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<H2> CATHPARSE documentation
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<!-- CONTENTS
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     Other subsections can be added for individual applications.
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<H2>CONTENTS </H2>
<b> <a href="#1.0">1.0     SUMMARY                   </a></b><br>
<b> <a href="#2.0">2.0     INPUTS & OUTPUTS          </a></b><br>
<b> <a href="#3.0">3.0     INPUT FILE FORMAT         </a></b><br>
<b> <a href="#4.0">4.0     OUTPUT FILE FORMAT        </a></b><br>
<b> <a href="#5.0">5.0     DATA FILES                </a></b><br>
<b> <a href="#6.0">6.0     USAGE                     </a></b><br>    
<b> <a href="#7.0">7.0     KNOWN BUGS & WARNINGS     </a></b><br>    
<b> <a href="#8.0">8.0     NOTES                     </a></b><br>
<b> <a href="#9.0">9.0     DESCRIPTION               </a></b><br>
<b> <a href="#10.0">10.0   ALGORITHM                 </a></b><br>
<b> <a href="#11.0">11.0   RELATED APPLICATIONS      </a></b><br>
<b> <a href="#12.0">12.0   DIAGNOSTIC ERROR MESSAGES </a></b><br>
<b> <a href="#13.0">13.0   AUTHORS                   </a></b><br>
<b> <a href="#14.0">14.0   REFERENCES                </a></b><br>

<!-- SUMMARY
     Succint description of the application, particularly its inputs, outputs
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     file and in the <documentation> attribute of the <application definition>
     of the ACD file.
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<a name="1.0"></a>
<br><br><br><H2> 1.0   SUMMARY  </H2>

Generate DCF file from raw CATH files
<!-- INPUTS & OUTPUTS
     Short summary of the application inputs and outputs in its different 
     modes of usage (if appropriate). More detail than the summary.
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<a name="2.0"></a>
<br><br><br><H2> 2.0   INPUTS & OUTPUTS          </H2>
CATHPARSE parses the CATH classification files, e.g. caths.list.v2.4, domlist.v2.4 and CAT.names.all.v2.4. 
These files are available by anonymous ftp from ftp.biochem.ucl.ac.uk (e.g. /pub/cathdata/v2.4)
The format of these files is explained in the README file available there.
CATHPARSE writes the CATH classification to a DCF file (EMBL-like format).  
No changes are made to the data other than changing the 
format in which it is held.  The input and output files are specified by the user.





<!-- INPUT FILE FORMAT 
     Description and example(s) of input file formats.  Should provide enough
     information to write and parse the file.  Should describe the format in 
     unusual cases - null input, etc.
     Use "<b>CATHPARSE</b> reads any normal sequence USAs." if
     appropriate.
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<a name="3.0"></a>
<br><br><br><H2> 3.0   INPUT FILE FORMAT         </H2>
An excerpt from the raw CATH classification files, of the type caths.list.vX.X (Figure 1), 
domlist.vX.X (Figure 2) and CAT.names.all.vX.X (Figure 3) is shown below.  The format of 
these files is explained in the CATH README file available by anonymous ftp from 
ftp.biochem.ucl.ac.uk (e.g. /pub/cathdata/v2.4).



<a name="input.1"></a>
<h3>Input files for usage example </h3>
<p><h3>File: caths.list.small</h3>
<table width="90%"><tr><td bgcolor="#FFCCFF">
<pre>
1cuk03    1  10   8  10   1   1   1  48 1.900
1hjp03    1  10   8  10   1   1   2  44 2.500
</pre>
</td></tr></table><p>
<p><h3>File: domlist.small</h3>
<table width="90%"><tr><td bgcolor="#FFCCFF">
<pre>
1cuk00  D03   F00    1  0   1 - 0  66 -    1  0  67 - 0 142 -    1  0 156 - 0 203 - 
1hjp00 D03 F01  1  0    1 - 0   66 -  1  0   67 - 0  158 -  1  0  159 - 0  202 -  0  203 - 0  203 - (1) 
</pre>
</td></tr></table><p>
<p><h3>File: CAT.names.all.small</h3>
<table width="90%"><tr><td bgcolor="#FFCCFF">
<pre>
1.10.8           1cuk03            :Helicase, Ruva Protein, domain 3	
1.10.8.10         1cuk03    :DNA helicase RuvA subunit, C-terminal domain 
0001             2ccyA0        :Mainly Alpha
0001.0010        1eca00          :Orthogonal Bundle
</pre>
</td></tr></table><p>

