Hi Friends,
I'm working on a perl script, which seems to be simpler. But I'm very new to PERL scripting.
I have a comma separated data file, from which I need to extract only the seventh field data out of available twenty fields to an array using perl.
Any help would be much appreciated.
... (17 Replies)
Guys,
Need you help, i have a a file content that look like this.
Nokia 3330 <spaces><spaces><more spaces>+76451883874
Nokia 3610 +87467361615
so on and so forth,
- there are so many spaces in between.
- e.g.... (5 Replies)
Hello Mates,
I have one txt file having commo seperated values. I have to insert string "FALSE" in 2nd field from the end. E.G
SE18 6RN,,,,5439070,1786840,,1000002148671600,123434
Out put should be:
SE18 6RN,,,,5439070,1786840,FALSE,1000002148671600,123434
Can some one help me to... (8 Replies)
Hi all,
I have the following files types:
FileA:
100,
23,
33,
FileB:
22,
45,
78,
and i want to make
File C:
100,22
23,45
33,78
any nice suggestions for making it easy. (3 Replies)
Hello there,
I have a comma separated csv , and all the text field is wrapped by double quote. Issue is some text field contain comma as well inside double quote. so it is difficult to process.
Input in the csv file is ,
1,234,"abc,12,gh","GH234TY",34
I need output like below,... (8 Replies)
Hi,
I have a large number of files which are written as csv (comma-separated values).
Does anyone know of simple sed/awk command do achieve this?
Thanks!
---------- Post updated at 10:59 AM ---------- Previous update was at 10:54 AM ----------
Guess I asked this too soon. Found the... (0 Replies)
Hi,
I am having the file with server names & its corresponding process, i need your help how to convert into comma separated output between server & app
#cat apps.txt
Server1
oracle
was
Server2
http
webadmin
Server3
tsm
db2
My requirement is like below.
Server1,oracle/was... (5 Replies)
Hi Experts,
Please support
I have below data in file in comma seperated, but 4th column is containing comma in between numbers, bcz of which when i tried to parse the file the column 6th value(5049641141) is being removed from the file and value(222.82) in column 5 becoming value of column6.
... (3 Replies)
can anyone help me!!!! How to I parse the CSV file
file name : abc.csv (csv file) The above file containing data like
abv,sfs,,hju,',',jkk wff,fst,,rgr,',',rgr ere,edf,erg,',',rgr,rgr I have a requirement like i have to extract different field and assign them into different... (4 Replies)
Discussion started by: J.Jena
4 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)