Thank you for yor assistance, I finally get the code and and since I have various files on my directory. With a for loop It can work on all my directory. Here is the code :
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Regards
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Last edited by RudiC; 06-07-2018 at 11:49 AM..
Reason: Added CODE tags.
Hello
when I try to run rm on multiple files I have problem to delete files with space.
I have this command :
find . -name "*.cmd" | xargs \rm -f
it doing the work fine but when it comes across files with spaces like : "my foo file.cmd"
it refuse to delete it
why? (1 Reply)
I'm trying some thing like this. But not working
It worked for bash files
Now I want some thing like that along with multiple input files by redirecting their outputs as inputs of next command like below
Could you guyz p0lz help me on this
#!/usr/bin/awk -f
BEGIN
{
}
script1a.awk... (2 Replies)
Hi,
I need help to split lines from a file into multiple files.
my input look like this:
13
23 45 45 6 7
33 44 55 66 7
13
34 5 6 7 87
45 7 8 8 9
13
44 55 66 77 8
44 66 88 99 6
I want to split every 3 lines from this file to be written to individual files. (3 Replies)
Hi guys,
say I have a few files in a directory (58 text files or somthing)
each one contains mulitple strings that I wish to replace with other strings
so in these 58 files I'm looking for say the following strings:
JAM (replace with BUTTER)
BREAD (replace with CRACKER)
SCOOP (replace... (19 Replies)
Hi,
I'd like to process multiple files. For example:
file1.txt
file2.txt
file3.txt
Each file contains several lines of data. I want to extract a piece of data and output it to a new file.
file1.txt ----> newfile1.txt
file2.txt ----> newfile2.txt
file3.txt ----> newfile3.txt
Here is... (3 Replies)
hi,
I have a directory "test" under which there are 3 files a.txt,b.txt and c.txt.
I need to rename those files to a.pl,b.pl and c.pl respectively.
is it possible to achieve this in a sed or awk one liner?
i have searched but many of them are scripts.
I need to do this in a one liner.
I... (2 Replies)
Hi everyone,
I'm new to the forums, as you can probably tell... I'm also pretty new to scripting and writing any type of code.
I needed to know exactly how I can grep for multiple strings, in files located in one directory, but I need each string to output to a separate file.
So I'd... (19 Replies)
How can I run the following command on multiple files and print out the corresponding multiple files.
perl script.pl genome.gff 1.txt > 1.gff
However, there are multiples files of 1.txt, from 1----100.txt
Thank you so much.
No duplicate posting! Continue here. (0 Replies)
How can I Run one script on multiple files and print out multiple files.
FOR EXAMPLE
i want to run script.pl on 100 files named 1.txt ....100.txt under same directory and print out corresponding file 1.gff ....100.gff.THANKS (4 Replies)
Dear folks
I have two data set which there names are "final.map" and "1.geno" and look like this structures:
final.map:
gi|358485511|ref|NC_006088.3| 2044
gi|358485511|ref|NC_006088.3| 2048
gi|358485511|ref|NC_006088.3| 2187
gi|358485511|ref|NC_006088.3| 17654
... (2 Replies)
Discussion started by: sajmar
2 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)