<!--

<br><br><b>Figure 1 Excerpt from raw CATH classification file, caths.list.vX.X (input) </b>
<table><td bgcolor="#CFCCFF">
<pre>
1cuk03    1  10   8  10   1   1   1  48 1.900
1hjp03    1  10   8  10   1   1   2  44 2.500
1a5t02    1  10   8  10   2   1   1  40 2.200
1bvsA3    1  10   8  10   3   1   1  44 3.000
1bvsB3    1  10   8  10   3   1   1  44 3.000
1bvsC3    1  10   8  10   3   1   1  44 3.000
1bvsD3    1  10   8  10   3   1   1  44 3.000
1bvsE3    1  10   8  10   3   1   1  44 3.000
1bvsG3    1  10   8  10   3   1   1  44 3.000
1bvsH3    1  10   8  10   3   1   1  44 3.000
1bvsF3    1  10   8  10   3   1   2  45 3.000
1dv0A0    1  10   8  10   4   1   1  45 999.000
1ubaA0    1  10   8  10   4   1   1  45 1000.000
1f4iA0    1  10   8  10   5   1   1  45 999.000
1aua02    1  10   8  20   1   1   1  83 2.500
1aipC3    1  10   8  30   1   1   1  53 3.000
1aipD3    1  10   8  30   1   1   1  53 3.000
1aipG3    1  10   8  30   1   1   1  53 3.000
1aipH3    1  10   8  30   1   1   2  52 3.000
1efuB1    1  10   8  30   1   2   1  54 2.500
1efuD1    1  10   8  30   1   2   1  54 2.500
1gab00    1  10   8  40   1   1   1  53 999.000
1prb00    1  10   8  40   1   1   1  53 999.000
1gjsA0    1  10   8  40   1   2   1  65 999.000
1gjtA0    1  10   8  40   1   2   1  65 999.000
1fjgM1    1  10   8  50   1   1   1  71 3.000
1d2nA2    1  10   8  60   1   1   1  67 1.750
1nsf02    1  10   8  60   1   1   1  67 1.900
1fnnA1    1  10   8  60   2   1   1 101 2.000
1fnnB1    1  10   8  60   2   1   1 101 2.000
</pre>
</table>

<br>
<br><br><b>Figure 2 Excerpt from raw CATH classification file,  domlist.vX.X (input) </b>
<table><td bgcolor="#CFCCFF">
<pre>
10gsA0 D02 F01  2  A    2 - A   78 -  A  187 - A  208 -  1  A   79 - A  186 -  A  209 - A  209 - (1) 
10gsB0 D02 F01  2  B    2 - B   78 -  B  187 - B  208 -  1  B   79 - B  186 -  B  209 - B  209 - (1) 
10mhA0 D02 F00  2  A    1 - A  186 -  A  285 - A  327 -  1  A  187 - A  284 - 
11gsA0 D02 F01  2  A    2 - A   78 -  A  187 - A  208 -  1  A   79 - A  186 -  A  209 - A  209 - (1) 
11gsB0 D02 F01  2  B    2 - B   78 -  B  187 - B  208 -  1  B   79 - B  186 -  B  209 - B  209 - (1) 
12e8H0 D02 F01  1  H    1 - H  113 -  1  H  114 - H  212 -  H  213 - H  214 - (2) 
12e8L0 D02 F01  1  L    1 - L  107 -  1  L  108 - L  211 -  L  212 - L  214 - (3) 
12e8M0 D02 F01  1  M    1 - M  107 -  1  M  108 - M  211 -  M  212 - M  214 - (3) 
12e8P0 D02 F01  1  P    1 - P  113 -  1  P  114 - P  212 -  P  213 - P  214 - (2) 
12gsA0 D02 F01  2  A    2 - A   78 -  A  187 - A  208 -  1  A   79 - A  186 -  A  209 - A  209 - (1) 
12gsB0 D02 F01  2  B    2 - B   78 -  B  187 - B  208 -  1  B   79 - B  186 -  B  209 - B  209 - (1) 
13gsA0 D02 F02  2  A    2 - A   78 -  A  187 - A  208 -  1  A   79 - A  186 -  A    0 - A    1 - (2)  A  209 - A  209 - (1) 
13gsB0 D02 F01  2  B    2 - B   78 -  B  187 - B  208 -  1  B   79 - B  186 -  B  209 - B  209 - (1) 
13pkA0 D02 F02  1  A    5 - A  192 -  1  A  199 - A  406 -  A  193 - A  198 - (6)  A  407 - A  419 - (13) 
13pkB0 D02 F02  1  B    5 - B  192 -  1  B  199 - B  406 -  B  193 - B  198 - (6)  B  407 - B  419 - (13) 
</pre>
</table>

<br>
<br><br><b>Figure 3 Excerpt from raw CATH classification file, CAT.names.all.vX.X (input) </b>
<table><td bgcolor="#CFCCFF">
<pre>
0001             2ccyA0        :Mainly Alpha
0001.0010        1eca00          :Orthogonal Bundle
0001.0020        2ccyA0          :Up-down Bundle
0001.0025        1lrv00          :Horshoe
0001.0040        1pprM1          :Alpha solenoid 
0001.0050        1cem00          :Alpha/alpha barrel
0002             2hlaB0        :Mainly Beta
0002.0010        1tpm00          :Ribbon
0002.0020        1rkd01          :Single Sheet
0002.0030        1pht00          :Roll
0002.0040        2por00          :Barrel
0002.0050        4bcl00          :Clam
0002.0060        2hlaB0          :Sandwich
0002.0070        1cdq00          :Distorted Sandwich
0002.0080        1afcA0          :Trefoil
0002.0090        1msaA0          :Orthogonal Prism
0002.0100        1vmoA0          :Aligned Prism
</pre>
</table>

-->



<!-- OUTPUT FILE FORMAT 
     Description and example(s) of output file formats.  Should provide enough
     information to write and parse the file.  Should describe the format in 
     unusual cases - null input, etc.  
     If the standard description of the avalable report formats is required, 
     use:   #include file="inc/reportformats.ihtml"
     Use "Outputs a graph to the specified graphics device."
     or  "outputs a report format file. The default format is ..."
     if appropriate.
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<a name="4.0"></a>
<br><br><br><H2> 4.0   OUTPUT FILE FORMAT         </H2>
An example of the DCF output file is shown in Figure 4.
The records used to describe an entry are as follows.  Records (5) to (8) 
are used to describe the position of the domain in the CATH hierarchy.
<br>
<UL>
<LI>(1)  ID - Domain identifier code.  This is a 6-character code that uniquely
identifies the domain in CATH. The first four characters are the PDB identifier code, 
the fifth character is the PDB chain identifier to which the domain belongs and the 
final character is the number of the domain in the chain (for chains comprising more 
than one domain). This character is '0' if the chain comprises a single 
domain only.
<LI>(2)  EN - PDB identifier code.  This is the 4-character PDB identifier code
of the PDB entry containing the domain.
<LI>(3) TY - domain type.  "CATH" or "SCOP" is given ("CATH" for DCF files 
generated by using CATHPARSE).
<LI>(4)  CI - CATH Classification Numbers. The integers preceeding the codes CL, AR, TP, SF,
FA, NI, IF are the CATH classification numbers for CLass, ARchitecture, ToPology,  
Homologous SuPerfamily, FAmily, Near Identical family and Identical Family respectively.    
These numbers uniquely identify the appropriate node in the CATH parsable files.
<LI>(5)  CL - Class.  It is the identical text taken from CAT.names.all.vX.X.
<LI>(6)  AR - Architecture. It is the identical text taken from CAT.names.all.vX.X.
<LI>(7)  TP - Topology. It is the identical text taken from CAT.names.all.vX.X.
<LI>(8)  SF - Homologous Superfamily. It is the identical text taken from CAT.names.all.vX.X. 
<LI>(9) DS - Sequence of the domain according to the PDB file.  This sequence
is taken from the domain CCF file (clean coordinate file) generated by DOMAINER.  The DS    
record will only be present if the DCF file has been processed using DOMAINSEQS.
<LI>(10)  NR - Number of residues in domain
<LI>(11) NC - Number of segments comprising the domain. All domains in CATH are from single chains.
If the number of segments is greater than 1, then the domain entry will have a 
section  containing a CN and a CH record (see below) for each segment.
<LI>(12) CN - Segment number.  The number given in brackets after this record 
indicates the start of the data for the relevent segment.
<LI>(13) CH - Domain definition.  The character given before CHAIN is the PDB 
chain identifier, the strings before START and END give the start and end positions 
respectively of the domain in the PDB file (a '.' is given in cases where a position 
was not specified).  Note that the start and end positions refer to residue numbering 
given in the original pdb file and therefore must be treated as strings.
(14) XX - used for spacing.
(15) // - used to delimit records for a domain.
</UL>


<a name="output.1"></a>
<h3>Output files for usage example </h3>
<p><h3>File: Ecath.dat</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
ID   1CUK03
XX
EN   1CUK
XX
TY   CATH
XX
CI   1 CL; 10 AR; 8 TP; 10 SF; 1 FA; 1 NI;1 IF;
XX
CL   Mainly Alpha
XX
AR   Orthogonal Bundle
XX
TP   Helicase, Ruva Protein, domain 3
XX
SF   DNA helicase RuvA subunit, C-terminal domain
XX
NR   48
XX
NC   1
XX
CN   [1]
XX
CH   0 CHAIN; 156 START; 203 END;
//
ID   1HJP03
XX
EN   1HJP
XX
TY   CATH
XX
CI   1 CL; 10 AR; 8 TP; 10 SF; 1 FA; 1 NI;2 IF;
XX
CL   Mainly Alpha
XX
AR   Orthogonal Bundle
XX
TP   Helicase, Ruva Protein, domain 3
XX
SF   DNA helicase RuvA subunit, C-terminal domain
XX
NR   44
XX
NC   1
XX
CN   [1]
XX
CH   0 CHAIN; 159 START; 202 END;
//
</pre>
</td></tr></table><p>
<p><h3>File: cathparse.log</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
1.10.8.10
1.10.8
0001.0010
0001
1.10.8.10
1.10.8
0001.0010
0001
</pre>
</td></tr></table><p>

<!--
<br>
<br><b>Figure 4 Excerpt from domain classification file</b>
<table><td bgcolor="#CFCCFF">
<pre>
ID   1CUK03
XX
EN   1CUK
XX
TY   CATH
XX
CI   1 CL; 10 AR; 8 TP; 10 SF; 1 FA; 1 NI;1 IF;
XX
CL   Mainly Alpha
XX
AR   Orthogonal Bundle
XX
TP   Helicase, Ruva Protein, domain 3
XX
SF   DNA helicase RuvA subunit, C-terminal domain
XX
NR   48
XX
NC   1
XX
CN   [1]
XX
CH   0 CHAIN; 156 START; 203 END;
//
ID   1HJP03
XX
EN   1HJP
XX
TY   CATH
XX
CI   1 CL; 10 AR; 8 TP; 10 SF; 1 FA; 1 NI;2 IF;
XX
CL   Mainly Alpha
XX
AR   Orthogonal Bundle
XX
TP   Helicase, Ruva Protein, domain 3
XX
SF   DNA helicase RuvA subunit, C-terminal domain
XX
NR   44
XX
NC   1
XX
CN   [1]
XX
CH   0 CHAIN; 159 START; 202 END;
//

</pre>
</table>


-->

<!-- DATA FILES         
     Any data files used (e.g. translation table file, substitution matrix 
     etc.  This includes example data file formats if they are not obvious.
     For a standard description of what data files are and how embossdata can
     be used to inspect and retrieve them, use:
     #include file="inc/localfiles.ihtml" 
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<a name="5.0"></a>
<br><br><br><H2> 5.0   DATA FILES                </H2>
None.


