Sponsored Content
Top Forums Shell Programming and Scripting reading information from a table and apply a command on multiple files Post 302708861 by @man on Tuesday 2nd of October 2012 10:29:46 AM
Old 10-02-2012
Thanks RudiC. It seems it's working just fine.
Now I have many files which I cannot open them. I believe it's because of their name:

one example:
gi|16799079|ref|NC_003212.1|:2769071-2769101.txt

How can I rename them all by replacing pipes and colons by underscore for example to have something like this:

gi_16799079_ref_NC_003212.1__2769071-2769101.txt

I appreciate your help!
 

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
X2SYS_MERGE(1gmt)					       Generic Mapping Tools						 X2SYS_MERGE(1gmt)

NAME
x2sys_merge - Merge an updated COEs tables SYNOPSIS
x2sys_merge -Amain_COElist.d -Mnew_COElist.d DESCRIPTION
x2sys_merge will read two crossovers data base and output the contents of the main one updated with the COEs in the second one. The second file should only contain updated COEs relatively to the first one. That is, it MUST NOT contain any new two tracks intersections (This point is NOT checked in the code). This program is useful when, for any good reason like file editing NAV correction or whatever, one had to recompute only the COEs between the edited files and the rest of the database. -A Specify the file main_COElist.d with the main crossover error data base. -M Specify the file new_COElist.d with the newly computed crossover error data base. OPTIONS
No space between the option flag and the associated arguments. EXAMPLES To update the main COE_data.txt with the new COEs estimations saved in the smaller COE_fresh.txt, try x2sys_merge -ACOE_data.txt -MCOE_fresh.txt > COE_updated.txt SEE ALSO
x2sys_binlist(1), x2sys_cross(1), x2sys_datalist(1), x2sys_get(1), x2sys_init(1), x2sys_list(1), x2sys_put(1), x2sys_report(1) GMT 4.5.7 15 Jul 2011 X2SYS_MERGE(1gmt)
All times are GMT -4. The time now is 02:02 PM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy