From 6f24bba0ca28bc3ea452de3d8359d994e59d1076 Mon Sep 17 00:00:00 2001 From: martinahansen Date: Tue, 1 Jul 2008 00:11:44 +0000 Subject: [PATCH] updating write_fasta.wiki git-svn-id: http://biopieces.googlecode.com/svn/trunk@80 74ccb610-7750-0410-82ae-013aeee3265d --- bp_usage/write_fasta | 26 -------------------------- bp_usage/write_fasta.wiki | 6 +++++- 2 files changed, 5 insertions(+), 27 deletions(-) delete mode 100644 bp_usage/write_fasta diff --git a/bp_usage/write_fasta b/bp_usage/write_fasta deleted file mode 100644 index 8c2fbda..0000000 --- a/bp_usage/write_fasta +++ /dev/null @@ -1,26 +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: Write sequences in FASTA format. - -Usage: ... | $script [options] - -Options: [-x | --no_stream] - Do not emit records. -Options: [-o | --data_out=] - Write result to file. -Options: [-w | --wrap=] - Wrap sequences to a given width. -Options: [-I | --stream_in=] - Read input from stream file - Default=STDIN -Options: [-O | --stream_out=] - Write output to stream file - Default=STDOUT -Options: [-Z | --compress] - Compress output using gzip. - -Examples: ... | $script -x -w 80 - Write entries wrapped to blocks of 80 to STDOUT. -Examples: ... | $script -x -o test.fna - Write entries to file 'test.fna'. -Examples: ... | $script -x -Z -o test.fna.gz - Write zipped entries to file 'test.fna.gz'. - -Keys in: SEQ_NAME - Sequence name. -Keys in: Q_ID - Used as sequence name if no SEQ_NAME. -Keys in: SEQ - Sequence. diff --git a/bp_usage/write_fasta.wiki b/bp_usage/write_fasta.wiki index 11ec7c4..dce18b4 100644 --- a/bp_usage/write_fasta.wiki +++ b/bp_usage/write_fasta.wiki @@ -6,7 +6,10 @@ 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. +*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: @@ -52,6 +55,7 @@ Write zipped entries to file 'test.fna.gz'. ==See also== [read_fasta] + [read_align] ==Author== -- 2.39.5