<!-- USAGE
     Example usage, as run from the command-line.
     Many examples illustrating different behaviours is good.
-->
<a name="6.0"></a>
<br><br><br><H2> 6.0   USAGE                     </H2>
<H3> 6.1   COMMAND LINE ARGUMENTS </H3>
 
 
<pre>
Generate DCF file from raw CATH files.
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers:
  [-listfile]          infile     [caths.list.v2.4] This option specifies the
                                  name of raw CATH classification file
                                  (caths.list.vX.X) (input). The raw CATH
                                  parsable files (classification and
                                  description files) available from
                                  ftp.biochem.ucl.ac.uk (/pub/cathdata/v2.4).
  [-domfile]           infile     [domlist.v2.4] This option specifies the
                                  name of raw CATH classification file
                                  (domlist.vX.X) (input). The raw CATH
                                  parsable files (classification and
                                  description files) available from
                                  ftp.biochem.ucl.ac.uk (/pub/cathdata/v2.4).
  [-namesfile]         infile     [CAT.names.all.v2.4] This option specifies
                                  the name of raw CATH classification file
                                  (CAT.names.all.vX.X) (input). The raw CATH
                                  parsable files (classification and
                                  description files) available from
                                  ftp.biochem.ucl.ac.uk (/pub/cathdata/v2.4).
  [-outfile]           outfile    [Ecath.dat] This option specifies the name
                                  of CATH DCF file (domain classification
                                  file) (output). A 'domain classification
                                  file' contains classification and other data
                                  for domains from SCOP or CATH, in DCF
                                  format (EMBL-like). The files are generated
                                  by using SCOPPARSE and CATHPARSE. Domain
                                  sequence information can be added to the
                                  file by using DOMAINSEQS.
   -logfile            outfile    [cathparse.log] This option specifies the
                                  name of the CATHPARSE log file.

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:

   "-outfile" associated qualifiers
   -odirectory4        string     Output directory

   "-logfile" associated qualifiers
   -odirectory         string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options and exit. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages
   -version            boolean    Report version number and exit

</pre>
</td></tr></table>
<P>
<table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
<tr bgcolor="#FFFFCC">
<th align="left">Qualifier</th>
<th align="left">Type</th>
<th align="left">Description</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Standard (Mandatory) qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td>[-listfile]<br>(Parameter 1)</td>
<td>infile</td>
<td>This option specifies the name of raw CATH classification file (caths.list.vX.X) (input). The raw CATH parsable files (classification and description files) available from ftp.biochem.ucl.ac.uk (/pub/cathdata/v2.4).</td>
<td>Input file</td>
<td>caths.list.v2.4</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>[-domfile]<br>(Parameter 2)</td>
<td>infile</td>
<td>This option specifies the name of raw CATH classification file (domlist.vX.X) (input). The raw CATH parsable files (classification and description files) available from ftp.biochem.ucl.ac.uk (/pub/cathdata/v2.4).</td>
<td>Input file</td>
<td>domlist.v2.4</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>[-namesfile]<br>(Parameter 3)</td>
<td>infile</td>
<td>This option specifies the name of raw CATH classification file (CAT.names.all.vX.X) (input). The raw CATH parsable files (classification and description files) available from ftp.biochem.ucl.ac.uk (/pub/cathdata/v2.4).</td>
<td>Input file</td>
<td>CAT.names.all.v2.4</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>[-outfile]<br>(Parameter 4)</td>
<td>outfile</td>
<td>This option specifies the name of CATH DCF file (domain classification file) (output). A 'domain classification file' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL-like). The files are generated by using SCOPPARSE and CATHPARSE. Domain sequence information can be added to the file by using DOMAINSEQS.</td>
<td>Output file</td>
<td>Ecath.dat</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-logfile</td>
<td>outfile</td>
<td>This option specifies the name of the CATHPARSE log file.</td>
<td>Output file</td>
<td>cathparse.log</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Additional (Optional) qualifiers</th>
</tr>

