Hello,
I have a logfile which is in this format:
1211667249500#3265
1211667266687#2875
1211667270781#1828
Is there a way to read the logfile line by line every time I execute the code and put the two numbers in the line in two separate variables?
Something like:
1211667249500#3265... (7 Replies)
I am reading file and extracting the paragraph between START and END tags.
contents of abc.txt
Remember that $ means the last line in a file. You can also specify a range based on two regexps. Try
START
Note that this prints all blocks starting with lines containing regexp1
through lines... (1 Reply)
hey gents,
I'm working on something that will use snmpwalk to query the devices on my network and retreive the device name, device IP, device model and device serial. I'm using Nmap for the enumeration and sed to clean up the results for use by snmpwalk. Once i get all the data organized I'm... (8 Replies)
I know this has been asked before but I just can't parse the syntax as explained. I have a set of files that has user information spread out over two lines that I wish to merge into one:
User1NameLast User1NameFirst User1Address
E-Mail:User1email
User2NameLast User2NameFirst User2Address... (11 Replies)
hello
i try this command in console mode
sed -e :a -e '/$/N; s/\(\)\n/\1 /; ta' test.txt > result.txt
i have in the output screen "Output line too long" for multiples lines
can you please tell me how can i retrieve those long lines during the execution ?
Another thing very... (5 Replies)
Hi
I've been trying to search but couldn't quite get the answer I was looking for.
I have a a file that's like this
Time, 9/1/12
0:00, 1033
0:10, 1044
...
23:50, 1050
How do I make it so the file will be like this?
9/1/12, 0:00, 1033
9/1/12, 0:10, 1044
...
9/1/12, 23:50, 1050
I... (4 Replies)
Hi,
I am running a script sample.sh in bash environment .In the script i am using sed and awk commands which when executed individually from terminal they are getting executed normally but when i give these sed and awk commands in the script it is giving the below errors :-
./sample.sh: line... (12 Replies)
I have file, i am extracting email address from file. but problem is that output is very ugly.
I am using this command
REMOVED "CSS OFFENDING CODE"...
While original filename have no such character. Please suggest. (20 Replies)
All, I appreciate any help you can offer here as this is well beyond my grasp of awk/sed...
I have an input file similar to:
&LOG
&LOG Part: "@DB/TC10000021855/--F"
&LOG
&LOG
&LOG Part: "@DB/TC10000021852/--F"
&LOG Cloning_Action: RETAIN
&LOG Part: "@DB/TCCP000010713/--A"
&LOG
&LOG... (5 Replies)
Sed command to replace a line in a file using line number from the output of a pipe.
Is it possible to replace a whole line piped from someother command into a file at paritcular line...
here is some basic execution flow..
the line number is 412
lineNo=412
Now i have a line... (1 Reply)
Discussion started by: vivek d r
1 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)