Select distinct sequences from fasta file and list
Hi
How can I extract sequences from a fasta file with respect a certain criteria? The beginning of my file (containing in total more than 1000 sequences) looks like this:
I want to extract the sequences containing the motif FDCIR? Can it be done with grep? Or do I need a pearl script?
In a next step: How could I even extract sequences with respect to fullfilling two or more criteria?
Looking forward getting your suggestions.
Cheers, Marion.
Last edited by jim mcnamara; 09-24-2014 at 04:55 PM..
Hi, buddies out there.
I have a text file ( only one column ) which I created using vi editor. The file contains duplicate rows and I would like to select distinct rows, how to go on it using unix command:
file content =
apple
apple
orange
watermelon
apple
orange
Can it be done... (7 Replies)
Hi ,
I have a similar problem.
Please can anyone help me with a shell script or a perl.
I have a flat file like this
fruit country
apple germany
apple india
banana pakistan
banana saudi
mango india
I want to get a output like
fruit country
apple ... (7 Replies)
Hi, I have the following file:
LOG:015608::ERR:2310:map_spsrec:Invalid parameter
LOG:015608::ERR:2471:map_dgdrec:Invalid parameter
LOG:015608::ERR:2487:map_nnmrec:Invalid number
LOG:015608::ERR:2310:map_nmrec:Invalid number
LOG:015608::ERR:2438:map_nmrec:Invalid number
As a delimiter I... (2 Replies)
Hi,
I am having a file of dna sequences in fasta format which look like this:
>admin_1_45
atatagcaga
>admin_1_46
atatagcagaatatatat
with many such thousands of sequences in a single file. I want to the replace the accession Id "admin_1_45" similarly in following sequences to... (5 Replies)
I have two files. File1 is shown below.
>153L:B|PDBID|CHAIN|SEQUENCE
RTDCYGNVNRIDTTGASCKTAKPEGLSYCGVSASKKIAERDLQAMDRYKTIIKKVGEKLCVEPAVIAGIISRESHAGKVL
KNGWGDRGNGFGLMQVDKRSHKPQGTWNGEVHITQGTTILINFIKTIQKKFPSWTKDQQLKGGISAYNAGAGNVRSYARM
DIGTTHDDYANDVVARAQYYKQHGY
>16VP:A|PDBID|CHAIN|SEQUENCE... (7 Replies)
I have a fasta file as follows
>sp|O15090|FABP4_HUMAN Fatty acid-binding protein, adipocyte OS=Homo sapiens GN=FABP4 PE=1 SV=3
MCDAFVGTWKLVSSENFDDYMKEVGVGFATRKVAGMAKPNMIISVNGDVITIKSESTFKN
TEISFILGQEFDEVTADDRKVKSTITLDGGVLVHVQKWDGKSTTIKRKREDDKLVVECVM
KGVTSTRVYERA
>sp|L18484|AP2A2_RAT AP-2... (3 Replies)
Hi,
I have a fasta file with multiple sequences. How can i get only unique sequences from the file.
For example
my_file.fasta
>seq1
TCTCAAAGAAAGCTGTGCTGCATACTGTACAAAACTTTGTCTGGAGAGATGGAGAATCTCATTGACTTTACAGGTGTGGACGGTCTTCAGAGATGGCTCAAGCTAACATTCCCTGACACACCTATAGGGAAAGAGCTAAC
>seq2... (3 Replies)
I could calculate the length of entire fasta sequences by following command,
awk '/^>/{if (l!="") print l; print; l=0; next}{l+=length($0)}END{print l}' unique.fasta
But, I need to calculate the length of a particular fasta sequence specified/listed in another txt file. The results to to be... (14 Replies)
I have a fasta file as follows
>sp|Q8WWQ8|STAB2_HUMAN Stabilin-2 OS=Homo sapiens OX=9606 GN=STAB2 PE=1 SV=3
MMLQHLVIFCLGLVVQNFCSPAETTGQARRCDRKSLLTIRTECRSCALNLGVKCPDGYTM
ITSGSVGVRDCRYTFEVRTYSLSLPGCRHICRKDYLQPRCCPGRWGPDCIECPGGAGSPC
NGRGSCAEGMEGNGTCSCQEGFGGTACETCADDNLFGPSCSSVCNCVHGVCNSGLDGDGT... (3 Replies)
Hi,
I have to add 7 bases of specific nucleotide at the beginning and ending of all the fasta sequences of a file. For example, I have a multi fasta file namely test.fasta as given below
test.fasta
>TalAA18_Xoo_CIAT_NZ_CP033194.1:_2936369-2939570:+1... (1 Reply)
Discussion started by: dineshkumarsrk
1 Replies
LEARN ABOUT NETBSD
ras
RAS(9) BSD Kernel Developer's Manual RAS(9)NAME
ras_lookup, ras_fork, ras_purgeall -- restartable atomic sequences
SYNOPSIS
#include <sys/types.h>
#include <sys/proc.h>
#include <sys/ras.h>
void *
ras_lookup(struct proc *p, void *addr);
int
ras_fork(struct proc *p1, struct proc *p2);
int
ras_purgeall(struct proc *p);
DESCRIPTION
Restartable atomic sequences are user code sequences which are guaranteed to execute without preemption. This property is assured by check-
ing the set of restartable atomic sequences registered for a process during cpu_switchto(9). If a process is found to have been preempted
during a restartable sequence, then its execution is rolled-back to the start of the sequence by resetting its program counter saved in its
process control block (PCB).
The RAS functionality is provided by a combination of the machine-independent routines discussed in this page and a machine-dependent compo-
nent in cpu_switchto(9). A port which supports restartable atomic sequences will define __HAVE_RAS in <machine/types.h> for machine-indepen-
dent code to conditionally provide RAS support.
A complicated side-effect of restartable atomic sequences is their interaction with the machine-dependent ptrace(2) support. Specifically,
single-step traps and/or the emulation of single-stepping must carefully consider the effect on restartable atomic sequences. A general
solution is to ignore these traps or disable them within restartable atomic sequences.
FUNCTIONS
The functions which operate on restartable atomic sequences are:
ras_lookup(p, addr)
This function searches the registered restartable atomic sequences for process p which contain the user address addr. If the
address addr is found within a RAS, then the restart address of the RAS is returned, otherwise -1 is returned.
ras_fork(p1, p2)
This function is used to copy all registered restartable atomic sequences for process p1 to process p2. It is primarily called from
fork1(9) when the sequences are inherited from the parent by the child.
ras_purgeall(p)
This function is used to remove all registered restartable atomic sequences for process p. It is primarily used to remove all reg-
istered restartable atomic sequences for a process during exec(3) and by rasctl(2).
CODE REFERENCES
The RAS framework itself is implemented within the file sys/kern/kern_ras.c. Data structures and function prototypes for the framework are
located in <sys/ras.h>. Machine-dependent portions are implemented within cpu_switchto(9) in the machine-dependent file
sys/arch/<arch>/<arch>/locore.S.
SEE ALSO rasctl(2), cpu_switchto(9), fork1(9)
Gregory McGarry, "An Implementation of User-level Restartable Atomic Sequences on the NetBSD Operating System", Proceedings of the FREENIX
Track: 2003 USENIX Annual Technical Conference, USENIX Association,
http://www.usenix.org/publications/library/proceedings/usenix03/tech/freenix03/full_papers/mcgarry/mcgarry.pdf, 311-322, June 9-14, 2003.
HISTORY
The RAS functionality first appeared in NetBSD 2.0.
BSD April 17, 2010 BSD