From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Tue, 1 Jul 2008 00:56:10 +0000 (+0000)
Subject: update wiki
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=9027c10642c4924a43b8c59e8564cf6c787dcd7b;p=biopieces.git

update wiki

git-svn-id: http://biopieces.googlecode.com/svn/trunk@87 74ccb610-7750-0410-82ae-013aeee3265d
---

diff --git a/bp_usage/read_bed b/bp_usage/read_bed
deleted file mode 100644
index 7058f73..0000000
--- a/bp_usage/read_bed
+++ /dev/null
@@ -1,35 +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:    Read BED data (Browser Extensible Data).
-
-Usage:          read_bed [options] -i <BED file(s)>
-
-Options:  [-i <file(s)> | --data_in=<file(s)>]  -  Read input data from file.
-Options:  [-n <int>     | --num=<int>]          -  Limit number of records to read.
-Options:  [-I <file>    | --stream_in=<file>]   -  Read input stream from file  -  Default=STDIN
-Options:  [-O <file>    | --stream_out=<file>]  -  Write output stream to file  -  Default=STDOUT
-
-Examples:  read_bed -i test1.bed,test2.bed
-Examples:  read_bed -i '*.bed'
-
-Keys out: CHR         -  Chromosome name.
-Keys out: CHR_BEG     -  Chromosome begin position.
-Keys out: CHR_END     -  Chromoeoms end position.
-Keys out: Q_ID        -  Query ID (feature name).
-Keys out: SCORE       -  Score.
-Keys out: STRAND      -  Strand.
-Keys out: THICK_BEG   -  The starting position at which the feature is drawn thickly.
-Keys out: THICK_END   -  The ending position at which the feature is drawn thickly.
-Keys out: ITEMRGB     -  An RGB value of the form R,G,B (e.g. 255,0,0).
-Keys out: BLOCKCOUNT  -  The number of blocks (exons) in the BED entry.
-Keys out: BLOCKSIZES  -  A comma separated list of the block sizes.
-Keys out: Q_BEGS      -  A comma separated list of block starts.
-Keys out: REC_TYPE    -  Record type.
-Keys out: BED_LEN     -  Length of BED entry.
-Keys out: BED_COLS    -  Number of columns in BED line.
diff --git a/bp_usage/read_bed.wiki b/bp_usage/read_bed.wiki
new file mode 100644
index 0000000..959a1d9
--- /dev/null
+++ b/bp_usage/read_bed.wiki
@@ -0,0 +1,121 @@
+=Biopiece: read_bed=
+
+==Synopsis==
+
+Read BED data (Browser Extensible Data).
+
+==Description==
+
+The BED (Browser Extensible Data) format is a tabular format for data pertaining to one of the Eukaryotic genomes in the UCSC genome brower. The BED format consists
+of up to 12 columns, where the first three are mandatory.
+
+  # CHR - the name of the chromosome.
+  # CHR_BEG  - the chromosome begin position.
+  # CHR_END  - the chromosome end position.
+  # Q_ID - the name of the feature.
+  # SCORE - a score between 0 and 1000.
+  # STRAND - the orientation of the feature.
+  # THICK_BEG - begin position of 'thick' drawing used for UTRs.
+  # THICK_END - end position of 'thick' drawing used for UTRs.
+  # ITEMRGB - RGB color code for feature.
+  # BLOCKCOUNT - number of exon blocks.
+  # BLOCKSIZES - list of block sizes.
+  # Q_BEGS - list of block begins.
+
+Furthermore, an extra three helper columns are added to the record by [read_bed]:
+
+  # REC_TYPE - the type of record, here BED.
+  # BED_LEN  - the length of the entire feature.
+  # BED_COLS - the number of BED columns (for speed).
+
+So a typical 12 column BED record looks like this:
+
+{{{
+STRAND: -
+Q_ID: AA695812
+CHR_END: 31601
+THICK_END: 31601
+SCORE: 0
+CHR_BEG: 31176
+BED_LEN: 426
+REC_TYPE: BED
+BLOCKCOUNT: 1
+CHR: chr4
+THICK_BEG: 31176
+Q_BEGS: 0,
+BLOCKSIZES: 426,
+ITEMRGB: 0
+BED_COLS: 12
+---
+}}}
+
+For more about the BED format:
+
+http://genome.ucsc.edu/FAQ/FAQformat#format1
+
+==Usage==
+
+{{{
+read_bed [options] -i <BED 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 BED entries from a file:
+
+{{{
+read_bed -i test.bed
+}}}
+
+To read in only 10 records from a BED file:
+
+{{{
+read_bed -n 10 -i test.bed
+}}}
+
+To read all BED entries from multiple files:
+
+{{{
+read_bed -i test1.bed,test2.bed
+}}}
+
+To read BED entries from multiple files using a glob expression:
+
+{{{
+read_bed -i '*.bed'
+}}}
+
+
+==See also==
+
+[write_bed]
+
+==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_bed] is part of the Biopieces framework.
+
+http://code.google.com/p/biopieces/
+
diff --git a/bp_usage/read_fasta.wiki b/bp_usage/read_fasta.wiki
index 087c8cf..71cb621 100644
--- a/bp_usage/read_fasta.wiki
+++ b/bp_usage/read_fasta.wiki
@@ -57,7 +57,7 @@ To read all FASTA entries from multiple files:
 read_fasta -i test1.fna,test2.fna
 }}}
 
-To read FASTS entries from multiple files using a glob expression:
+To read FASTA entries from multiple files using a glob expression:
 
 {{{
 read_fasta -i '*.fna'