From a112a9d22fbbbeaee1077ea24bb14e0edeb6a6c2 Mon Sep 17 00:00:00 2001
From: tcarver <tjc@sanger.ac.uk>
Date: Mon, 12 Nov 2012 14:21:20 +0000
Subject: [PATCH] add section on sequence and annotation file formats
---
docs/file_menu.sgml | 66 +--------------------------------------------
1 file changed, 1 insertion(+), 65 deletions(-)
diff --git a/docs/file_menu.sgml b/docs/file_menu.sgml
index 64cc961f3..d9c1a5033 100644
--- a/docs/file_menu.sgml
+++ b/docs/file_menu.sgml
@@ -25,74 +25,10 @@ LINKEND="CONCEPTS-ACTIVEENTRY">) and will be the new default entry (see <XREF
LINKEND="CONCEPTS-DEFAULTENTRY">).
</PARA>
<PARA>
+See <XREF LINKEND="FILETYPES">.
This function only reads the feature section of the input file - the sequence
(if any) is ignored.
</PARA>
- <PARA>
-&prog; can read these feature file formats:
- </PARA>
- <ITEMIZEDLIST>
- <LISTITEM>
- <PARA>
- <ULINK URL="http://www.ebi.ac.uk/embl/Documentation/">EMBL or GenBank feature tables</ULINK>
- </PARA>
- </LISTITEM>
- <LISTITEM>
- <PARA>
- <ULINK URL="http://www.sequenceontology.org/gff3.shtml">GFF Version 3 files</ULINK>
- </PARA>
- </LISTITEM>
- <LISTITEM>
- <PARA>
- FASTA files
- </PARA>
- </LISTITEM>
- <LISTITEM>
- <PARA>
- Indexed FASTA files can be read in. The files are indexed
-using <ULINK URL="http://samtools.sourceforge.net/">SAMtools</ULINK>:
- </PARA>
- <SYNOPSIS>
-samtools faidx ref.fasta
- </SYNOPSIS>
- </LISTITEM>
- <LISTITEM>
- <PARA>
-The indexed FASTA can be used with an indexed GFF to overlay annotation on the sequence.
-To index the GFF first sort and bgzip the file and then use tabix with "-p gff" option (see the
-<ULINK URL="http://samtools.sourceforge.net/tabix.shtml">tabix manual</ULINK>):
- </PARA>
- <SYNOPSIS>
-(grep ^"#" in.gff; grep -v ^"#" in.gff | sort -k1,1 -k4,4n) | bgzip > sorted.gff.gz;
-tabix -p gff sorted.gff.gz
- </SYNOPSIS>
- <PARA>
-A drop down menu of the contigs or chromosomes sequences is provided in the Entry toolbar
-to select the sequence. Using indexed FASTA and indexed GFF files improves the memory management
-and enables large genomes to be viewed. Note that as it is indexed the sequence and annotation are
-read-only and cannot be edited. When there are many contigs to select from it can be easier
-to display the one of interest by typing the name into the drop down list.
- </PARA>
- </LISTITEM>
- <LISTITEM>
- <PARA>
-The output of <ULINK
-URL="http://sonnhammer.sbc.su.se/download/software/MSPcrunch+Blixem/"><COMMAND>MSPcrunch</COMMAND></ULINK>.
-<COMMAND>MSPcrunch</COMMAND> must be run with the <COMMAND>-x</COMMAND> or
-<COMMAND>-d</COMMAND> flags.
- </PARA>
- </LISTITEM>
- <LISTITEM>
- <PARA>
-The output of <ULINK URL="http://www.ncbi.nlm.nih.gov/blast/">blastall version
-2.2.2</ULINK> or better. <COMMAND>blastall</COMMAND> must be run with the
-<COMMAND>-m 8</COMMAND> flag which generates one line of information per HSP.
-Note that currently &prog; displays each Blast HSP as a separate feature
-rather than displaying each BLAST hit as a feature.
- </PARA>
- </LISTITEM>
- </ITEMIZEDLIST>
- </SECT2>
<SECT2 ID="FILEMENU-READ-ENTRY-INTO">
<TITLE>Read Entry Into</TITLE>
--
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