Rename text file with a specific pattern in directory Post: 302991428

Sponsored Content

Top Forums Shell Programming and Scripting Rename text file with a specific pattern in directory Post 302991428 by drysdalk on Friday 10th of February 2017 11:20:55 AM

02-10-2017

Registered User

Hi,

I've come up with the following script which does what you need, I think:

Code:

#!/bin/bash

pattern1="variant_strandbias_readcount.vcf."
pattern2_old="hg19_multianno"
pattern2_new="hg19multianno"
pattern3="_dbremoved_removed_final_index_inheritence_import_classify"

for file in `/bin/ls *.txt`
do
        newname=`echo $file | /bin/sed s/$pattern1//g | /bin/sed s/$pattern2_old/$pattern2_new/g | /bin/sed s/$pattern3//g`
        /bin/mv -fv $file $newname
done

If I run it, this is what I get:

Code:

$ ls -1
16-0000_File-A_variant_strandbias_readcount.vcf.hg19_multianno_dbremoved_removed_final_index_inheritence_import_classify.txt
16-0002_File-B_variant_strandbias_readcount.vcf.hg19_multianno_dbremoved_removed_final_index_inheritence_import_classify.txt
16-0005_File-C_variant_strandbias_readcount.vcf.hg19_multianno_dbremoved_removed_final_index_inheritence_import_classify.txt
script.sh
$ ./script.sh 
'16-0000_File-A_variant_strandbias_readcount.vcf.hg19_multianno_dbremoved_removed_final_index_inheritence_import_classify.txt' -> '16-0000_File-A_hg19multianno.txt'
'16-0002_File-B_variant_strandbias_readcount.vcf.hg19_multianno_dbremoved_removed_final_index_inheritence_import_classify.txt' -> '16-0002_File-B_hg19multianno.txt'
'16-0005_File-C_variant_strandbias_readcount.vcf.hg19_multianno_dbremoved_removed_final_index_inheritence_import_classify.txt' -> '16-0005_File-C_hg19multianno.txt'
$ ls -1
16-0000_File-A_hg19multianno.txt
16-0002_File-B_hg19multianno.txt
16-0005_File-C_hg19multianno.txt
script.sh
$

Hope this helps.

This User Gave Thanks to drysdalk For This Post:

drysdalk

View Public Profile for drysdalk

Find all posts by drysdalk

10 More Discussions You Might Find Interesting

1. UNIX for Dummies Questions & Answers

extracting text and reusing the text to rename file

Hi, I have some ps files where I want to ectract/copy a certain number from and use that number to rename the ps file. eg: 'file.ps' contains following text: 14 (09 01 932688 0)t the text can be variable, the only fixed element is the '14 ('. The problem is that the fixed element can appear...

2. Shell Programming and Scripting

How can i break a text file into parts that occur between a specific pattern

How can i break a text file into parts that occur between a specific pattern? I have text file having various xml many tags like which starts with the tag "<?xml version="1.0" encoding="utf-8"?>" . I have to break the whole file into several xmls by looking for the above pattern. All the...

3. Shell Programming and Scripting

extract specific string and rename file

Hi all, I am working on a small prog.. i have a file.txt which contains random data... K LINES V4 ADD CODE `COMPANY` ADD CODE `DISTRIBUTOR` SEQ NAME^K LINES V5 SEQ NAME^K LINES V6 ADD `PACK-LDATE` SEQ NAME^K^KCOMMAND END^KHEADINFO...

4. Shell Programming and Scripting

Help with remove last text of a file that have specific pattern

Input file matrix-remodelling_associated_8_ aurora_interacting_1_ L20 von_factor_A_domain_1 ATP_containing_3B_ . . Output file matrix-remodelling_associated_8 aurora_interacting_1 L20 von_factor_A_domain_1 ATP_containing_3B . .

5. UNIX for Dummies Questions & Answers

look for file size greater than "0" of specific pattern and move those to another directory

Hi , i have some files of specific pattern ...i need to look for files which are having size greater than zero and move those files to another directory.. Ex... abc_0702, abc_0709, abc_782 abc_1234 ...etc need to find out which is having the size >0 and move those to target directory.....

6. Shell Programming and Scripting

Rename the file with specific pattern

Hello I am making a script where I need to rename the files but with different names.The file name could be change according to the product I made a logic but that is not working properly arr=$(echo a@b@c | tr "@" "\n") echo $arr output is a b c arry=$(echo d@e@f | tr "@" "\n") ...

7. Shell Programming and Scripting

Extract specific line in an html file starting and ending with specific pattern to a text file

Hi This is my first post and I'm just a beginner. So please be nice to me. I have a couple of html files where a pattern beginning with "http://www.site.com" and ending with "/resource.dat" is present on every 241st line. How do I extract this to a new text file? I have tried sed -n 241,241p...

8. Shell Programming and Scripting

Rename specific file extension in directory with match to another file in bash

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...

9. UNIX for Beginners Questions & Answers

How to zip csv files having specific pattern in a directory using UNIX shell script?

I have files in a Linux directory . Some of the file is listed below -rw-rw-r--. 1 roots roots 0 Dec 23 02:17 zzz_123_00000_A_1.csv -rw-rw-r--. 1 roots roots 0 Dec 23 02:18 zzz_121_00000_A_2.csv -rw-rw-r--. 1 roots roots 0 Dec 23 02:18 zzz_124_00000_A_3.csv drwxrwxr-x. 2 roots roots 6 Dec 23...

10. Shell Programming and Scripting

Match all lines in file where specific text pattern is less than

In the below file I am trying to grep or similar, all lines where only AF= is less than 0.4.. Thank you :). grep grep "AF=" ,+ .4 file file 12 112036782 . T C 34.0248 PASS ...

LEARN ABOUT DEBIAN

vcf-compare

VCF-COMPARE(1)							   User Commands						    VCF-COMPARE(1)

NAME

       vcf-compare - compare bgzipped and tabix indexed VCF files

SYNOPSIS

       compare-vcf [OPTIONS] file1.vcf file2.vcf ...

DESCRIPTION

       About: Compare bgzipped and tabix indexed VCF files. (E.g. bgzip file.vcf; tabix -p vcf file.vcf.gz)

OPTIONS

       -c, --chromosomes <list|file>
	      Same as -r, left for backward compatibility. Please do not use as it will be dropped in the future.

       -d, --debug
	      Debugging information. Giving the option multiple times increases verbosity

       -H, --cmp-haplotypes
	      Compare haplotypes, not only positions

       -m, --name-mapping <list|file>
	      Use  with -H when comparing files with differing column names. The argument to this options is a comma-separated list or one mapping
	      per line in a file. The names are colon separated and must appear in the same order as the files on the command line.

       -R, --refseq <file>
	      Compare the actual sequence, not just positions. Use with -w to compare indels.

       -r, --regions <list|file>
	      Process the given regions (comma-separated list or one region per line in a file).

       -s, --samples <list>
	      Process only the listed samples. Excluding unwanted samples may increase performance considerably.

       -w, --win <int>
	      In repetitive sequences, the same indel can be called at different positions. Consider records this far apart as matching (be  it  a
	      SNP or an indel).

       -h, -?, --help
	      This help message.

vcf-compare 0.1.5						     July 2011							    VCF-COMPARE(1)