Hi Xterra,
Maybe something like:
which produces the output:
I'm sure you could write this as a 1-liner, but I much prefer something I can see on a screen (and debug).
If there's anything here you can't figure out, ask questions about what you don't understand.
Hope this helps,
Don
These 2 Users Gave Thanks to Don Cragun For This Post:
Hi all,
if for example I had a variable containing the string 'hello', is the any way I can output, for example, the e and the 2nd l based on their position in the string not their character (in this case 2 and 4)?
any general pointers in the right direction will be much appreciated, at... (3 Replies)
Hi Please help me to refine my syntax. I want to delete the excess characters from the out put below.
-bash-3.00$ top -b -n2 -d 00.20 |grep Cpu|tail -1 | awk -F ":" '{ print $2 }' | cut -d, -f1
4.4% us
now i want to delete the % and us. How wil i do that to make it just 4.4.
Thanks (7 Replies)
Hi,
I've a csv file seperated by '|' from which I'm trying to remove the excess '|' characters more than the existing fields. My CSV looks like as below.
HRLOAD|Service|AddChange|EN
PERSONID|STATUS|LASTNAME|FIRSTNAME|ITDCLIENTUSERID|ADDRESSLINE1
10000001|ACTIVE|Testazar1|Testore1|20041|||... (24 Replies)
sed -e "s// /g" old.txt > new.txt
While I do know some control characters need to be escaped, can normal characters also be escaped and still work the same way? Basically I do not know all control characters that have a special meaning, for example, ?, ., % have a meaning and have to be escaped... (11 Replies)
helloo
I wonder if there's a way to cut characters out of a string and keep only
the last 2 by using sed.
For example if there's the todays' date:
2012-05-06
and we only want to keep the last 2 characters which are the day.
Is there a quick way to do it with sed? (2 Replies)
Hey guys,
I know that title is a mouthful - I'll try to better explain my struggles a little better...
What I'm trying to do is:
1. Query a db and output to a file, a list of column data.
2. Then, for each line in this file, repeat these values but wrap them with:
ITEM{
... (3 Replies)
Hi,
I have a xml file (Config.xml)
<Header name="" TDate="" PDate="">
<Config>
{"config" { "Nation" "Pri:|Sec:"}}
</Config>
</Header>
Now I wanted to printed all the strings between "". I tried the following
cat Config.xml | sed -n 's/.*\.*//p'
... (8 Replies)
Hi,
I hope you can help me out please?
I need to replace from character 8-16 with AAAAAAAA and the rest should stay the same after character 16
gtwrhtrd11111111rjytwyejtyjejetjyetgeaEHT
wrehrhw22222222hytekutkyukrylryilruilrGEQTH
hrwjyety33333333gtrhwrjrgkreglqeriugn;RUGNEURGU
... (4 Replies)
I have a file that looks like this:
>ID 1
AATAATTCCGGATCGTGC
>ID 2
TTTGACAGTAGAC
>ID 3
AGACGATGACGAT
I am using the following script to report if AATTCCGGATCG is present in any sequence:
awk 'FNR==1{n=substr(FILENAME,1,index(FILENAME,".")-1)} { print n "\t"... (10 Replies)
Discussion started by: Xterra
10 Replies
LEARN ABOUT DEBIAN
tigr-long-orfs
LONG-ORFS(1) General Commands Manual LONG-ORFS(1)NAME
long-orfs -- Find/Score potential genes in genome-file using the probability model in icm-file
SYNOPSIS
tigr-long-orgs [genome-file options]
DESCRIPTION
Program long-orfs takes a sequence file (in FASTA format) and outputs a list of all long "potential genes" in it that do not overlap by too
much. By "potential gene" I mean the portion of an orf from the first start codon to the stop codon at the end.
The first few lines of output specify the settings of various parameters in the program:
Minimum gene length is the length of the smallest fragment considered to be a gene. The length is measured from the first base of the
start codon to the last base *before* the stop codon. This value can be specified when running the program with the -g option. By
default, the program now (April 2003) will compute an optimal length for this parameter, where "optimal" is the value that produces the
greatest number of long ORFs, thereby increasing the amount of data used for training.
