EMBASSY: CATHPARSE documentation.

CATHPARSE documentation

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

Generate DCF file from raw CATH files

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.

(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.
(2) EN - PDB identifier code. This is the 4-character PDB identifier code of the PDB entry containing the domain.
(3) TY - domain type. "CATH" or "SCOP" is given ("CATH" for DCF files generated by using CATHPARSE).
(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.
(5) CL - Class. It is the identical text taken from CAT.names.all.vX.X.
(6) AR - Architecture. It is the identical text taken from CAT.names.all.vX.X.
(7) TP - Topology. It is the identical text taken from CAT.names.all.vX.X.
(8) SF - Homologous Superfamily. It is the identical text taken from CAT.names.all.vX.X.
(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.
(10) NR - Number of residues in domain
(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.
(12) CN - Segment number. The number given in brackets after this record indicates the start of the data for the relevent segment.
(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.

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

5.0 DATA FILES

None.

6.0 USAGE

6.1 COMMAND LINE ARGUMENTS

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

Qualifier Type Description Allowed values Default

Standard (Mandatory) qualifiers

[-listfile]
(Parameter 1) 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). Input file caths.list.v2.4

[-domfile]
(Parameter 2) 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). Input file domlist.v2.4

[-namesfile]
(Parameter 3) 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). Input file CAT.names.all.v2.4

[-outfile]
(Parameter 4) 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. Output file Ecath.dat

-logfile outfile This option specifies the name of the CATHPARSE log file. Output file cathparse.log

Additional (Optional) qualifiers

(none)

Advanced (Unprompted) qualifiers

(none)

Associated qualifiers

"-outfile" associated outfile qualifiers

-odirectory4
-odirectory_outfile string Output directory Any string

"-logfile" associated outfile qualifiers

-odirectory string Output directory Any string

General qualifiers

-auto boolean Turn off prompts Boolean value Yes/No N

-stdout boolean Write first file to standard output Boolean value Yes/No N

-filter boolean Read first file from standard input, write first file to standard output Boolean value Yes/No N

-options boolean Prompt for standard and additional values Boolean value Yes/No N

-debug boolean Write debug output to program.dbg Boolean value Yes/No N

-verbose boolean Report some/full command line options Boolean value Yes/No Y

-help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose Boolean value Yes/No N

-warning boolean Report warnings Boolean value Yes/No Y

-error boolean Report errors Boolean value Yes/No Y

-fatal boolean Report fatal errors Boolean value Yes/No Y

-die boolean Report dying program messages Boolean value Yes/No Y

-version boolean Report version number and exit Boolean value Yes/No N

Qualifier	Type	Description	Allowed values	Default
Standard (Mandatory) qualifiers
[-listfile] (Parameter 1)	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).	Input file	caths.list.v2.4
[-domfile] (Parameter 2)	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).	Input file	domlist.v2.4
[-namesfile] (Parameter 3)	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).	Input file	CAT.names.all.v2.4
[-outfile] (Parameter 4)	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.	Output file	Ecath.dat
-logfile	outfile	This option specifies the name of the CATHPARSE log file.	Output file	cathparse.log
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
(none)
Associated qualifiers
"-outfile" associated outfile qualifiers
-odirectory4 -odirectory_outfile	string	Output directory	Any string
"-logfile" associated outfile qualifiers
-odirectory	string	Output directory	Any string
General qualifiers
-auto	boolean	Turn off prompts	Boolean value Yes/No	N
-stdout	boolean	Write first file to standard output	Boolean value Yes/No	N
-filter	boolean	Read first file from standard input, write first file to standard output	Boolean value Yes/No	N
-options	boolean	Prompt for standard and additional values	Boolean value Yes/No	N
-debug	boolean	Write debug output to program.dbg	Boolean value Yes/No	N
-verbose	boolean	Report some/full command line options	Boolean value Yes/No	Y
-help	boolean	Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose	Boolean value Yes/No	N
-warning	boolean	Report warnings	Boolean value Yes/No	Y
-error	boolean	Report errors	Boolean value Yes/No	Y
-fatal	boolean	Report fatal errors	Boolean value Yes/No	Y
-die	boolean	Report dying program messages	Boolean value Yes/No	Y
-version	boolean	Report version number and exit	Boolean value Yes/No	N

6.2 EXAMPLE SESSION

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

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

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

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

Program name	Description
aaindexextract	Extract amino acid property data from AAINDEX
allversusall	Sequence similarity data from all-versus-all comparison
cutgextract	Extract codon usage tables from CUTG database
domainalign	Generate alignments (DAF file) for nodes in a DCF file
domainer	Generate domain CCF files from protein CCF files
domainnr	Remove redundant domains from a DCF file
domainrep	Reorder DCF file to identify representative structures
domainseqs	Add sequence records to a DCF file
domainsse	Add secondary structure records to a DCF file
helixturnhelix	Identify nucleic acid-binding motifs in protein sequences
hetparse	Convert heterogen group dictionary to EMBL-like format
jaspextract	Extract data from JASPAR
libgen	Generate discriminating elements from alignments
matgen3d	Generate a 3D-1D scoring matrix from CCF files
pdbparse	Parse PDB files and writes protein CCF files
pdbplus	Add accessibility and secondary structure to a CCF file
pdbtosp	Convert swissprot:PDB codes file to EMBL-like format
pepcoil	Predict coiled coil regions in protein sequences
printsextract	Extract data from PRINTS database for use by pscan
prosextract	Process the PROSITE motif database for use by patmatmotifs
rebaseextract	Process the REBASE database for use by restriction enzyme applications
rocon	Generate a hits file from comparing two DHF files
rocplot	Perform ROC analysis on hits files
scopparse	Generate DCF file from raw SCOP files
seqalign	Extend alignments (DAF file) with sequences (DHF file)
seqfraggle	Remove fragment sequences from DHF files
seqnr	Remove redundancy from DHF files
seqsort	Remove ambiguous classified sequences from DHF files
seqwords	Generate DHF files from keyword search of UniProt
sites	Generate residue-ligand CON files from CCF files
ssematch	Search a DCF file for secondary structure matches
tfextract	Process TRANSFAC transcription factor database for use by tfscan

12.0 DIAGNOSTIC ERROR MESSAGES

None.

13.0 AUTHORS

Mike Hurley
Jon Ison (jison@ebi.ac.uk)
The European Bioinformatics Institute Wellcome Trust Genome Campus Cambridge CB10 1SD UK

14.0 REFERENCES

Please cite the authors and EMBOSS. Please cite the authors and EMBOSS.

Rice P, Longden I and Bleasby A (2000) "EMBOSS - The European Molecular Biology Open Software Suite" