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Full Discussion: Using multiple pipe output
Top Forums UNIX for Dummies Questions & Answers Using multiple pipe output Post 302682611 by jrymer on Monday 6th of August 2012 01:32:30 PM
Old 08-06-2012
Using multiple pipe output
I have a script that finds all sffs and extracts them into .fastq file types. What I need to do is change the .fastq to .fasta using the below script. How can I change the input.fastq and output.fasta to mirror the file's name? Would I use an array and use the default iterator?

Code:
#!/bin/bash

find . -type f -name \*.sff | xargs python /usr/local/bin/sff_extract.py

find . -type f -name \*.fastq | xargs awk 'BEGIN{P=1}{if(P==1||P==2){gsub(/^[@]/,">");print}; if(P==4)P=0; P++}' input.fastq > output.fasta

 

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LEARN ABOUT DEBIAN

bio::seqio::fasta

Bio::SeqIO::fasta(3pm)					User Contributed Perl Documentation				    Bio::SeqIO::fasta(3pm)

NAME

       Bio::SeqIO::fasta - fasta sequence input/output stream

SYNOPSIS

       Do not use this module directly.  Use it via the Bio::SeqIO class.

DESCRIPTION

       This object can transform Bio::Seq objects to and from fasta flat file databases.

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 one
       of the Bioperl mailing lists.  Your participation is much appreciated.

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

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address
       it. Please include a thorough description of the problem with code and data examples if at all possible.

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

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

AUTHORS - Ewan Birney &; Lincoln Stein
       Email: birney@ebi.ac.uk
	      lstein@cshl.org

CONTRIBUTORS

       Jason Stajich, jason-at-bioperl.org

APPENDIX

       The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

   next_seq
	Title	: next_seq
	Usage	: $seq = $stream->next_seq()
	Function: returns the next sequence in the stream
	Returns : Bio::Seq object, or nothing if no more available
	Args	: NONE

   write_seq
	Title	: write_seq
	Usage	: $stream->write_seq(@seq)
	Function: Writes the $seq object into the stream
	Returns : 1 for success and 0 for error
	Args	: Array of 1 or more Bio::PrimarySeqI objects

   width
	Title	: width
	Usage	: $obj->width($newval)
	Function: Get/Set the line width for FASTA output
	Returns : value of width
	Args	: newvalue (optional)

   preferred_id_type
	Title	: preferred_id_type
	Usage	: $obj->preferred_id_type('accession')
	Function: Get/Set the preferred type of identifier to use in the ">ID" position
		  for FASTA output.
	Returns : string, one of values defined in @Bio::SeqIO::fasta::SEQ_ID_TYPES.
		  Default = $Bio::SeqIO::fasta::DEFAULT_SEQ_ID_TYPE ('display').
	Args	: string when setting. This must be one of values defined in
		  @Bio::SeqIO::fasta::SEQ_ID_TYPES. Allowable values:
		  accession, accession.version, display, primary
	Throws	: fatal exception if the supplied id type is not in @SEQ_ID_TYPES.

perl v5.14.2							    2012-03-02						    Bio::SeqIO::fasta(3pm)
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