<tr>
<td colspan=5>(none)</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Advanced (Unprompted) qualifiers</th>
</tr>

<tr>
<td colspan=5>(none)</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Associated qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td align="left" colspan=5>"-outfile" associated outfile qualifiers
</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -odirectory4<br>-odirectory_outfile</td>
<td>string</td>
<td>Output directory</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td align="left" colspan=5>"-logfile" associated outfile qualifiers
</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -odirectory</td>
<td>string</td>
<td>Output directory</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>General qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td> -auto</td>
<td>boolean</td>
<td>Turn off prompts</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -stdout</td>
<td>boolean</td>
<td>Write first file to standard output</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -filter</td>
<td>boolean</td>
<td>Read first file from standard input, write first file to standard output</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -options</td>
<td>boolean</td>
<td>Prompt for standard and additional values</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -debug</td>
<td>boolean</td>
<td>Write debug output to program.dbg</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -verbose</td>
<td>boolean</td>
<td>Report some/full command line options</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -help</td>
<td>boolean</td>
<td>Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -warning</td>
<td>boolean</td>
<td>Report warnings</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -error</td>
<td>boolean</td>
<td>Report errors</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -fatal</td>
<td>boolean</td>
<td>Report fatal errors</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -die</td>
<td>boolean</td>
<td>Report dying program messages</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -version</td>
<td>boolean</td>
<td>Report version number and exit</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

</table>


<H3> 6.2 EXAMPLE SESSION </H3>

<br>An example of interactive use of CATHPARSE is shown below.

Here is a sample session with <b>cathparse</b>
<p>

<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>

% <b>cathparse </b>
Generate DCF file from raw CATH files.
Raw cath list file [caths.list.v2.4]: <b>caths.list.small</b>
Raw cath domlist file [domlist.v2.4]: <b>domlist.small</b>
Raw cath names file [CAT.names.all.v2.4]: <b>CAT.names.all.small</b>
Domain classification output file [Ecath.dat]: <b></b>
Domainatrix log output file [cathparse.log]: <b></b>

</pre></td></tr></table><p>
<p>
<a href="#input.1">Go to the input files for this example</a><br><a href="#output.1">Go to the output files for this example</a><p><p>

<!--
<br>The raw CATH classification files caths.list.small, domlist.small and CAT.names.all.small were read from test_data/ directory and and a domain classification file in DCF format called /test_data/cathparse/all.scop was written.  The log file test_data/cathparse/CATHPARSE.log was written. -->



<!-- KNOWN BUGS & WARNINGS
     Bugs that have not yet been fixed, easily missued features, problems
     and caveats etc. Potentially stupid things the program will let you do.
-->
<a name="7.0"></a>
<br><br><br><H2> 7.0   KNOWN BUGS & WARNINGS     </H2>



<!-- NOTES
     Important general remarks, including:
       Restrictions.
       Interesting behaviour.
       Useful things you can do with this program.
       Future plans.
       etc.
-->
<a name="8.0"></a>
<br><br><br><H2> 8.0   NOTES                     </H2>
A future implementation will give the option of omitting from the output file 
domains that consist of more than one segment.
<br><br>
CATH includes several minor classes which are not appropriate for some
anaylses.  A future implementation will give the option to omit domains from 
minor classes. 


<H3> 8.1   GLOSSARY OF FILE TYPES    </H2>
<table BORDER CELLSPACING=5 CELLPADDING=5 BGCOLOR="#f5f5ff" >
<tr>
<td><b>FILE TYPE</b></td>
<td><b>FORMAT</b></td>
<td><b>DESCRIPTION</b></td>
<td><b>CREATED BY <b></td>
<td><b>SEE ALSO</b></td>
</tr>
<tr>
<td><b>SCOP parsable files</b></td>
<td> CATH format. </td>
<td> Raw CATH classification data.  </td>
<td> Available from ftp.biochem.ucl.ac.uk (e.g. /pub/cathdata/v2.4)</a> </td>
<td> N.A.  </td>
</tr>
<tr>
<td><b> Domain classification file (for CATH)</b></td>
<td> DCF format (EMBL-like). </td>
<td> Classification and other data for domains from CATH.  </td>
<td> <a href="cathparse.html">CATHPARSE</a> </td>
<td> Domain sequence information can be added to the file by using DOMAINSEQS.  </td>
</tr>
</table>



<!-- DESCRIPTION
     A complete, non-technical, user-level description of the application.
-->
<a name="9.0"></a>
<br><br><br><H2> 9.0   DESCRIPTION               </H2>
The raw CATH classification files are inconvenient for some uses because 
the text describing the domain classification is given in a different file
to the classification itself, the file formats are not easily extended and
differ from other related classifications such as SCOP.
CATHPARSE reads the raw CATH classification files and writes a single file
in DCF (EMBL-like) format, which is an easier format to work with, is more 
human-readable and is more extensible than the native CATH database format.



<!-- ALGORITHM
     A technical description of algorithmic aspects, describing exactly how
     the key aspects of the application work.
-->
<a name="10.0"></a>
<br><br><br><H2> 10.0  ALGORITHM                 </H2>
None.





<!-- RELATED APPLICATIONS
     Other applications that either generate the input, use the output or 
     are in some other way related to the application are described here. 
-->
<a name="11.0"></a>
<br><br><br><H2> 11.0  RELATED APPLICATIONS      </H2>

<h2><a name="See also">See also</a></h2>
<table border cellpadding=4 bgcolor="#FFFFF0">
<tr><th>Program name</th>
<th>Description</th></tr>
<tr>
<td><a href="../../emboss/apps/aaindexextract.html">aaindexextract</a></td>
<td>Extract amino acid property data from AAINDEX</td>
</tr>

<tr>
<td><a href="../domalign/allversusall.html">allversusall</a></td>
<td>Sequence similarity data from all-versus-all comparison</td>
</tr>

<tr>
<td><a href="../../emboss/apps/cutgextract.html">cutgextract</a></td>
<td>Extract codon usage tables from CUTG database</td>
</tr>

<tr>
<td><a href="../domalign/domainalign.html">domainalign</a></td>
<td>Generate alignments (DAF file) for nodes in a DCF file</td>
</tr>

<tr>
<td><a href="../structure/domainer.html">domainer</a></td>
<td>Generate domain CCF files from protein CCF files</td>
</tr>

<tr>
<td><a href="domainnr.html">domainnr</a></td>
<td>Remove redundant domains from a DCF file</td>
</tr>

<tr>
<td><a href="../domalign/domainrep.html">domainrep</a></td>
<td>Reorder DCF file to identify representative structures</td>
</tr>

<tr>
<td><a href="domainseqs.html">domainseqs</a></td>
<td>Add sequence records to a DCF file</td>
</tr>

<tr>
<td><a href="domainsse.html">domainsse</a></td>
<td>Add secondary structure records to a DCF file</td>
</tr>

<tr>
<td><a href="../../emboss/apps/helixturnhelix.html">helixturnhelix</a></td>
<td>Identify nucleic acid-binding motifs in protein sequences</td>
</tr>

<tr>
<td><a href="../structure/hetparse.html">hetparse</a></td>
<td>Convert heterogen group dictionary to EMBL-like format</td>
</tr>

<tr>
<td><a href="../../emboss/apps/jaspextract.html">jaspextract</a></td>
<td>Extract data from JASPAR</td>
</tr>

<tr>
<td><a href="../signature/libgen.html">libgen</a></td>
<td>Generate discriminating elements from alignments</td>
</tr>

<tr>
<td><a href="../signature/matgen3d.html">matgen3d</a></td>
<td>Generate a 3D-1D scoring matrix from CCF files</td>
</tr>

<tr>
<td><a href="../structure/pdbparse.html">pdbparse</a></td>
<td>Parse PDB files and writes protein CCF files</td>
</tr>

<tr>
<td><a href="../structure/pdbplus.html">pdbplus</a></td>
<td>Add accessibility and secondary structure to a CCF file</td>
</tr>

