Hi,
i want to append a character '|' at end of each line of a file abc.txt.
for example if the file abc.txt conatins:
a|b|c
1|2|33
w|2|11
i want result file xyz.txt
a|b|c|
1|2|33|
w|2|11|
I know this is simple but sumhow i am not able to reach end of line.
its urgent, thanks for... (4 Replies)
I have a comma delimited text file and need to appened ",000000" to the end of every line. For example:
Before:
"D700000","2006" ,"5000","Open Year" ,"Conversion" ,"Wk64","Productive Payroll $" ,1103.45
After:
"D700000","2006" ,"5000","Open Year" ,"Conversion" ,"Wk64","Productive Payroll... (3 Replies)
Hi,
I have a command "get_data" with some parameters in few *.text files of a directory. I want to first find those files that contain this command and then append the following parameter to the end of the command.
example of an entry in the file :-
get_data -x -m50 /etc/web/getid
this... (1 Reply)
Hi, guys. I have one question:
I have a file called "group", the contents of it is below:
********************************
...
test:x:203:
sales:x:204:
repair:x:205:
research:x:206:brownj
...
***********
Now I want to add string ",sherrys" at the end of "research:x:206:brownj", so... (5 Replies)
Hello all,
I have a stumper of a problem. I am trying to append a ^M or "newline" to the end of each 129 character string in a huge file in unix.
Each string starts with A00.
I am trying to get the file to go from...
A00vswjdv1 Test Junk Junk A00vswjdv2 Test Junk Junk ... (6 Replies)
Hi Friends, I have a file with many lines as shown below.
/START SAMPLE LINE/
M:\mmarimut_v6.4.0_pit_01\java\build.xml@@\main\v6.4.0_pit_a
M:\mmarimut_v6.4.0_pit_01\port\Post.java@@\main\v6.4.0_pit_a
M:\mmarimut_v6.4.0_pit_01\switchview\View.java@@\main\v6.4.0_pit_a
/END SAMPLE LINE/
I... (1 Reply)
Hi friends,
I have a file containing many lines as follows.
M:\mmarimut_v6.4.0_pit_01\java\build.xml@@\main\v6.4.0_pit_a
M:\mmarimut_v6.4.0_pit_01\ADBasicView.java@@\main\v6.4.0_pit_a
I would like to append the string "\0" at the end of each line in the file. The output should look... (10 Replies)
Hi,
I have a File, which have multiple rows.
Like below
123456 Test1 FNAME JRW#$% PB MO Approver XXXXXX. YYYY
123457 Test2 FNAME JRW#$% PB MO Super XXXXXX. YYYY
123458 Test3 FNAME JRW#$% PB MO Approver XXXXXX. YYYY
I want to search a line which contains PB MO Approver and append... (2 Replies)
Platform: Solaris 10
I have a file like below
$ cat languages.txt
Spanish
Norwegian
English
Persian
German
Portugese
Chinese
Korean
Hindi
Malayalam
Bengali
Italian
Greek
Arabic
I want to append the string " is a great language" at end of each line in this file. (3 Replies)
hi,
i need a help in the script , need to append a string at the end of each line of a files , and append the files into a single file vertically.
eg
file1 has the following columns
abc,def,aaa
aaa,aa,aaa
files 2 has the following rows and columns
abc,def,aaa
aaa,aa,aaa
i... (3 Replies)
Discussion started by: senkerth
3 Replies
LEARN ABOUT DEBIAN
psi-cd-hit-2d-g1
PSI-CD-HIT-2D-G1.PL(1) User Commands PSI-CD-HIT-2D-G1.PL(1)NAME
psi-cd-hit-2d-g1.pl - runs similar algorithm like CD-HIT but using BLAST to calculate similarities in db1 or db2 format
DESCRIPTION
Usage psi-cd-hit-2d [Options]
Options
-i in_dbname, required
-o out_dbname, required
-c clustering threshold (sequence identity), default 0.3
-ce clustering threshold (blast expect), default -1,
it means by default it doesn't use expect threshold, but with positive value, the program cluster seqs if similarities meet either
identity threshold or expect threshold
-L coverage of shorter sequence ( aligned / full), default 0.0
-M coverage of longer sequence ( aligned / full), default 0.0
-R (1/0) use psi-blast profile? default 0 perform psi-blast / pdb-blast type search
-G (1/0) use global identity? default 1 sequence identity calculated as
total identical residues of local alignments / length of shorter seq
if you prefer to use -G 0, it is suggested that you also use -L, such as -L 0.8, to prevent very short matches.
-d length of description line in the .clstr file, default 30 if set to 0, it takes the fasta defline and stops at first space
-l length_of_throw_away_sequences, default 10
-p profile search para, default
"-a 2 -d nr80 -j 3 -F F -e 0.001 -b 500 -v 500"
-bfdb profile database, default nr80
-s blast search para, default
"-F F -e 0.000001 -b 100000 -v 100000"
-be blast expect cutoff, default 0.000001
-b filename of list of hosts to run this program in parallel with ssh calls, you need provide a list of hosts
-pbs No of jobs to send each time by PBS querying system
you can not use both ssh and pbs at same time
-k (1/0) keep blast raw output file, default 1
-rs steps of save restart file and clustering output, default 5000
everytime after process 5000 sequences, program write a restart file and current clustering information
-restart restart file, readin a restart file
if program crash, stoped, termitated, you can restart it by add a option "-restart sth.restart"
-rf steps of re format blast database, default 200,000
if program clustered 200,000 seqs, it remove them from seq pool, and re format blast db to save time
-local dir of local blast db,
when run in parallel with ssh (not pbs), I can copy blast dbs to local drives on each node to save blast db reading time BUT, IT MAY
NOT FASTER
-J job, job_file, exe specific jobs like parse blast outonly DON'T use it, it is only used by this program itself
-single files of ids those you known that they are singletons
so I won't run them as queries
-i2 second input database
-blastn run blastn, default 0
-lo how long can seq in db2 > db1 in a cluster, default 0
means, that seq in db2 should <= seqs in db1 in a cluster
============================== by Weizhong Li, liwz@sdsc.edu ==============================
If you find cd-hit useful, please kindly cite:
"Clustering of highly homologous sequences to reduce thesize of large protein database", Weizhong Li, Lukasz Jaroszewski & Adam
GodzikBioinformatics, (2001) 17:282-283 "Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide
sequences", Weizhong Li & Adam Godzik Bioinformatics, (2006) 22:1658-1659
psi-cd-hit-2d-g1.pl 4.6-2012-04-25 April 2012 PSI-CD-HIT-2D-G1.PL(1)