=Biopiece: read_fasta=

==Synopsis==

Read FASTA entries from one or more files.

==Description==

[read_fasta] read in sequence entries from FASTA files. Each sequence entry consists of a
sequence name prefixed by a '>' followed by the sequence name on a line of its own, followed
by one or my lines of sequence until the next entry or the end of the file. The resulting
biopiece record consists of the following record type:

{{{
SEQ_NAME: test
SEQ_LEN: 10
SEQ: ATCGATCGAC
---
}}}

For more about the FASTA format:

http://en.wikipedia.org/wiki/Fasta_format

==Usage==

{{{
read_fasta [options] -i <FASTA file(s)>
}}}

==Options==

{{{
[-i <file(s)> | --data_in=<file(s)>]  -  Comma separated list of files or glob expression to read.
[-n <int>     | --num=<int>]          -  Limit number of records to read.
[-I <file>    | --stream_in=<file>]   -  Read input stream from file  -  Default=STDIN
[-O <file>    | --stream_out=<file>]  -  Write output stream to file  -  Default=STDOUT
}}}

==Examples==

To read all FASTA entries from a file:

{{{
read_fasta -i test.fna
}}}

To read in only 10 records from a FASTA file:

{{{
read_fasta -n 10 -i test.fna
}}}

To read all FASTA entries from multiple files:

{{{
read_fasta -i test1.fna,test2.fna
}}}

To read FASTA entries from multiple files using a glob expression:

{{{
read_fasta -i '*.fna'
}}}


==See also==

[read_align]

[write_fasta]

==Author==

Martin Asser Hansen - Copyright (C) - All rights reserved.

mail@maasha.dk

August 2007

==License==

GNU General Public License version 2

http://www.gnu.org/copyleft/gpl.html

==Help==

[read_fasta] is part of the Biopieces framework.

http://code.google.com/p/biopieces/