10 More Discussions You Might Find Interesting
1. Shell Programming and Scripting
What is an efficient way of counting the number of unique values in a 400 column by 1000 row array and outputting the counts per column, assuming the unique values in the array are:
A, B, C, D
In other words the output should look like: Value COL1 COL2 COL3
A 50 51 52... (16 Replies)
Discussion started by: Geneanalyst
16 Replies
2. UNIX for Dummies Questions & Answers
Hi !
input:
A|B|C|D
A|F|C|E
A|B|I|C
A|T|I|B
As the title of the thread says, I would need to get:
1|3|2|4
I tried different variants of this command, but I don't manage to obtain what I need:
gawk 'BEGIN{FS=OFS="|"}{for(i=1; i<=NF; i++) a++} END {for (b in a) print b}' input
... (2 Replies)
Discussion started by: beca123456
2 Replies
3. Shell Programming and Scripting
Hi i have data like
abchd 124 ldskc aattggcc
each separated by tab space i want to count number of characters in 4th column and print it in new column with tabspace for every line can anyone help me how to do it.
Thanks. (3 Replies)
Discussion started by: bhargavpbk88
3 Replies
4. Shell Programming and Scripting
Hi
I was going through the below thread
https://www.unix.com/shell-programming-scripting/48535-how-count-number-fields-record.html
I too have something similar requirement as specified in this thread but the number of columns in my case can be very high, so I am getting following error.
... (3 Replies)
Discussion started by: shekharjchandra
3 Replies
5. Shell Programming and Scripting
This is the source file, we called it errorlist.out
196 server_a server_unix_2 CD
196 server_b server_win_1 CD
196 server_c server_win_2 CD
196 server_bd server_unix_2 CD
196 server_d server_unix_2 CD
196 server_es server_win_1 CD
196 ... (14 Replies)
Discussion started by: sQew
14 Replies
6. UNIX for Dummies Questions & Answers
Could anybody help with this?
I have input below .....
david,39
david,39
emelie,40
clarissa,22
bob,42
bob,42
tim,32
bob,39
david,38
emelie,47
what i want to do is count how many names there are with different ages, so output would be like this ....
david,2
emelie,2
clarissa,1... (3 Replies)
Discussion started by: itsme999
3 Replies
7. Shell Programming and Scripting
im trying to count the number of occurences of column 2 value(starting from KKK*) of the below file, file.txt
using the code cat file.txt | awk ' BEGIN { print "Category Counts"} {FS=","} {NR > 2} { cats = cats + 1} END { for(c in cats) { print c, "=", cats} } '
but its returning as
... (6 Replies)
Discussion started by: michaelrozar17
6 Replies
8. UNIX for Dummies Questions & Answers
Hi All,
I have the following input which i want to process using AWK.
Rows,NC,amount
1,1202,0.192387
2,1201,0.111111
3,1201,0.123456
i want the following output
count of rows = 3 ,sum of amount = 0.426954
Many thanks (2 Replies)
Discussion started by: pistachio
2 Replies
9. Shell Programming and Scripting
Hi,
I am a beginner in awk scripting! I need your help; I want to replace the fifth column number (which is 15 here) here in this file for example :
ATOM 142 N PRO A 15
ATOM 143 CD PRO A 15
ATOM 144 HD1 PRO A 15
ATOM ... (5 Replies)
Discussion started by: adak
5 Replies
10. Shell Programming and Scripting
Hi All,
I have an input below and i would want to do a count on all the term "aaa" and count only once if the number in first column is the same.
For eg, if i use a "grep -c aaa input" command, the count will be "8".
However, i would want the count to be "6" instead since 2 numbers in the 1st... (7 Replies)
Discussion started by: Raynon
7 Replies
tabix(1) Bioinformatics tools tabix(1)
NAME
bgzip - Block compression/decompression utility
tabix - Generic indexer for TAB-delimited genome position files
SYNOPSIS
bgzip [-cdhB] [-b virtualOffset] [-s size] [file]
tabix [-0lf] [-p gff|bed|sam|vcf] [-s seqCol] [-b begCol] [-e endCol] [-S lineSkip] [-c metaChar] in.tab.bgz [region1 [region2 [...]]]
DESCRIPTION
Tabix indexes a TAB-delimited genome position file in.tab.bgz and creates an index file in.tab.bgz.tbi when region is absent from the com-
mand-line. The input data file must be position sorted and compressed by bgzip which has a gzip(1) like interface. After indexing, tabix is
able to quickly retrieve data lines overlapping regions specified in the format "chr:beginPos-endPos". Fast data retrieval also works over
network if URI is given as a file name and in this case the index file will be downloaded if it is not present locally.
OPTIONS OF TABIX
-p STR Input format for indexing. Valid values are: gff, bed, sam, vcf and psltab. This option should not be applied together with any
of -s, -b, -e, -c and -0; it is not used for data retrieval because this setting is stored in the index file. [gff]
-s INT Column of sequence name. Option -s, -b, -e, -S, -c and -0 are all stored in the index file and thus not used in data retrieval.
[1]
-b INT Column of start chromosomal position. [4]
-e INT Column of end chromosomal position. The end column can be the same as the start column. [5]
-S INT Skip first INT lines in the data file. [0]
-c CHAR Skip lines started with character CHAR. [#]
-0 Specify that the position in the data file is 0-based (e.g. UCSC files) rather than 1-based.
-h Print the header/meta lines.
-B The second argument is a BED file. When this option is in use, the input file may not be sorted or indexed. The entire input will
be read sequentially. Nonetheless, with this option, the format of the input must be specificed correctly on the command line.
-f Force to overwrite the index file if it is present.
-l List the sequence names stored in the index file.
EXAMPLE
(grep ^"#" in.gff; grep -v ^"#" in.gff | sort -k1,1 -k4,4n) | bgzip > sorted.gff.gz;
tabix -p gff sorted.gff.gz;
tabix sorted.gff.gz chr1:10,000,000-20,000,000;
NOTES
It is straightforward to achieve overlap queries using the standard B-tree index (with or without binning) implemented in all SQL data-
bases, or the R-tree index in PostgreSQL and Oracle. But there are still many reasons to use tabix. Firstly, tabix directly works with a
lot of widely used TAB-delimited formats such as GFF/GTF and BED. We do not need to design database schema or specialized binary formats.
Data do not need to be duplicated in different formats, either. Secondly, tabix works on compressed data files while most SQL databases do
not. The GenCode annotation GTF can be compressed down to 4%. Thirdly, tabix is fast. The same indexing algorithm is known to work effi-
ciently for an alignment with a few billion short reads. SQL databases probably cannot easily handle data at this scale. Last but not the
least, tabix supports remote data retrieval. One can put the data file and the index at an FTP or HTTP server, and other users or even web
services will be able to get a slice without downloading the entire file.
AUTHOR
Tabix was written by Heng Li. The BGZF library was originally implemented by Bob Handsaker and modified by Heng Li for remote file access
and in-memory caching.
SEE ALSO
samtools(1)
tabix-0.2.0 11 May 2010 tabix(1)