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Full Discussion: Remove empty records
Top Forums Shell Programming and Scripting Remove empty records Post 302639107 by yifangt on Friday 11th of May 2012 08:17:45 AM
Old 05-11-2012
Remove empty records
Hello:
Is there a simple way to remove empty records of FASTA format file?
A FASTA format consists of two parts: header and sequence (for non-biologist, Wiki for details of course!). The header always start with ">" for the name of the sequence. The header must be in this ONLY single line. Following the header are the sequence that can be in single or multiple rows. Example:
Code:
>header1
ACGATAGCTCTAGCTAGCTA
>header2
GGCGCTATG
>other header name
GCGGCGGGGCGTTTAAA
ATCGAT

I have a file some of which only have headers but not sequence (i.e. empty sequences). I need to remove them.
Input file:
Code:
>head1
ACGATAGCTCTAGCTAGCTA
>header2
GGCGCTATGGCGACTGATCAGC
CCGAAAGATGCT
>other header name
>some thing maybe long but single line for sure
GCTAGCTAGCA
>something 
>strange header 2
AGCTAGCTGAGGGAGGAGGGA
>some description  
>other description  2
CGTAGCTAGGTAGATTTA
>something not good for me

ouput
Code:
>head1
ACGATAGCTCTAGCTAGCTA
 >header2
 GGCGCTATGGCGACTGATCAGC
CCGAAAGATGCT
 >some thing maybe long but single line for sure
GCTAGCTAGCA
>strange header 2
AGCTAGCTGAGGGAGGAGGGA
 >other description  2
 CGTAGCTAGGTAGATTTA

There are bioperl scripts and other tools to do the job. I was thinking there must be a simpler handy way with sed or awk to do it, especially on the terminal for smaller files. Perl oneliner works too, but I have problem with the "$/" variable as the input sequence can be different multiple rows.
Could not figure this out by myself. Post it here for to get experts' ideas. Thanks in advance!
Yifang
 

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LEARN ABOUT DEBIAN

hhconsensus

HHCONSENSUS(1)							   User Commands						    HHCONSENSUS(1)

NAME

       hhconsensus - calculate the consensus sequence for an A3M/FASTA input file

SYNOPSIS

       hhconsensus -i <file> [options]

DESCRIPTION

       HHconsensus  version  2.0.15  (June 2012) Calculate the consensus sequence for an A3M/FASTA input file.	(C) Johannes Soeding, Michael Rem-
       mert, Andreas Biegert, Andreas Hauser Remmert M, Biegert A, Hauser A, and Soding J.  HHblits:  Lightning-fast  iterative  protein  sequence
       searching by HMM-HMM alignment.	Nat. Methods 9:173-175 (2011).

       -i <file>
	      query alignment (A2M, A3M, or FASTA), or query HMM

   Output options:
       -s <file>
	      append consensus sequence in FASTA (default=<infile.seq>)

       -o <file>
	      write alignment with consensus sequence in A3M

       -oa3m <file>
	      same

       -oa2m <file>
	      write alignment with consensus sequence in A2M

       -ofas <file>
	      write alignment with consensus sequence in FASTA

       -v <int>
	      verbose mode: 0:no screen output	1:only warings	2: verbose

   Filter input alignment (options can be combined):
       -id    [0,100] maximum pairwise sequence identity (%) (def=100)

       -diff [0,inf[ filter most diverse set of sequences, keeping at least this

	      many sequences in each block of >50 columns (def=0)

       -cov   [0,100] minimum coverage with query (%) (def=0)

       -qid   [0,100] minimum sequence identity with query (%) (def=0)

       -qsc   [0,100] minimum score per column with query  (def=-20.0)

   Input alignment format:
       -M a2m use A2M/A3M (default): upper case = Match; lower case = Insert; '-' = Delete; '.' = gaps aligned to inserts (may be omitted)

       -M first
	      use FASTA: columns with residue in 1st sequence are match states

       -M [0,100]
	      use FASTA: columns with fewer than X% gaps are match states

   Other options:
       -addss add predicted secondary structure information from PSIPRED

       Example: hhconsensus -i stdin -s stdout

hhconsensus 2.0.15						     June 2012							    HHCONSENSUS(1)
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