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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
CD-HIT-EST-2D(1) User Commands CD-HIT-EST-2D(1)
NAME
cdhit-est-2d - run CD-HIT algorithm on RNA/DNA sequences in db1 or db2 format
SYNOPSIS
cdhit-est-2d [Options]
DESCRIPTION
====== CD-HIT version 4.6 (built on Apr 26 2012) ======
Options
-i input filename for db1 in fasta format, required
-i2 input filename for db2 in fasta format, required
-o output filename, required
-c sequence identity threshold, default 0.9 this is the default cd-hit's "global sequence identity" calculated as: number of identical
amino acids in alignment divided by the full length of the shorter sequence
-G use global sequence identity, default 1 if set to 0, then use local sequence identity, calculated as : number of identical amino
acids in alignment divided by the length of the alignment NOTE!!! don't use -G 0 unless you use alignment coverage controls see
options -aL, -AL, -aS, -AS
-b band_width of alignment, default 20
-M memory limit (in MB) for the program, default 800; 0 for unlimitted;
-T number of threads, default 1; with 0, all CPUs will be used
-n word_length, default 10, see user's guide for choosing it
-l length of throw_away_sequences, default 10
-d length of description in .clstr file, default 20 if set to 0, it takes the fasta defline and stops at first space
-s length difference cutoff, default 0.0 if set to 0.9, the shorter sequences need to be at least 90% length of the representative of
the cluster
-S length difference cutoff in amino acid, default 999999 if set to 60, the length difference between the shorter sequences and the
representative of the cluster can not be bigger than 60
-s2 length difference cutoff for db1, default 1.0 by default, seqs in db1 >= seqs in db2 in a same cluster if set to 0.9, seqs in db1
may just >= 90% seqs in db2
-S2 length difference cutoff, default 0 by default, seqs in db1 >= seqs in db2 in a same cluster if set to 60, seqs in db2 may 60aa
longer than seqs in db1
-aL alignment coverage for the longer sequence, default 0.0 if set to 0.9, the alignment must covers 90% of the sequence
-AL alignment coverage control for the longer sequence, default 99999999 if set to 60, and the length of the sequence is 400, then the
alignment must be >= 340 (400-60) residues
-aS alignment coverage for the shorter sequence, default 0.0 if set to 0.9, the alignment must covers 90% of the sequence
-AS alignment coverage control for the shorter sequence, default 99999999 if set to 60, and the length of the sequence is 400, then the
alignment must be >= 340 (400-60) residues
-A minimal alignment coverage control for the both sequences, default 0 alignment must cover >= this value for both sequences
-uL maximum unmatched percentage for the longer sequence, default 1.0 if set to 0.1, the unmatched region (excluding leading and tailing
gaps) must not be more than 10% of the sequence
-uS maximum unmatched percentage for the shorter sequence, default 1.0 if set to 0.1, the unmatched region (excluding leading and tail-
ing gaps) must not be more than 10% of the sequence
-U maximum unmatched length, default 99999999 if set to 10, the unmatched region (excluding leading and tailing gaps) must not be more
than 10 bases
-B 1 or 0, default 0, by default, sequences are stored in RAM if set to 1, sequence are stored on hard drive it is recommended to use
-B 1 for huge databases
-p 1 or 0, default 0 if set to 1, print alignment overlap in .clstr file
-g 1 or 0, default 0 by cd-hit's default algorithm, a sequence is clustered to the first cluster that meet the threshold (fast clus-
ter). If set to 1, the program will cluster it into the most similar cluster that meet the threshold (accurate but slow mode) but
either 1 or 0 won't change the representatives of final clusters
-r 1 or 0, default 1, by default do both +/+ & +/- alignments if set to 0, only +/+ strand alignment
-mask masking letters (e.g. -mask NX, to mask out both 'N' and 'X')
-match matching score, default 2 (1 for T-U and N-N)
-mismatch
mismatching score, default -2
-gap gap opening score, default -6
-gap-ext
gap extension score, default -1
-bak write backup cluster file (1 or 0, default 0)
-h print this help
Questions, bugs, contact Limin Fu at l2fu@ucsd.edu, or Weizhong Li at liwz@sdsc.edu For updated versions and information, please
visit: http://cd-hit.org
cd-hit web server is also available from http://cd-hit.org
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
Godzik. Bioinformatics, (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
cd-hit-est-2d 4.6-2012-04-25 April 2012 CD-HIT-EST-2D(1)