I have a file which is having fileds separtaed by delimiter.
Ex:
C;4498;qwa;cghy;;;;40;;222122
C;4498;sample;city;;;;34 2;;222123
C;4498;qwe;xcbv;;;;34-2;;222124
C;4498;jj;sffz;;;;41;;222120
C;4498;eert;qwq;;;;34 A;;222125
C;4498;jj;szxzzd;;;;34;;222127
out of these records I... (3 Replies)
I want to filter records in one of my file using AWK command (or anyother command). I am using the below code
awk -F@ '$1=="0003"&&"$2==20100402" print {$0}' $INPUT > $OUTPUT
I want to pass the 0003 and 20100402 values through a variable. How can I do this?
Any help is much... (1 Reply)
Dear members..
I have a fixed width file. Requirement is as below:-
1. Scan each record from this fixed width file
2. Check for value under field no "6" equals to "ABC". If yes, then filter this record into the output file
Please suggest a unix command to achieve this, my guess awk might... (6 Replies)
Hi Folks,
I have a text file with lots of rows with duplicates in the first column, i want to filter out records based on filter columns in a different filter text file.
bash scripting is what i need.
Data.txt
Name OrderID Quantity
Sam 123 300
Jay 342 498
Kev 78 2500
Sam 420 50
Vic 10... (3 Replies)
Not sure if this is the correct forum for this question. I have two files. file1.zip, file2
Input:
file1.zip
col1, col2 , col3
a , b , 0:0:0:0:0:c436:9346:d40b
x, y, 0:0:0:0:0:880:39f9:c9a7
m, n , 0:0:0:0:0:80c7:9161:fe00
file2.txt
col1
c4:36:93:46:d4:0b... (1 Reply)
Hello
I have a tab text file with many columns and have to filter rows ONLY if column 22 has the value of '0', '1', '2' or '3' (out of 0-5).
If Column 22 has value '0','1', '2' or '3' (highlighted below), then remove anything less than 10 and greater 100 (based on column 5) AND remove anything... (1 Reply)
I have two files and would need to filter out records based on certain criteria, these column are of variable lengths, but the lengths are uniform throughout all the records of the file. I have shown a sample of three records below. Line 1-9 is the item number "0227546_1" in the case of the first... (15 Replies)
I have csv file with 30, 40 columns
Pasting just three column for problem description
I want to filter record if column 1 matches CN or DN then,
check for values in column 2 if column contain 1235, 1235 then in column 3 values must be sequence of 2345, 2345
and if column 2 contains 6789, 6789... (5 Replies)
Hi Experts,
I have csv file with 30, 40 columns
Pasting just 2 column for problem description.
Need to print error if below combination is not present in file
check for column-1 (DocumentNumber) and filter columns where value in DocumentNumber field is same.
For all such rows, the field... (7 Replies)
Dear Experts,
I have a log file that contains a timestamp, I would like to filter record from that file based on timestamp. For example refer below file -
cat sample.txt
Jan 19 20:51:48 mukul-Vostro-14-3468 systemd: pam_unix(systemd-user:session): session opened for user root by (uid=0)... (6 Replies)
Discussion started by: mukulverma2408
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)