<tr>
<td><a href="../structure/pdbtosp.html">pdbtosp</a></td>
<td>Convert swissprot:PDB codes file to EMBL-like format</td>
</tr>

<tr>
<td><a href="../../emboss/apps/pepcoil.html">pepcoil</a></td>
<td>Predict coiled coil regions in protein sequences</td>
</tr>

<tr>
<td><a href="../../emboss/apps/printsextract.html">printsextract</a></td>
<td>Extract data from PRINTS database for use by pscan</td>
</tr>

<tr>
<td><a href="../../emboss/apps/prosextract.html">prosextract</a></td>
<td>Process the PROSITE motif database for use by patmatmotifs</td>
</tr>

<tr>
<td><a href="../../emboss/apps/rebaseextract.html">rebaseextract</a></td>
<td>Process the REBASE database for use by restriction enzyme applications</td>
</tr>

<tr>
<td><a href="../signature/rocon.html">rocon</a></td>
<td>Generate a hits file from comparing two DHF files</td>
</tr>

<tr>
<td><a href="../signature/rocplot.html">rocplot</a></td>
<td>Perform ROC analysis on hits files</td>
</tr>

<tr>
<td><a href="scopparse.html">scopparse</a></td>
<td>Generate DCF file from raw SCOP files</td>
</tr>

<tr>
<td><a href="../domalign/seqalign.html">seqalign</a></td>
<td>Extend alignments (DAF file) with sequences (DHF file)</td>
</tr>

<tr>
<td><a href="../domsearch/seqfraggle.html">seqfraggle</a></td>
<td>Remove fragment sequences from DHF files</td>
</tr>

<tr>
<td><a href="../domsearch/seqnr.html">seqnr</a></td>
<td>Remove redundancy from DHF files</td>
</tr>

<tr>
<td><a href="../domsearch/seqsort.html">seqsort</a></td>
<td>Remove ambiguous classified sequences from DHF files</td>
</tr>

<tr>
<td><a href="../domsearch/seqwords.html">seqwords</a></td>
<td>Generate DHF files from keyword search of UniProt</td>
</tr>

<tr>
<td><a href="../structure/sites.html">sites</a></td>
<td>Generate residue-ligand CON files from CCF files</td>
</tr>

<tr>
<td><a href="ssematch.html">ssematch</a></td>
<td>Search a DCF file for secondary structure matches</td>
</tr>

<tr>
<td><a href="../../emboss/apps/tfextract.html">tfextract</a></td>
<td>Process TRANSFAC transcription factor database for use by tfscan</td>
</tr>

</table>


<!-- DIAGNOSTIC ERROR MESSAGES
     Description of error messages or log file, if one is written.
-->
<a name="12.0"></a>
<br><br><br><H2> 12.0  DIAGNOSTIC ERROR MESSAGES </H2>
None.



<!-- AUTHORS
     The main author first then all others. 
-->
<a name="13.0"></a>
<br><br><br><H2> 13.0  AUTHORS                   </H2>
<!-- #include file="inc/jison.address" -->

Mike Hurley 

<br>Jon Ison <a href="mailto:jison@ebi.ac.uk">(jison@ebi.ac.uk)</a>
<br>
The European Bioinformatics Institute 
Wellcome Trust Genome Campus 
Cambridge CB10 1SD 
UK 



<!-- REFERENCES
     Quote the paper where the application was first published, described, used etc. 
-->
<a name="14.0"></a>
<br><br><br><H2> 14.0  REFERENCES                </H2>
Please cite the authors and EMBOSS.
Please cite the authors and EMBOSS.
<br><br>
<i>Rice P, Longden I and Bleasby A (2000) "EMBOSS - The European
Molecular Biology Open Software Suite"  Trends in Genetics,
15:276-278.

<p>
See also <a href="http://emboss.sourceforge.net/">http://emboss.sourceforge.net/</a></i>


<H3>14.1 Other useful references  </H3>
1. Conte, L.L., Ailey, B., Hubbard, T.J. Brenner, S.E., Murzin, A.G. and Chothia, C. (2000) SCOP: a structural classification of proteins database. Nucleic Acids Res. 28, 257-259.


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