Hi there,
I'm wanting to produce a shell script that will check through some file names and identify a skip in sequence (four digit seq num in file name).
I have played on the idea of havng a file that has a sorted list of file names which I can read line at a time and cut out the sequence... (1 Reply)
Hello,
I might require some help here.
I have a file, ITEMS with the below data :
A1 20 A2 A3
B1 40 B2 B3
C1 70 C2 C3
D1 90 D2 D3
I need the output as :
A2 A3 20
B2 B3 40
C2 C3 70
D2 D3 90
i.e, I need the sequence of columns to be changed and only 3 fields to be... (5 Replies)
I have a txt file as database. when i run my program what it does is it ask me for 3 name and stored in the file as
name1:name2:name3:1
when u enter 3 name it add those in file as above format and add 1 at the end. I what i want is if i enter same names again it changes that 1 to 2 and so... (3 Replies)
Hi,
I have a string like:
DBMS stats (Number Used | Percentage of total): 10 | 1.00%
I have a sed command to extract numbers from this string:
sed "s///g;s/^$/-1/;"
Output: 10100
However what I want the sed command to return is only the first number(regardless of its size) i.e.... (3 Replies)
Dear Perl users,
I need your help to solve my problem below.
I want to print the sequence number without missing number within the range.
E.g. my sequence number :
1 2 3 4 5 6 7 8 11 12 13 14
my desired output:
1 -8 , 11-14
my code below but still problem with the result:
1 - 14
1 -... (2 Replies)
Am using unix aix KSH...
I have the files called
MMRR0106.DAT
MMRR0206.DAT
MMRR0406.DAT
MMRR0506.DAT
MMRR0806.DAT
....
...
MMRR3006.DAT
MMRR0207.DAT
These files are in one dircetory /venky ?
I want the output like this ?
Missing files are :
MMRR0306.DAT
MMRR0606.DAT... (7 Replies)
Hi all,
I have a file like this
ID 3BP5L_HUMAN Reviewed; 393 AA.
AC Q7L8J4; Q96FI5; Q9BQH8; Q9C0E3;
DT 05-FEB-2008, integrated into UniProtKB/Swiss-Prot.
DT 05-JUL-2004, sequence version 1.
DT 05-SEP-2012, entry version 71.
FT COILED 59 140 ... (1 Reply)
Hi All ,
I have a file which contains data(comma separated) in below format :
500,Sourav ,kolkata ,8745775020,700091
505,ram,delhi ,9875645874,600032
510 ,madhu ,mumbai ,5698756430 ,500042
515 ,ramesh ,blore ,8769045601 ,400092
I want to add unique sequence number at the start of each... (7 Replies)
Hi,
Need to add sequnce number to one of the csv file and please find below
actual requirement.
Input file
ABC,500
XXQ,700
ADF,400,
ART,200
Out put file should be
1,ABC,500
2,XXQ,700
3,ADF,400,
4,ART,200 (3 Replies)
Discussion started by: siva83
3 Replies
LEARN ABOUT DEBIAN
bp_sreformat
BP_SREFORMAT(1p) User Contributed Perl Documentation BP_SREFORMAT(1p)NAME
bpsreformat - convert sequence formats
DESCRIPTION
This script uses the SeqIO system that allows conversion of sequence formats either sequence data or multiple sequence alignment data. The
name comes from the fact that Sean Eddy's program sreformat (part of the HMMER pkg) already does this. Sean's program tries to guess the
input formats while in our code we currently require your to specify what the input and output formats are and if the data is from a
multiple sequence alignment or from straight sequence files.
Usage:
bpsreformat -if INFORMAT -of OUTFORMAT -i FILENAME -o output.FORMAT
-h/--help Print this help
-if/--informat Specify the input format
-of/--outformat Specify the output format
-i/--input Specify the input file name
(to pass in data on STDIN use minus sign as filename)
-o/--output Specify the output file name
(to pass data out on STDOUT use minus sign as filename)
--msa Specify this is multiple sequence alignment data
--special Will pass on special parameters to the AlignIO/SeqIO
object -- most of these are for Bio::AlignIO objects
Comma separated list of the following
nointerleaved -- for phylip,non-interleaved format
idlinebreak -- for phylip, makes it molphy format
percentages -- for clustalw, show % id per line
perl v5.14.2 2012-03-02 BP_SREFORMAT(1p)