even more wikis

git-svn-id: http://biopieces.googlecode.com/svn/trunk@100 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_usage/complement_seq b/bp_usage/complement_seq
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--- a/bp_usage/complement_seq
+++ /dev/null
@@ -1,16 +0,0 @@
-Author:         Martin Asser Hansen - Copyright (C) - All rights reserved
-
-Contact:        mail@maasha.dk
-
-Date:           August 2007
-
-License:        GNU General Public License version 2 (http://www.gnu.org/copyleft/gpl.html)
-
-Description:    Complement sequences in stream.
-
-Usage:          ... | $script [options]
-
-Options:  [-I <file> | --stream_in=<file>]   -  Read input from stream file   -  Default=STDIN
-Options:  [-O <file> | --stream_out=<file>]  -  Write output to stream file   -  Default=STDOUT
-
-Examples:  ... | $script  -  Complements all sequences in stream.

diff --git a/bp_usage/complement_seq.wiki b/bp_usage/complement_seq.wiki
new file mode 100644 (file)
index 0000000..fb573bc
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+++ b/bp_usage/complement_seq.wiki
@@ -0,0 +1,56 @@
+=Biopiece: complement_seq=
+
+==Synopsis==
+
+Complement nucleotide sequences in the stream.
+
+==Description==
+
+[complement_seq] complements nucleotide sequences in the stream which along with [reverse_seq]
+results in reverse/complemented sequence.
+
+==Usage==
+
+{{{
+... | complement_seq [options]
+}}}
+
+==Options==
+
+{{{
+[-I <file> | --stream_in=<file>]   -  Read input from stream file   -  Default=STDIN
+[-O <file> | --stream_out=<file>]  -  Write output to stream file   -  Default=STDOUT
+}}}
+
+==Examples==
+
+To reverse complement sequence first reverse the sequence with [reverse_seq] and then
+complement it using [complement_seq] (or visa versa):
+
+{{{
+... | complement_seq | reverse_seq
+}}}
+
+==See also==
+
+[reverse_seq]
+
+==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==
+
+[complement_seq] is part of the Biopieces framework.
+
+http://code.google.com/p/biopieces/

diff --git a/bp_usage/count_records b/bp_usage/count_records
deleted file mode 100644 (file)
index 8662a50..0000000
--- a/bp_usage/count_records
+++ /dev/null
@@ -1,19 +0,0 @@
-Author:         Martin Asser Hansen - Copyright (C) - All rights reserved
-
-Contact:        mail@maasha.dk
-
-Date:           August 2007
-
-License:        GNU General Public License version 2 (http://www.gnu.org/copyleft/gpl.html)
-
-Description:    Count the number of records in stream.
-
-Usage:          ... | count_records [options]
-
-Options:   [-x        | --no_stream]          -  Do not emit records.
-Options:   [-o <file> | --data_out=<file>]    -  Write result to file.
-Options:   [-I <file> | --stream_in=<file>]   -  Read input from stream file  -  Default=STDIN
-Options:   [-O <file> | --stream_out=<file>]  -  Write output to stream file  -  Default=STDOUT
-
-Examples:  ... | count_records -x -o count.txt  -  Count records in stream and write result to 'count.txt'
-

diff --git a/bp_usage/count_records.wiki b/bp_usage/count_records.wiki
new file mode 100644 (file)
index 0000000..53b802b
--- /dev/null
+++ b/bp_usage/count_records.wiki
@@ -0,0 +1,65 @@
+=Biopiece: count_records=
+
+==Synopsis==
+
+Count the number of records in the stream.
+
+==Description==
+
+[count_records] count the number of records in the stream and outputs the count as a
+record who's count is _not_ included. Using [count_recrods] with the `-x` switch is
+a lot faster because this prevents the need for parsing and emitting the records.
+
+==Usage==
+
+{{{
+... | count_records [options]
+}}}
+
+==Options==
+
+{{{
+[-x        | --no_stream]          -  Do not emit records.
+[-o <file> | --data_out=<file>]    -  Write result to file.
+[-I <file> | --stream_in=<file>]   -  Read input from stream file  -  Default=STDIN
+[-O <file> | --stream_out=<file>]  -  Write output to stream file  -  Default=STDOUT
+}}}
+
+==Examples==
+
+To count the records in the stream and saving the result to file, do:
+
+{{{
+... | count_record -o <file>
+}}}
+
+The resulting file will then contain some thing like this:
+
+{{{
+count_records: 1234
+---
+}}}
+
+==See also==
+
+[count_vals]
+
+==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==
+
+[count_records] is part of the Biopieces framework.
+
+http://code.google.com/p/biopieces/

