In a nutshell, I need to work out how to return the last matching pattern from an awk //,// search. I can bring back the first, but am unsure how to obtain the last, and a simple tail won't work as the match could be over multiple lines.
Secondly I would like some way of pattern matching, a... (10 Replies)
Dear Team,
How do we match two patterns on the same line using awk?Are there any logical operators which i could use in awk like awk '\gokul && chennai\' <filename>
Eg:
Input file:
gokul,10/11/1986,coimbatore.
gokul,10/11/1986,bangalore.
gokul,12/04/2008,chennai.... (2 Replies)
Hi,
How can I tell awk to print all lines/columns if column number 5 contains the word Monday?
I have tried
nawk -F, '$5==Monday' OFS=, myfile > outputfile
but that doesn't work (I am a newb!!)
Thanks, (7 Replies)
Hello all,
I am trying to sort thru a database and print all the customers whose first names are only four characters. I just want to pull the first name only from the database.
the database records appear like this in file:
Mike Harrington:(510) 548-1278:250:100:175; first is name Mike... (4 Replies)
Hello ,
I have comma delimited file with over 20 fileds that i need to do some validations on. I have to check if certain fields are null and then write the line containing the null field into a new file and then delete the line from the current file.
Can someone tell me how i could go... (2 Replies)
can somebody provide me with some ksh code that will return true if my the contents in my variable match anyone of these strings ORA|ERROR|SP2
variable="Error:ORA-01017: Invalid username/password; logon denied\nSP2-0640:Not connected"
I tried this and it does not seem to work for me
... (3 Replies)
Hi I am trying to find a pattern match with column one containing 3 numbers.
input file tmp.lst
abcd456|1|23123|123123|23423
kumadff|a|dadfadf|adfd|adfadfadf
xxxd999|d|adfdfs|adfadf|adfdasfadf
admin|a|dafdf|adfadfa|||
output file tmp4.lst
abcd456|1|23123|123123|23423... (3 Replies)
I have two files, want to compare file1 data with file2 second column and print line which are not matching. Need help in matching the pattern, file2 second column number can be leading 0 or 00 or 000.
Example:
file1
1
2
3
file2
a,0001
b,02
c,000
d,01
e,2
f,0005
Expected output:... (20 Replies)
Hi,
I have input file whose first column needs(match.txt) to be matched with the first column of the input file with min & max length as defined in match.txt. But conditions are not matching. Please help on the changes in the code below as for multiple enteries in match.txt complete match.txt will... (3 Replies)
Hi
I need to do a patten match between files .
I am new to shell scripting and have come up with this so far. It take 50 seconds to process files of 2mb size . I need to tune this code as file size will be around 50mb and need to save time.
Main issue is that I need to search the pattern from... (2 Replies)
Discussion started by: nitin_daharwal
2 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)