Minimum overlap length is a lower bound on the number of bases overlap between 2 genes that is considered a problem. Overlaps shorter than
this are ignored.
Minimum overlap percent is another lower bound on the number of bases overlap that is considered a problem. Overlaps shorter than this
percentage of *both* genes are ignored.
The next portion of the output is a list of potential genes:
Column 1 is an ID number for reference purposes. It is assigned sequentially starting with 1 to all long potential genes. If overlap-
ping genes are eliminated, gaps in the numbers will occur. The ID prefix is specified in the constant ID_PREFIX .
Column 2 is the position of the first base of the first start codon in the orf. Currently I use atg, and gtg as start codons. This is
easily changed in the function Is_Start () .
Column 3 is the position of the last base *before* the stop codon. Stop codons are taa, tag, and tga. Note that for orfs in the reverse
reading frames have their start position higher than the end position. The order in which orfs are listed is in increasing order by Max
{OrfStart, End}, i.e., the highest numbered position in the orf, except for orfs that "wrap around" the end of the sequence.
When two genes with ID numbers overlap by at least a sufficient amount (as determined by Min_Olap and Min_Olap_Percent ), they are elimi-
nated and do not appear in the output.
The final output of the program (sent to the standard error file so it does not show up when output is redirected to a file) is the length
of the longest orf found.
Specifying Different Start and Stop Codons:
To specify different sets of start and stop codons, modify the file gene.h . Specifically, the functions:
Is_Forward_Start Is_Reverse_Start Is_Start Is_Forward_Stop Is_Reverse_Stop Is_Stop
are used to determine what is used for start and stop codons.
Is_Start and Is_Stop do simple string comparisons to specify which patterns are used. To add a new pattern, just add the comparison for
it. To remove a pattern, comment out or delete the comparison for it.
The other four functions use a bit comparison to determine start and stop patterns. They represent a codon as a 12-bit pattern, with 4
bits for each base, one bit for each possible value of the bases, T, G, C or A. Thus the bit pattern 0010 0101 1100 represents the base
pattern [C] [A or G] [G or T]. By doing bit operations (& | ~) and comparisons, more complicated patterns involving ambiguous reads can
be tested efficiently. Simple patterns can be tested as in the current code.
For example, to insert an additional start codon of CAT requires 3 changes: 1. The line || (Codon & 0x218) == Codon should be inserted into
Is_Forward_Start , since 0x218 = 0010 0001 1000 represents CAT. 2. The line || (Codon & 0x184) == Codon should be inserted into
Is_Reverse_Start , since 0x184 = 0001 1000 0100 represents ATG, which is the reverse-complement of CAT. Alternately, the #define constant
ATG_MASK could be used. 3. The line || strncmp (S, "cat", 3) == 0 should be inserted into Is_Start .
OPTIONS -g n Set minimum gene length to n. Default is to compute an optimal value automatically. Don't change this unless you know what
you're doing.
-l Regard the genome as linear (not circular), i.e., do not allow genes to "wrap around" the end of the genome. This option works
on both glimmer and long-orfs . The default behavior is to regard the genome as circular.
-o n Set maximum overlap length to n. Overlaps shorter than this are permitted. (Default is 0 bp.)
-p n Set maximum overlap percentage to n%. Overlaps shorter than this percentage of *both* strings are ignored. (Default is 10%.)
SEE ALSO
tigr-glimmer3 (1), tigr-adjust (1), tigr-anomaly (1), tigr-build-icm (1), tigr-check (1), tigr-codon-usage (1), tigr-compare-lists (1),
tigr-extract (1), tigr-generate (1), tigr-get-len (1), tigr-get-putative (1),
http://www.tigr.org/software/glimmer/
Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer3.
AUTHOR
This manual page was quickly copied from the glimmer web site by Steffen Moeller moeller@debian.org for the Debian system.
LONG-ORFS(1)