diff --git a/bp_usage/reverse_seq b/bp_usage/reverse_seq
deleted file mode 100644 (file)
index 594ec8b..0000000
--- a/bp_usage/reverse_seq
+++ /dev/null
@@ -1,17 +0,0 @@
-Author:         Martin Asser Hansen - Copyright (C) - All rights reserved
-
-Contact:        mail@maasha.dk
-
-Date:           August 2007
-
-License:        GNU General Public License version 2 (http://www.gnu.org/copyleft/gpl.html)
-
-Description:    Reverse sequences in stream.
-
-Usage:          ... | reverse_seq [options]
-
-Options:   [-I <file> | --stream_in=<file>]   -  Read input from stream file   -  Default=STDIN
-Options:   [-O <file> | --stream_out=<file>]  -  Write output to stream file   -  Default=STDOUT
-
-Examples: ... | reverse_seq  -  Reverses all sequences in stream.
-

diff --git a/bp_usage/reverse_seq.wiki b/bp_usage/reverse_seq.wiki
new file mode 100644 (file)
index 0000000..41d9225
--- /dev/null
+++ b/bp_usage/reverse_seq.wiki
@@ -0,0 +1,71 @@
+=Biopiece: reverse_seq=
+
+==Synopsis==
+
+Reverse sequences in the stream.
+
+==Description==
+
+[reverse_seq] reverses sequences in the stream which is useful for extracting subsequences
+[extract_seq] or reverse complementing sequence [complement_seq].
+
+==Usage==
+
+{{{
+... | reverse_seq [options]
+}}}
+
+==Options==
+
+{{{
+[-I <file> | --stream_in=<file>]   -  Read input from stream file   -  Default=STDIN
+[-O <file> | --stream_out=<file>]  -  Write output to stream file   -  Default=STDOUT
+}}}
+
+==Examples==
+
+To reverse sequences simply pipe the stream through [reverse_seq]:
+
+{{{
+... | reverse_seq
+}}}
+
+To reverse complement sequence first reverse the sequence with [reverse_seq] and then
+complement it using [complement_seq] (or visa versa):
+
+{{{
+... | reverse_seq | complement_seq
+}}}
+
+To obtain the last  e.g. five residues from all sequences, first use [reverse_seq], then [extract_seq],
+and then re-reverse with [reverse_seq]:
+
+{{{
+... | reverse_seq | extract_seq -l 5 | reverse_seq
+}}}
+
+==See also==
+
+[complement_seq]
+
+[extract_seq]
+
+==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==
+
+[reverse_seq] is part of the Biopieces framework.
+
+http://code.google.com/p/biopieces/

diff --git a/bp_usage/uppercase_seq b/bp_usage/uppercase_seq
deleted file mode 100644 (file)
index bc7c441..0000000
--- a/bp_usage/uppercase_seq
+++ /dev/null
@@ -1,17 +0,0 @@
-Author:         Martin Asser Hansen - Copyright (C) - All rights reserved
-
-Contact:        mail@maasha.dk
-
-Date:           August 2007
-
-License:        GNU General Public License version 2 (http://www.gnu.org/copyleft/gpl.html)
-
-Description:    Uppercases sequences in stream.
-
-Usage:          ... | uppercase_seq [options]
-
-Options:   [-I <file> | --stream_in=<file>]   -  Read input from stream file  -  Default=STDIN
-Options:   [-O <file> | --stream_out=<file>]  -  Write output to file         -  Default=STDOUT
-
-Examples:  ... | uppercase_seq  -  Uppercases all sequences in stream.
-

diff --git a/bp_usage/uppercase_seq.wiki b/bp_usage/uppercase_seq.wiki
new file mode 100644 (file)
index 0000000..4813153
--- /dev/null
+++ b/bp_usage/uppercase_seq.wiki
@@ -0,0 +1,70 @@
+=Biopiece: uppercase_seq=
+
+==Synopsis==
+
+Uppercases sequences in stream.
+
+==Description==
+
+[upppercase_seq] changes all lowercase letter in sequences to uppercase letters.
+
+==Usage==
+
+{{{
+... | uppercase_seq [options]
+}}}
+
+==Options==
+
+{{{
+[-I <file> | --stream_in=<file>]   -  Read input from stream file   -  Default=STDIN
+[-O <file> | --stream_out=<file>]  -  Write output to stream file   -  Default=STDOUT
+}}}
+
+==Examples==
+
+Consider the following sequence entry in FASTA format in the file `test.fna`:
+
+{{{
+>test
+ACGACGCATNNNNNNactgatcga
+}}}
+
+To read in this sequence use [read_fasta] and then [uppercase_seq] to uppercase all letters:
+
+{{{
+read_fasta -i test.fna | uppercase_seq 
+
+SEQ: ACGACGCATNNNNNNACTGATCGA
+SEQ_NAME: test
+SEQ_LEN: 24
+---
+}}}
+
+==See also==
+
+[read_fasta]
+
+[transliterate_seq]
+
+[transliterate_vals]
+
+==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==
+
+[uppercase_seq] is part of the Biopieces framework.
+
+http://code.google.com/p/biopieces/