CATHPARSE documentation

CONTENTS

1.0 SUMMARY
2.0 INPUTS & OUTPUTS
3.0 INPUT FILE FORMAT
4.0 OUTPUT FILE FORMAT
5.0 DATA FILES
6.0 USAGE
7.0 KNOWN BUGS & WARNINGS
8.0 NOTES
9.0 DESCRIPTION
10.0 ALGORITHM
11.0 RELATED APPLICATIONS
12.0 DIAGNOSTIC ERROR MESSAGES
13.0 AUTHORS
14.0 REFERENCES

1.0 SUMMARY

Reads raw CATH classification files and writes DCF file (domain classification file)

2.0 INPUTS & OUTPUTS

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.

3.0 INPUT FILE FORMAT

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).

Input files for usage example

File: caths.list.small

1cuk03    1  10   8  10   1   1   1  48 1.900
1hjp03    1  10   8  10   1   1   2  44 2.500

File: domlist.small

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) 

File: CAT.names.all.small

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

4.0 OUTPUT FILE FORMAT

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.

Output files for usage example

File: Ecath.dat

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;
//

File: CATHPARSE.log

1.10.8.10
1.10.8
0001.0010
0001
1.10.8.10
1.10.8
0001.0010
0001

5.0 DATA FILES

None.

6.0 USAGE

6.1 COMMAND LINE ARGUMENTS

   Standard (Mandatory) qualifiers:
  [-listfile]          infile     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     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     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    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    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 standard output
   -filter             boolean    Read standard input, write 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. 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 deaths


Standard (Mandatory) qualifiers Allowed values Default
[-listfile]
(Parameter 1)
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"). Input file caths.list.v2.4
[-domfile]
(Parameter 2)
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"). Input file domlist.v2.4
[-namesfile]
(Parameter 3)
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"). Input file CAT.names.all.v2.4
[-outfile]
(Parameter 4)
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. Output file Ecath.dat
-logfile This option specifies the name of the CATHPARSE log file. Output file CATHPARSE.log
Additional (Optional) qualifiers Allowed values Default
(none)
Advanced (Unprompted) qualifiers Allowed values Default
(none)

6.2 EXAMPLE SESSION


An example of interactive use of CATHPARSE is shown below. Here is a sample session with cathparse


% cathparse 
Reads raw CATH classification files and writes DCF file (domain
classification file).
Name of raw CATH classification file (caths.list.vX.X) (input). [caths.list.v2.4]: caths.list.small
Name of raw CATH classification file (domlist.vX.X) (input). [domlist.v2.4]: domlist.small
Name of raw CATH classification file (CAT.names.all.vX.X) (input). [CAT.names.all.v2.4]: CAT.names.all.small
Name of CATH DCF file (domain classification file) (output). [Ecath.dat]: 
Name of CATHPARSE log file [CATHPARSE.log]: 

Go to the input files for this example
Go to the output files for this example


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.

7.0 KNOWN BUGS & WARNINGS

8.0 NOTES

A future implementation will give the option of omitting from the output file domains that consist of more than one segment.

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.

8.1 GLOSSARY OF FILE TYPES

FILE TYPE FORMAT DESCRIPTION CREATED BY SEE ALSO
SCOP parsable files CATH format. Raw CATH classification data. Available from ftp.biochem.ucl.ac.uk (e.g. /pub/cathdata/v2.4) N.A.
Domain classification file (for CATH) DCF format (EMBL-like). Classification and other data for domains from CATH. CATHPARSE Domain sequence information can be added to the file by using DOMAINSEQS.

9.0 DESCRIPTION

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.

10.0 ALGORITHM

None.

11.0 RELATED APPLICATIONS

See also

Program nameDescription
aaindexextractExtract data from AAINDEX
allversusallDoes an all-versus-all global alignment for each set of sequences in an input directory and writes files of sequence similarity values
cutgextractExtract data from CUTG
domainerReads CCF files (clean coordinate files) for proteins and writes CCF files for domains, taken from a DCF file (domain classification file)
domainnrRemoves redundant domains from a DCF file (domain classification file). The file must contain domain sequence information, which can be added by using DOMAINSEQS
domainseqsAdds sequence records to a DCF file (domain classification file)
domainsseAdds secondary structure records to a DCF file (domain classification file)
hetparseConverts raw dictionary of heterogen groups to a file in EMBL-like format
pdbparseParses PDB files and writes CCF files (clean coordinate files) for proteins
pdbplusAdd residue solvent accessibility and secondary structure data to a CCF file (clean coordinate file) for a protein or domain
pdbtospConvert raw swissprot:PDB equivalence file to EMBL-like format
printsextractExtract data from PRINTS
prosextractBuilds the PROSITE motif database for patmatmotifs to search
rebaseextractExtract data from REBASE
scopparseReads raw SCOP classification files and writes a DCF file (domain classification file)
seqnrRemoves redundancy from DHF files (domain hits files) or other files of sequences
sitesReads CCF files (clean coordinate files) and writes CON files (contact files) of residue-ligand contact data for domains in a DCF file (domain classification file)
ssematchSearches a DCF file (domain classification file) for secondary structure matches
tfextractExtract data from TRANSFAC

12.0 DIAGNOSTIC ERROR MESSAGES

None.

13.0 AUTHORS

Mike Hurley (mhurley@rfcgr.mrc.ac.uk)
Jon Ison (jison@rfcgr.mrc.ac.uk)
MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK

14.0 REFERENCES

Please cite the authors and EMBOSS.

Rice P, Bleasby A.J. 2000. EMBOSS - The European Molecular Biology Open Software Suite. Trends in Genetics, 15:276-278. See also http://www.uk.embnet.org/Software/EMBOSS

14.1 Other useful references

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.