As long as a mv operation is performed on the same file system -
.
.
.
Even if the file is moved between file systems, there should not be a problem as long as the file is kept open. Even though the file and it's contents ARE moved by the mv command, the OS keeps the file readable until it is closed and unlinked. See below, using nezabudka's one liner extended by mv's -v (--verbose) option
and the respective lsof output (before and after (but before file closing) the mv operation) :
Even though attributed "deleted", the file's contents is still available and readable. Of course, once unlinked, the file can't be reopened / reused in its original location.
I am on a HP-UX machine I have a directory called "/u01/blobs" and the files look like this:
ls -1
7398
7399
7400
I need to produce a comma delimited file with the following format:
filename,location/filename
i.e:
7398,/u01/blobs/7398
7399,/u01/blobs/7399
7400,/u01/blobs/7400
What... (3 Replies)
Hello guys, thank God that I found this forum.
I hope that someone can help me because I don't have any idea on how to start it. I know that for some of you this is a very simple task but I'm not as advance on shell scripting like many people out there.
I got this file with a permanent... (10 Replies)
Hello all.
I am new to this forum (and somewhat new to UNIX / LINUX - I started using ubuntu 1 year ago).:b:
I have the following problem that I have not been able to figure out how to take care of and I was wondering if anyone could help me out.:confused:
I have all of my music stored in... (7 Replies)
Hi guys, I am a newbie here :wall:
I need a script that can search for a file in a directory and copy the contents of that file in a new file.
Please help me. :confused: Thanks in advance~ (6 Replies)
I hope some one can help me
I have multiple files in a directory with out extension like as below mentioned. But i want to change all the file names along .DDMMYYYYHHMISS format. And all files should have same DDMMYYYYHHMISS.
Scenario:
direcory name = /vol/best/srcfiles
files in a... (4 Replies)
I have to write a script to rename the every last sub-directory in a directory structure if the last sub-directory name doesn't contain "submitted".
eg:
given directory path:/u01/home/somedir
somedir can have many subdirectories and each subdirectory inturn has many subdirectories.
somedir... (3 Replies)
Hello All,
Can you help me in writing a script for reading the specific position data in a file and if that data found in that file that particular file should be renamed.
Ex: Folder : C:\\test
and Filename : CLSACK_112214.txt,CLSACK_112314.txt,CLSACK_112414.txt
Contents in the file would... (3 Replies)
I am trying to use the two files shown below to either remove or rename contents in one of those files. If in file1.txt $5 matches $5 of file2.txt and the value in $1 of file1.txt is not "No Match" then that value is substituted for all values in $5 and $1 of file2.txt. If however in $1 ... (5 Replies)
I have a specific set (all ending with .bam) of downloaded files in a directory /home/cmccabe/Desktop/NGS/API/2-15-2016. What I am trying to do is use a match to $2 in name to rename the downloaded files. To make things a more involved the date of the folder is unique and in the header of name... (1 Reply)
Hi All,
Just started learning unix and stuck into below issue.
Suppose i have folder structure as below.
Dir1/Dir2/Dir3/File1.msg
I am looking to rename the file name from File1.msg to File2.msg but from the parent Dir1
From Dir3 i can easily run the command like
mv File1.msg... (2 Replies)
Discussion started by: Gurjeet Singh
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)