parse fasta file to tabular file Post: 302584570

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Top Forums Shell Programming and Scripting parse fasta file to tabular file Post 302584570 by yifangt on Friday 23rd of December 2011 04:55:17 PM

12-23-2011

Registered User

parse fasta file to tabular file

Hello,
A bioperl problem I thought could be done with awk: convert the fasta format (Note: the length of each row is not the same for each entry as they were combined from different files!) to tabular format.

Code:

input.fasta:

>YAL069W-1.334 Putative promoter sequence
CCACACCACACCCACACACCCACACACCACACCACACACC
ACACCACACCCACACACACACATCCTAACACTACCCTAAC
ACAGCCCTAATCTAACCCTGGCCAACCTGTCTCTCAACTT
>YAL068C-7235.2170 Putative promoter sequence
TACGAGAATAATTTCTCATCATCCAGCTTTAACACAAAAT
ACGTAAATGAAGTTTATATATAAATTTCCTTTTTATTGGA
>gi|31044174|gb|AY143560.1| Tintinnopsis fimbriata 18S ribosomal RNA gene, partial sequence
GAAACTGCGAATGGCTCATTAAAACAGTTATAGTTTATTTGGTAATCAAACTTACATGGATAACCGTGG
TAATTCTAGAGCTAATACATGCTGTTGTGCCCGACTCACGAAGGGCGGTATTTATTAGATATCAGCCAATA
AGCATCTGCTATTGTGGTGACTCATAGTAACTTAATCGGATCGCATGGGCTTGTCCCGCGACAAACCATT
>gi|31044185|gb|AY143571.1| Codonellopsis americana 18S ribosomal RNA gene, partial sequence
ATTACCCAATCCTGACTCAGGGAGGTAGTGACAAGAAATAATGGGTCGGGGTTCTGCCCCGGGACTGCA
GGGCACCACCAGGCGTGGAGCTTGCGGCTCAATTTGACTCAACACGGGGAAACTTACCAGGTCCAGACAT

I want to convert it to the tabular format as:

Code:

output.tab:

>YAL069W-1.334 Putative promoter sequence CCACACCACACCCACACACCCACACA......CACAGCCCTAATCTAACCCTGGCCAACCTGTCTCTCAACTT
>YAL068C-7235.2170 Putative promoter sequence TACGAGAATAATTTCTCATCATCCAG......CATTTTCTTATGACGTAAATGAAGTTTATATATAAATTTCCTTTTTATTGGA
>gi|31044174|gb|AY143560.1| Tintinnopsis fimbriata 18S ribosomal RNA gene, partial sequence GAAACTGCGAATGGCTCA......ATTGTGGTGACTCATAGTAACTTAATCGGATCGCATGGGCTTGTCCCGCGACAAACCATT
>gi|31044185|gb|AY143571.1| Codonellopsis americana 18S ribosomal RNA gene, partial sequence ATTACCCAATCCTGACTC......CCAGGCGTGGAGCTTGCGGCTCAATTTGACTCAACACGGGGAAACTTACCAGGTCCAGACAT

i.e. each row has two columns: the first one is the header for the sequence name and description, the second column is the DNA sequence. This is quite common in bioinformatics daily task.
I am aware bioperl is the right tool to do the job, but I am trying to level up my awk when I read the RS variable. Not sure how to handle this situation for the RS and the FS variables.
Thanks a lot!

yifangt

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LEARN ABOUT DEBIAN

bp_aacomp

BP_AACOMP(1p)						User Contributed Perl Documentation					     BP_AACOMP(1p)

NAME

       aacomp - amino acid composition of protein sequences

SYNOPSIS

	 aacomp [-f/--format FORMAT] [-h/--help] filename
	 or
	 aacomp [-f/--format FORMAT] < filename
	 or
	 aacomp [-f/--format FORMAT] -i filename

DESCRIPTION

       This scripts prints out the count of amino acids over all protein sequences from the input file.

OPTIONS

       The default sequence format is fasta.

       The sequence input can be provided using any of the three methods:

       unnamed argument
	    aacomp filename

       named argument
	    aacomp -i filename

       standard input
	    aacomp < filename

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the
       Bioperl mailing list.  Your participation is much appreciated.

	 bioperl-l@bioperl.org			- General discussion
	 http://bioperl.org/wiki/Mailing_lists	- About the mailing lists

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the
       web:

	 https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Jason Stajich
       Email jason@bioperl.org

HISTORY

       Based on aacomp.c from an old version of EMBOSS

perl v5.14.2							    2012-03-02							     BP_AACOMP(1p)