reading information from a table and apply a command on multiple files
Hey gyuz,
I wanna calculate the number of mapped reads of a bam file in a region of interest. I used this code to do so :
This will store all the reads from given bam file within the region of interest in region1.txt
Now I have several bam files and several regions for each which are different. (regions are not the same in all bam files)
I prepared a list of them like below:
bam1 region1
bam1 region2
bam1 region3
bam2 region4
bam2 region4
bam3 region5
I want the script to read from the table and apply the function on proper bam file and regions and report the output for each region in a single file. region1.txt, region2.txt, region3.txt,.....
If you can help me with this you saved my time so much!!
Hi all,
Can you please help me in this aspect. I devoloped a FTP script to copy a directory to remote server. Now i got stuck-up in changing the file permissions for all the files in directory. I tried to change the permissions of single file and I did it but failed in changing... (3 Replies)
Hi everyone!!
I have a database table, which has file_name as one of its fields.
Example:
File_ID File_Name Directory Size
0001 UNO_1232 /apps/opt 234
0002 UNO_1234 /apps/opt 788
0003 UNO_1235 /apps/opt 897
0004 UNO_1236 /apps/opt 568
I have to... (3 Replies)
Hi All,
I am using the awk command to replace ',' by '\t' (tabs) in a csv file. I would like to apply this to all .csv files in a directory and create .txt files with the tabs.
How would I do this in a script?
I have the following script called "csvtabs":
awk 'BEGIN {
FS... (4 Replies)
Hi,
I have a bunch of records within a directory where each one has this form:
(example file1)
1 2 50 90 80 90 43512 98 0909 79869 -9 7878 33222 8787 9090 89898 7878 8989 7878 6767 89 89 78676 9898 000 7878 5656 5454 5454
and i want for all of these files to be... (3 Replies)
Hello there,
I am trying to extract (string) information ( a list words) from 4 files and then put the results into 1 file. Currently I am doing this using grep -f list.txt file1 . and repeat the process for the other 3 files. The reasons i am doing that (a) I do know how to code (b) each file... (4 Replies)
Hi ,
I have searched through the forum but not able to find out any help :(
i have a directory having lot of files which contains sql statemtns
eg : file 1 contains
select from table_name1 where .....................
select from
table_name2 where ..........
select
from ... (3 Replies)
hi everyone,
im stuck in here with shell :) can you help me??
i have a directory with alot files (genbank files ... all ended in .gbk ) more than 1000 for sure ... and i want to read each one of them and search for some information and if i found the right one i save in new file with new... (6 Replies)
Hi,
I need to load data from two files to a single table.
My requirement is that I get two files in which a few column data are manadatory.
These files are identified based on the file name.
For example, I have two files ABCFile and BCDFile. ABCFile has mandatory data in column 3 and 4... (0 Replies)
Hi all!
I have this command
grep -E '^\To: |^\Date: |^\Subject: ' fileA.txt > fileA_1.txt && grep -v '^\To: |^\Date: |^\Subject: ' fileA.txt >> fileA_1.txt && rm fileA.txt && sed -i -e 's/\(Date: \|Subject: \|To: \)//g' fileA_1.txtHow do I apply it to all the files in the folder (each file has a... (7 Replies)
Hi ,
Can any please help the below requirement on all multiple servers and multiple dbs.
update configuration set value='yes' ;1)
the above statement apply on 31 Databases at a time on different Ip address
eg : 10.104.1.12 (unix ip address )
the above ip box contains 4 db's eg : db... (2 Replies)
Discussion started by: venkat918
2 Replies
LEARN ABOUT REDHAT
dos2unix
dos2unix(1) General Commands Manual dos2unix(1)NAME
dos2unix - DOS/MAC to UNIX text file format converter
SYNOPSYS
dos2unix [options] [-c convmode] [-o file ...] [-n infile outfile ...]
Options:
[-hkqV] [--help] [--keepdate] [--quiet] [--version]
DESCRIPTION
This manual page documents dos2unix, the program that converts plain text files in DOS/MAC format to UNIX format.
OPTIONS
The following options are available:
-h --help
Print online help.
-k --keepdate
Keep the date stamp of output file same as input file.
-q --quiet
Quiet mode. Suppress all warning and messages.
-V --version
Prints version information.
-c --convmode convmode
Sets conversion mode. Simulates dos2unix under SunOS.
-o --oldfile file ...
Old file mode. Convert the file and write output to it. The program default to run in this mode. Wildcard names may be used.
-n --newfile infile outfile ...
New file mode. Convert the infile and write output to outfile. File names must be given in pairs and wildcard names should NOT be
used or you WILL lost your files.
EXAMPLES
Get input from stdin and write output to stdout.
dos2unix
Convert and replace a.txt. Convert and replace b.txt.
dos2unix a.txt b.txt
dos2unix -o a.txt b.txt
Convert and replace a.txt in ASCII conversion mode. Convert and replace b.txt in ISO conversion mode. Convert c.txt from Mac to Unix
ascii format.
dos2unix a.txt -c iso b.txt
dos2unix -c ascii a.txt -c iso b.txt
dos2unix -c mac a.txt b.txt
Convert and replace a.txt while keeping original date stamp.
dos2unix -k a.txt
dos2unix -k -o a.txt
Convert a.txt and write to e.txt.
dos2unix -n a.txt e.txt
Convert a.txt and write to e.txt, keep date stamp of e.txt same as a.txt.
dos2unix -k -n a.txt e.txt
Convert and replace a.txt. Convert b.txt and write to e.txt.
dos2unix a.txt -n b.txt e.txt
dos2unix -o a.txt -n b.txt e.txt
Convert c.txt and write to e.txt. Convert and replace a.txt. Convert and replace b.txt. Convert d.txt and write to f.txt.
dos2unix -n c.txt e.txt -o a.txt b.txt -n d.txt f.txt
DIAGNOSTICS BUGS
The program does not work properly under MSDOS in stdio processing mode. If you know why is that so, please tell me.
AUTHORS
Benjamin Lin - <blin@socs.uts.edu.au>
Bernd Johannes Wuebben (mac2unix mode) <wuebben@kde.org>
MISCELLANY
Tested environment:
Linux 1.2.0 with GNU C 2.5.8
SunOS 4.1.3 with GNU C 2.6.3
MS-DOS 6.20 with Borland C++ 4.02
Suggestions and bug reports are welcome.
SEE ALSO unix2dos(1)mac2unix(1)1995.03.31 dos2unix v3.0 dos2unix(1)