Merge pull request #10 from Rfam/add-rfam-ftp-help

Add rfam ftp help

docs/source/database.rst

@@ -1,3 +1,4 @@
+.. _ftp_help_link:
 Public MySQL Database
 ======================
 

docs/source/ftp-help.rst

@@ -0,0 +1,43 @@
+Rfam FTP Site
+=============
+
+The following list describes a few of the important files in the
+Rfam `FTP site <ftp://ftp.ebi.ac.uk/pub/databases/Rfam>`_.
+Some of these files may be very large (of the order of several hundred megabytes).
+Please check the sizes before trying to download them over a slow connection.
+
+Documentation
+-------------
+
+`README <ftp://ftp.ebi.ac.uk/pub/databases/Rfam/CURRENT/README>`_
+  Release Notes
+`COPYING <ftp://ftp.ebi.ac.uk/pub/databases/Rfam/CURRENT/COPYING>`_
+  Public Domain Information for Rfam
+`USERMAN <ftp://ftp.ebi.ac.uk/pub/databases/Rfam/CURRENT/USERMAN>`_
+  A description of the Rfam flatfile formats
+
+Sequences, Alignments, Models and Trees
+---------------------------------------
+
+`Rfam.tar.gz <ftp://ftp.ebi.ac.uk/pub/databases/Rfam/CURRENT/Rfam.tar.gz>`_
+  Rfam covariance models in ascii INFERNAL format
+`Rfam.seed.gz <ftp://ftp.ebi.ac.uk/pub/databases/Rfam/CURRENT/Rfam.seed.gz>`_
+  Annotated seed alignments in STOCKHOLM format
+`Rfam.seed_tree.tar.gz <ftp://ftp.ebi.ac.uk/pub/databases/Rfam/CURRENT/Rfam.seed_tree.tar.gz>`_
+  Annotated tree files for each seed alignment
+`Rfam.full_region.gz <ftp://ftp.ebi.ac.uk/pub/databases/Rfam/CURRENT/Rfam.full_region.gz>`_
+  List of sequence regions making up the full family membership for each family
+`fasta_files <ftp://ftp.ebi.ac.uk/pub/databases/Rfam/CURRENT/fasta_files>`_
+  Directory containing the sequences for all significant hits per family
+
+Rfam database dumps
+-------------------
+
+`database_files <ftp://ftp.ebi.ac.uk/pub/databases/Rfam/CURRENT/database_files>`_
+  Directory containing MYSQL dump of the the Rfam database data, tables and mysql database schema
+
+.. hint:: For direct access to the database please visit :ref:`Public MySQL Database <ftp_help_link>`
+
+
+
+

docs/source/index.rst

@@ -28,6 +28,7 @@ Contents
    glossary
    genome-annotation
    linking-rfam
+   ftp-help
    rest-api
    database
    rfam-team