Commit 1777b873 authored by Carsten Kemena's avatar Carsten Kemena

updated UserManual

parent 479797f2
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......@@ -109,7 +109,7 @@ htmlhelp_basename = 'RADSdoc'
latex_elements = {
'sphinxsetup':'VerbatimColor={rgb}{0.87,0.87,0.87},verbatimwithframe=false',
'classoptions': ',openany,oneside'
'classoptions': ',openany'
# The paper size ('letterpaper' or 'a4paper').
#
# 'papersize': 'letterpaper',
......
......@@ -32,11 +32,15 @@ The basic options
.. option:: -I <FILE>, --InterPro <FILE>
Used to turn the InterPro annotation file (match\_complete.xml.gz) found on https://www.ebi.ac.uk/interpro/download.html into a RADS database. This option is used to compute the precomputed InterPro databases. Use the :option:`--database` option to extract the domain arrangements of a single database.
Used to turn the InterPro annotation file (match\_complete.xml.gz) found on https://www.ebi.ac.uk/interpro/download.html into a RADS database.
This option is used to compute the precomputed InterPro databases. Use the :option:`--database` option to extract the domain arrangements
of a single database.
.. option:: -s <FILE>, --seqs <FILE>
Sequence files. Are used in combination with the domain arrangement files. If none is given all sequence lengths are set to 0.
Sequence files. Are used in combination with the domain arrangement files. If none is given all sequence lengths are set to 0. If you provide a
sequence file you need to provide as many files as you provide domain annotation files. It is necessary that the order of the sequence files is
the same as for the domain files: seqFile1 for domFile1, seqFile2 for domFile2, ...
.. option:: -o <FILE>, --out <FILE>
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......@@ -125,7 +125,8 @@ These options can be used to filter the hits that are reported.
Output format
===============
The output is in a simple text file format and contains two parts. The first part is a summary of the process containing the date of execution, The version of RADS and the parameters used. The second part of the file contains the result. The hits are listed in a table of five \emph{tab} separated columns. The first column contains the alignment score and the second the normalized version. The third column contains the the target id followed by the sequence length in the fourth column.
The output is in a simple text file format and contains two parts. The first part is a summary of the process containing the date of execution, The version
of RADS and the parameters used. The second part of the file contains the result. The hits are listed in a table of five `tab` separated columns. The first column contains the alignment score and the second the normalized version. The third column contains the the target id followed by the sequence length in the fourth column.
The table is sorted according to the first column.
.. code-block:: text
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