I have a big file with blast results (if you know what this means, otherwise look at it just as a text file with a specific form).
I am trying to extract some ids from within this file, which have certain parameters.
For example, some Of my IDs have the term 'No hit results' connected to them.
This is what I am trying to extract.
this is how it looks loike:
In the complete file I have 15517 'Query=' and for 389 of them I can also find 'No hits found'.
My Qeustion is how can I found out which Queries are connected to this 'No hits'.
I tried it with :
But this doesn't work.
I just don't understand how to grep in many files and than pipe it to a second grep option.
Hi,
I did not understand why the following did not work out as I expected:
find . -name "pqp.txt" | grep -v "Permission"
I thought I would be able to catch whichever paths containing my pqp.txt file without receiving the display of messages such as "find: cannot access... Permisson... (1 Reply)
Howdy folks,
I am fairly new to scripting but have lost of expirience in c++, pascal, and a few other. I am trying to complete a file search script that is sent a file name containing data to search that is arranged like this
"id","name","rating"
"1","bob","7"
etc
and an argument to... (1 Reply)
Hi all.
I have a problem at work which I have managed to break down into a simple test scenario:
I have written a monitoring script that outputs every second the status of various processes, but for now, lets just print the date
input.sh:
while true
do
date
sleep 1
done
This... (9 Replies)
Hi,
I need to use a double grep so to speak. I need to grep for a particular item say BOB and then for each successful result I need to grep for another item say SMITH.
I tried grep "BOB" filename | grep "SMITH"
but it does not seem to work.
I can achieve my desired result using an... (12 Replies)
$>cat file.txt
123 d3
234 abc 3
zyf 23
124 def 8
ghi kz0
...
...
I have the following output on the screen through <some command>.
$> <some command>
abc
def
ghi
...
...
I have to search for each of these patterns in the file.txt and print the lines in file.txt matching the... (4 Replies)
Hi everybody,
I have a big file with blast results (if you know what this means, otherwise look at it just as a text file with a specific form).
I am trying to extract some ids from within this file, which have certain parameters.
For example, some Of my IDs have the term 'No hit results'... (6 Replies)
I am trying to extract the file names alone, for example "TVLI_STATS_NRT_XLSTWS03_20120215_132629.csv", from below output
which was given by the grep.
sam:/data/log: grep "C10_Subscribe.000|subscribe|newfile|" PDEWG511_TVLI_JOB_STATS.ksh.201202*
Output:
... (6 Replies)
Hi,
I have a number of files containing the information below.
"""""
Fundallinfo
6.3950 14.9715 14.0482
"""""
I would like to grep for Fundallinfo and use it to read the next line? I ideally would like to read the three numbers that follow in the next line and... (2 Replies)
So, this is weird... I'm running this command:
iotop -o -P -k -bt -d 5
I'd like to save the output relelvant to rsyslogd to a file, so I do this:
iotop -o -P -k -bt -d 5 | grep rsyslogd >> /var/log/rsyslogd
Nothing is written to the file! I can write the full output to the file:
... (2 Replies)
cat file
1 aaa
2 bbb
3 ccc
4 ddd
In TextEdit, I then copy the characters “ccc” to the clipboard. The problem is that the following command gives no output:
bash-3.2$ pbpaste | grep - file
Desired output:
3 ccc
What should the syntax be for that command? I am using MacOS El... (3 Replies)
Discussion started by: palex
3 Replies
LEARN ABOUT DEBIAN
mclindex
mclindex(7) MISCELLANEOUS mclindex(7)
NAME
mclindex - a list of the utilities and modules present in the MCL distribution.
For more information, consult mclfamily(7).
Generic stuff
mcl(1)
the mcl manual page
mclfaq(7)
the mcl FAQ
mcxio(5)
the mcl matrix format specification
mclpipeline(1)
generic pipeline (parsing/matrix creation/clustering/display)
mcx(1)
interface to basic matrix operations
mcxassemble(1)
prepare input matrix from cooccurrence scores
mcxdump(1)
dump matrices, optionally map indices to labels
mcxarray(1)
transform array data to MCL matrices
mcxconvert(1)
convert between ascii/binary storage types
Dealing with clustering results
clmformat(1)
display clusterings in browsable format
clmdist(1)
compute distances between clusterings
clminfo(1)
performance measures for clusterings
clmmeet(1)
compute intersection of clusterings
clmmate(1)
compute best matches between two clusterings
clmimac(1)
Interpret Matrices (c.q. MCL iterands) As Clusterings
clmresidue(1)
extend subgraph clusterings onto encompassing graph
clmorder(1)
reorder indices to represent blocks from different clusterings
clmclose(1)
fetch connected components from graphs or subgraphs
Dealing with matrices
mcxio(5)
the mcl matrix format specification
mcx(1)
interface to basic matrix operations
mcxsubs(1)
extract submatrices by specifiying sets of nodes and clusters
mcxmap(1)
remap matrix indices / relabel graph nodes
mcxassemble(1)
prepare input matrix from cooccurrence scores
Application specific parsers and wrappers
BLAST package - Documentation only available if installed with --enable-blast
__________________
mclblastline(1)
pipeline for clustering from blast files
mcxdeblast(1)
prepare input from blast files
mclindex 12-068 8 Mar 2012 mclindex(7)