Sponsored Content
Top Forums Shell Programming and Scripting reading information from a table and apply a command on multiple files Post 302708837 by RudiC on Tuesday 2nd of October 2012 09:57:43 AM
Old 10-02-2012
Try this:
Code:
while read BAM REGION; do samtools view $BAM chrname:$REGION >> $REGION.txt; done <file

remove the region*.txt files before use.
This User Gave Thanks to RudiC For This Post:
 

10 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

Apply `chmod` for multiple files through FTP

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)
Discussion started by: Chanakya.m
3 Replies

2. Shell Programming and Scripting

How to Pull out multiple files from DB table and redirect all those files to a differetn directory?

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)
Discussion started by: ss3944
3 Replies

3. Shell Programming and Scripting

Apply 'awk' to all files in a directory or individual files from a command line

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)
Discussion started by: ScKaSx
4 Replies

4. Shell Programming and Scripting

apply record separator to multiple files within a directory using awk

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)
Discussion started by: amarn
3 Replies

5. Shell Programming and Scripting

extracting information from multiple files

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)
Discussion started by: houkto
4 Replies

6. UNIX for Dummies Questions & Answers

Reading Table name from a list of files in a Directory

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)
Discussion started by: Trendz
3 Replies

7. Shell Programming and Scripting

search information in multiple files and save in new files

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)
Discussion started by: andreia
6 Replies

8. UNIX for Dummies Questions & Answers

Load multiple files into a table

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)
Discussion started by: reshma15193
0 Replies

9. Shell Programming and Scripting

Apply command to all files in folder

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)
Discussion started by: guilliber
7 Replies

10. UNIX for Beginners Questions & Answers

How to apply the update statement in multiple servers on multiple dbs at a time .?

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
BAM(1)								   User Commands							    BAM(1)

NAME
bam - fast and flexible build system SYNOPSIS
bam [OPTION]... [VARIABLE=VALUE]... [TARGET]... DESCRIPTION
Builds applications using the bam build system. Execution: -a abort on error -c clean targets -d build targets that is dependent given targets --dry dry run, don't run any jobs -j sets the number of threads to use (default: 0, disabled) -s bam file to use (default: bam.lua) Lua: -l print local variables in backtrace -t print backtrace when an error occurs Output: -r build progress report format (default: s) b = progress bar c = use ansi colors s = build steps -v be verbose Other: -n don't use cache -h, --help prints this help Debug: --debug-nodes prints all the nodes with dependencies --debug-detail prints all the nodes with dependencies and details --debug-jobs prints all the jobs that exist --debug-dot prints all nodes as a graphviz dot file --debug-jobs-dot prints all jobs as a graphviz dot file --debug-trace-vm prints a line for every instruction the vm makes --debug-dump-int prints the internals scripts to stdout --debug-no-int don't load internal scripts bam by Magnus Auvinen (magnus.auvinen@gmail.com) bam May 2011 BAM(1)
All times are GMT -4. The time now is 10:14 AM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy