a single <key>. The first field on each line of the <keyfile> is used as
a retrieval <key> (an HMM name or accession). Blank lines and comment lines (that start with a # character) are ignored.
-o <f> Output HMM(s) to file <f> instead of to standard output.
-O Output HMM(s) to individual file(s) named <key> instead of standard output. With the -f option, this can result in many files being
created.
--index
Instead of retrieving one or more profiles from <hmmfile>, index the <hmmfile> for future retrievals. This creates a <hmmfile>.ssi
binary index 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@ hmmfetch(1)