zzz

git-svn-id: http://biopieces.googlecode.com/svn/trunk@78 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_usage/read_fasta.wiki b/bp_usage/read_fasta.wiki
index 45a065aa0d810ce4cc904fd8987a19a05f51276a..c76e81085cc7376cb40e2d333d4ad2c70ea291db 100644 (file)
--- a/bp_usage/read_fasta.wiki
+++ b/bp_usage/read_fasta.wiki
@@ -35,7 +35,7 @@ read_fasta [options] -i <FASTA file(s)>
 [-O <file>    | --stream_out=<file>]  -  Write output stream to file  -  Default=STDOUT
 }}}
 
-==Examples=
+==Examples==
 
 To read all FASTA entries from a file:
 

diff --git a/bp_usage/write_fasta.wiki b/bp_usage/write_fasta.wiki
new file mode 100644 (file)
index 0000000..11ec7c4
--- /dev/null
+++ b/bp_usage/write_fasta.wiki
@@ -0,0 +1,76 @@
+=Biopiece: write_fasta=
+
+==Synopsis==
+
+Write sequences from stream in FASTA format.
+
+==Description==
+
+*write_fasta* writes sequence from the data stream in FASTA format. However, a FASTA entry will only be written if a SEQ key and a SEQ_NAME key is present. If a SEQ key is present and not SEQ_NAME, then the Q_ID key will be used as SEQ_NAME - if such a key is found.
+
+For more about the FASTA format:
+
+http://en.wikipedia.org/wiki/Fasta_format
+
+==Usage==
+
+{{{
+... | write_fasta [options]
+}}}
+
+==Options==
+
+{{{
+[-x        | --no_stream]          -  Do not emit records.
+[-o <file> | --data_out=<file>]    -  Write result to file.
+[-w <int>  | --wrap=<int>]         -  Wrap sequences to a given width.
+[-I <file> | --stream_in=<file>]   -  Read input from stream file  -  Default=STDIN
+[-O <file> | --stream_out=<file>]  -  Write output to stream file  -  Default=STDOUT
+[-Z        | --compress]           -  Compress output using gzip.
+}}}
+
+==Examples==
+
+Writing entries wrapped to blocks of 80 to STDOUT.
+
+{{{
+... | write_fasta -x -w 80
+}}}
+
+Writing entries to file 'test.fna'.
+
+{{{
+... | write_fasta -x -o test.fna
+}}}
+
+Write zipped entries to file 'test.fna.gz'.
+
+{{{
+... | write_fasta -x -Z -o test.fna.gz
+}}}
+
+==See also==
+
+[read_fasta]
+[read_align]
+
+==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==
+
+*write_fasta* is part of the Biopieces framework.
+
+http://code.google.com/p/biopieces/
+