Hi,
I am new to this forum and new to awk.
I have a file that contains 2 columns.
Heres an example of what it looks like:
10 +
20 +
40 +
50 -
70 -
So the file is tab-delimited. What I want to do is add 10 to column 1 whenever column 2 is + and substract 10 from column 1... (1 Reply)
Dear All,
I would like to split a file of the following format into multiple files based on the number in the 6th column (numbers 1, 2, 3...):
ATOM 1 N GLY A 1 -3.198 27.537 -5.958 1.00 0.00 N
ATOM 2 CA GLY A 1 -2.199 28.399 -6.617 1.00 0.00 ... (3 Replies)
Hi,
I have a file sample_1.txt (300k rows) which has data like below:
* Also each record is around 64k bytes
11|1|abc|102553|125589|64k bytes of data
10|2|def|123452|123356|......
13|2|geh|144351|121123|...
25|4|fgh|165250|118890|..
14|1|abc|186149|116657|......... (6 Replies)
I have a following inputfile
MT,AP,CDM,TTML,MUM,GS,SUCC,3
MT,AP,CDM,TTSL,AP,GS,FAIL,9
MT,AP,CDM,RCom,MAH,GS,SUCC,3
MT,AP,CDM,RTL,HP,GS,SUCC,1
MT,AP,CDM,Uni,UPE,GS,SUCC,2
MT,AP,CDM,Uni,MUM,GS,SUCC,2
TTSL,AP,GS,MT,MAH,CDM,SUCC,20
TTML,AP,GS,MT,MAH,CDM,FAIL,10... (2 Replies)
Hi,
I have a similar input format-
A_1 2
B_0 4
A_1 1
B_2 5
A_4 1
and looking to print in this output format with headers. can you suggest in awk?awk because i am doing some pattern matching from parent file to print column 1 of my input using awk already.Thanks!
letter number_of_letters... (5 Replies)
Hi,
I have a table to be imported for R as matrix or data.frame but I first need to edit it because I've got several lines with the same identifier (1st column), so I want to sum the each column (2nd -nth) of each identifier (1st column)
The input is for example, after sorted:
K00001 1 1 4 3... (8 Replies)
please write a shell script
Table
--------------------------
1 2 3 a b c
3 4 5 c d e
7 8 9 f g h
Output should be like this
---------------
1 2 3
3 4 5
7 8 9
a b c
c d e
f g h (1 Reply)
Split column data if the table has n number of column's with some record then how to split n number of colmn's line by line with records
Table
---------
Col1 col2 col3 col4 ....................col20
1 2 3 4 .................... 20
a b c d .................... v
... (11 Replies)
Hello,
I am trying to store sum of a column as a new column inside a file but have to find the column names dynamically
I/p
c1,c2,c3,c4,c5
10,20,30,40,50
20,30,40,50,60
If i want to find sum only column c1, c3 and output it as c6,c7
O/p
c1,c2,c3,c4,c5,c6,c7
10,20,30,40,50,30,70... (6 Replies)
Hi All,
I have a file as below and want to sum based on the id in the first column
Input
10264;ATE; 12
10265;SES;11
10266AUT;50
10264;ATE;10
10265;SES;13
10266AUT;89
10264;ATE;1
10265;SES;15
10266AUT;78
Output
10264;ATE; 23
10265;SES;39
10266AUT;139 (6 Replies)
Discussion started by: arunkumar_mca
6 Replies
LEARN ABOUT DEBIAN
tabix
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)