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Full Discussion: Concatenate lines between lines starting with a specific pattern
Top Forums Shell Programming and Scripting Concatenate lines between lines starting with a specific pattern Post 302465492 by s052866 on Friday 22nd of October 2010 02:54:07 PM
Old 10-22-2010
Concatenate lines between lines starting with a specific pattern
Hi,

I have a file such as:
---
>contig00001 length=35524 numreads=2944
gACGCCGCGCGCCGCGGCCAGGGCTGGCCCA
CAGGCCGCGCGGCGTCGGCTGGCTGAG
>contig00002 length=4242 numreads=43423
ATGCCGAAGGTCCGCCTGGGGCTGG
CGCCGGGAGCATGTAGCG
---
I would like to concatenate the lines not starting with ">" (concatenate any lines between lines starting with ">"). My wanted output is:
---
>contig00001 length=35524 numreads=2944
gACGCCGCGCGCCGCGGCCAGGGCTGGCCCACAGGCCGCGCGGCGTCGGCTGGCTGAG
>contig00002 length=4242 numreads=43423
ATGCCGAAGGTCCGCCTGGGGCTGGCGCCGGGAGCATGTAGCG
---

Thanks



---------- Post updated at 01:54 PM ---------- Previous update was at 01:48 PM ----------




I have tried like this:
% awk '{if(substr($0,1)==">") print $0"\n";else printf("%s",$0);}' test2.fna | fold -w60
But my output looks like:
Code:
>contig00001 length=35524   numreads=2944gACGCCGCGCGCCGCGGCC
AGGGCTGGCCCACGGCCcTCTTCCGGCGCGCTGCGCAGGCGTTCGGCCAGGCCGCGCGGC
GTCGGCTGGCTGAGCGCCCAGCGTAGCAGGCGATCGAACGGATGCCGACGGGCGCTTTCC
AGTCGTTCGCGCAAACGGGCGATCAACTGGGCGATCAACAGCGAGTCGCCGCCAGCCCCG
AAGAAGTCTTGCTCGACGCCCAGCGACGGGTTGTCCAGCACCTCCCGCCAGAGTGCCAGC

Instead of what I want which is like this:
Code:
>contig00001 length=35524   numreads=2944
gACGCCGCGCGCCGCGGCCAGGGCTGGCCCACGGCCcTCTTCCGGCGCGCTGCGCAGGCG
TTCGGCCAGGCCGCGCGGCGTCGGCTGGCTGAGCGCCCAGCGTAGCAGGCGATCGAACGG
ATGCCGACGGGCGCTTTCCAGTCGTTCGCGCAAACGGGCGATCAACTGGGCGATCAACAG
CGAGTCGCCGCCAGCCCCGAAGAAGTCTTGCTCGACGCCCAGCGACGGGTTGTCCAGCAC
CTCCCGCCAGAGTGCCAGC

 

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LEARN ABOUT OPENSOLARIS

lptest

lptest(1B)					     SunOS/BSD Compatibility Package Commands						lptest(1B)

NAME

       lptest - generate line printer ripple pattern

SYNOPSIS

       /usr/ucb/lptest [length [count]]

DESCRIPTION

       The  lptest  utility  writes the traditional ripple test pattern to the standard output. In 96 lines, the ripple test pattern prints all 96
       printable ASCII characters in each position. The ripple test pattern was originally created to test printers.  It is also useful for  test-
       ing terminals, driving terminal ports, debugging, and performing tasks that require a quick supply of random data.

       This command is obsolete.

OPTIONS

       length	 Specifies the length of the output line in characters. 79 characters is the default.

       count	 Specifies the number of output lines. 200 lines is the default. If  count is specified, length must also be specified.

EXIT STATUS

       The following exit values are returned:

       0	   Successful completion.

       non-zero    An error occurred.

ATTRIBUTES

       See attributes(5) for descriptions of the following attributes:

       +-----------------------------+-----------------------------+
       |      ATTRIBUTE TYPE	     |	    ATTRIBUTE VALUE	   |
       +-----------------------------+-----------------------------+
       |Availability		     |SUNWscplp 		   |
       +-----------------------------+-----------------------------+

SEE ALSO

       attributes(5)

SunOS 5.11							    9 Sep 1996								lptest(1B)
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