10 More Discussions You Might Find Interesting
1. Programming
Hi All,
I would like get the minimum value in the certain column with respect to other column.
For example, I have a text file like this.
ATOM 1 QSS SPH S 0 -2.790 -1.180 -2.282 2.28 2.28
ATOM 1 QSS SPH S 1 -2.915 -1.024 -2.032 2.31 2.31
ATOM 1 ... (4 Replies)
Discussion started by: bala06
4 Replies
2. Shell Programming and Scripting
Need your support for below. Please help to get required output
If column 5 is INV then only consider column1 and take out duplicates/identical rows/values from column1 and then put minimum value of column6 in column7 and put maximum value in column 8 and then need to do subtract values of... (7 Replies)
Discussion started by: as7951
7 Replies
3. Shell Programming and Scripting
Hello,
I need to find out the minimum and maximum values based on specific column, and then print out the entire row with the max value.
Infile.txt:
scf6 290173 290416 . + X_047241 T_00113118-1
scf6 290491 290957 . + X_047241 T_00113118-2
scf6 290898 290957 . + X_047241 T_00113119-3
scf6... (2 Replies)
Discussion started by: yifangt
2 Replies
4. Shell Programming and Scripting
input
1 2 3 4 5 2 8
2 1 1 1 4 2 1
5 4 4 4 2 1 3
2 2 6 7 4 5 4
5 5 5 4 3 3 5
I woud like to print a min of each row such that my output would look like
1
1
1
2
3 (5 Replies)
Discussion started by: johnkim0806
5 Replies
5. Shell Programming and Scripting
Hi Friends,
I have an input file like this
chr1 100 200 1 2 3 4
chr1 150 200 4 5 6 7
chr2 300 400 9 6 7 1
chr2 300 410 -10 21 -11 13
chr3 700 900 -21 -22 130 165
Now, my output file is
chr1 100 200 1
chr1 150 200 4
chr2 300 400 1
chr2 300 410 10
chr3 700 900 21
Remove... (5 Replies)
Discussion started by: jacobs.smith
5 Replies
6. Shell Programming and Scripting
Hello,
I have this file file1.csv
Element1;23-10-2012;1,450;1,564;1,428
Element2;23-10-2012;1,448;1,565;1,427
Element3;23-10-2012;1,453;1,570;1,424
Element4;23-10-2012;1,428;1,542;1,405
Element5;23-10-2012;1,461;;1,453
Element6;23-10-2012;1,438;1,555;1,417... (6 Replies)
Discussion started by: saba01
6 Replies
7. Shell Programming and Scripting
Hi all,
I am having multiple files with the pattern given below:
I need to find the minimum value of 5th column if column 1 is x and 2nd column is awh or vbn or ... (20 different strings).
the output must be like:
Kindly help me to figure out this prob....
Thanks in... (4 Replies)
Discussion started by: CAch
4 Replies
8. Shell Programming and Scripting
Hi there
I have generated a column containing 100.000 values. Sample:
94.971
101.468
73.120
100.601
102.329
I need to find the minimum value in this file and I must know which row it is in (no sorting).
I hope you can help!
Thanks! (16 Replies)
Discussion started by: cno
16 Replies
9. Shell Programming and Scripting
Input
10 8 20 8 10 9 20 9
10 12 20 19 10 10 20 40
Output1
10 8 2 20 8 12 10 9 1 20 9 11
10 12 -2 20 19 1 10 10 0 20 40 -20
Output2
10 9 ... (0 Replies)
Discussion started by: repinementer
0 Replies
10. Shell Programming and Scripting
Hi,
Suppose I have a space delimited file like this:
Serial# 1970 1971 1972 1973 1974
193532 21 2 X X X
200201 20 30 X X 40
200201 X X 13 15 X
393666 66 3 X X 5 ... (2 Replies)
Discussion started by: grossgermany
2 Replies
BP_MASK_BY_SEARCH(1p) User Contributed Perl Documentation BP_MASK_BY_SEARCH(1p)
NAME
mask_by_search - mask sequence(s) based on its alignment results
SYNOPSIS
mask_by_search.pl -f blast genomefile blastfile.bls > maskedgenome.fa
DESCRIPTION
Mask sequence based on significant alignments of another sequence. You need to provide the report file and the entire sequence data which
you want to mask. By default this will assume you have done a TBLASTN (or TFASTY) and try and mask the hit sequence assuming you've
provided the sequence file for the hit database. If you would like to do the reverse and mask the query sequence specify the -t/--type
query flag.
This is going to read in the whole sequence file into memory so for large genomes this may fall over. I'm using DB_File to prevent keeping
everything in memory, one solution is to split the genome into pieces (BEFORE you run the DB search though, you want to use the exact file
you BLASTed with as input to this program).
Below the double dash (--) options are of the form --format=fasta or --format fasta or you can just say -f fasta
By -f/--format I mean either are acceptable options. The =s or =n or =c specify these arguments expect a 'string'
Options:
-f/--format=s Search report format (fasta,blast,axt,hmmer,etc)
-sf/--sformat=s Sequence format (fasta,genbank,embl,swissprot)
--hardmask (booelean) Hard mask the sequence
with the maskchar [default is lowercase mask]
--maskchar=c Character to mask with [default is N], change
to 'X' for protein sequences
-e/--evalue=n Evalue cutoff for HSPs and Hits, only
mask sequence if alignment has specified evalue
or better
-o/--out/
--outfile=file Output file to save the masked sequence to.
-t/--type=s Alignment seq type you want to mask, the
'hit' or the 'query' sequence. [default is 'hit']
--minlen=n Minimum length of an HSP for it to be used
in masking [default 0]
-h/--help See this help information
AUTHOR - Jason Stajich
Jason Stajich, jason-at-bioperl-dot-org.
perl v5.14.2 2012-03-02 BP_MASK_BY_SEARCH(1p)