Login or Register to Ask a Question and Join Our Community

Sponsored Content
Full Discussion: Concatenating sequence length to another file
Top Forums UNIX for Beginners Questions & Answers Concatenating sequence length to another file Post 303031922 by rdrtx1 on Thursday 7th of March 2019 03:14:42 PM
Old 03-07-2019
Code:
for file in *.fa;
do
  awk '
  NR==FNR {
     if ($0 ~ /^>/ && why_print_seqlen_for_this_line) {if (seqlen) print seqlen; next;}
     # is there a record separator /^>/ in the *.fa files not mentioned in samples?

     seqlen += length($0);
     next;
  }
  {print FNR, $0, seqlen}
  ' OFS="\t" $file ${file%.*}_pos.txt > t_$$

  mv -f t_$$ ${file%.*}_pos.txt
done

This User Gave Thanks to rdrtx1 For This Post:
Ibk
 

10 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

Concatenating values in a File

Hi All, I have a ',' delimited file and i would like concatenate a new value at a specific column. Example :- xXXX,XYZ,20071005,ABC,DEF,123 xXXX,XYZ,20071005,ABC,DEF,123 xXXX,XYZ,20071005,ABC,DEF,123 The output that i want is xXXX,XYZ,20071005001,ABC,DEF,123... (7 Replies)
Discussion started by: amitkhiare
7 Replies

2. Shell Programming and Scripting

Concatenating the two lines in a file

hi My requirement is i have a file with some records like this file name ::xyz a=1 b=100,200 ,300,400 ,500,600 c=700,800 d=900 i want to change my file a=1 b=100,200,300,400 c=700,800 d=900 if record starts with " , " that line should fallows the previous line.please give... (6 Replies)
Discussion started by: srivsn
6 Replies

3. UNIX for Dummies Questions & Answers

What the command to find out the record length of a fixed length file?

I want to find out the record length of a fixed length file? I forgot the command. Any body know? (9 Replies)
Discussion started by: tranq01
9 Replies

4. UNIX for Dummies Questions & Answers

Convert a tab delimited/variable length file to fixed length file

Hi, all. I need to convert a file tab delimited/variable length file in AIX to a fixed lenght file delimited by spaces. This is the input file: 10200002<tab>US$ COM<tab>16/12/2008<tab>2,3775<tab>2,3783 19300978<tab>EURO<tab>16/12/2008<tab>3,28523<tab>3,28657 And this is the expected... (2 Replies)
Discussion started by: Everton_Silveir
2 Replies

5. Shell Programming and Scripting

Concatenating File and String for Sendmail

I want o add a variable in addition to a file which will be send with sendmail. I have problems to find the correct syntax for concatenating this variable called $MyVariable. sendmail mai@domain.com </tmp/errormessage.txt $MyVariable] Thanks for your help! (2 Replies)
Discussion started by: high5
2 Replies

6. Shell Programming and Scripting

Concatenating fixed length lines in shell script

I have a peculiar file with record format like given below. Each line is wrapped to next lines after certain number of characters. I want to concatenate all wrapped lines into 1. Input:(wrapped after 10 columns) This is li ne1 This is li ne2 and this line is too lo ng Shortline ... (8 Replies)
Discussion started by: kmanyam
8 Replies

7. Shell Programming and Scripting

Flat file-make field length equal to header length

Hello Everyone, I am stuck with one issue while working on abstract flat file which i have to use as input and load data to table. Input Data- ------ ------------------------ ---- ----------------- WFI001 Xxxxxx Control Work Item A Number of Records ------ ------------------------... (5 Replies)
Discussion started by: sonali.s.more
5 Replies

8. Shell Programming and Scripting

find common entries and match the number with long sequence and cut that sequence in output

Hi all, I have a file like this ID 3BP5L_HUMAN Reviewed; 393 AA. AC Q7L8J4; Q96FI5; Q9BQH8; Q9C0E3; DT 05-FEB-2008, integrated into UniProtKB/Swiss-Prot. DT 05-JUL-2004, sequence version 1. DT 05-SEP-2012, entry version 71. FT COILED 59 140 ... (1 Reply)
Discussion started by: manigrover
1 Replies

9. Shell Programming and Scripting

Concatenating 3 files into a single file

I have 3 files File1 C1 C2 c3 File 2 C1 c2 c3 File 3 C1 c2 c3 Now i want to have File1 as C1 c2 c3 I File2 as C1 c2 c3 O File3 as c1 c2 c3 D and these 3 files should be concatenated into a single file how can it be done in unix script? (3 Replies)
Discussion started by: Codesearcher
3 Replies

10. UNIX for Dummies Questions & Answers

ConCATenating binaries but excluding last bytes from each file

Hi there, shameful Linux Newbie here :p I was wondering if you could help with my problem... I have plenty of files I'd like to concatenate. I know how to basically use cat command but that won't be enough from what I need : excluding the last xx bytes from files before assembling since there's... (4 Replies)
Discussion started by: grolido
4 Replies

LEARN ABOUT REDHAT

mac2unix

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)
All times are GMT -4. The time now is 06:46 AM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy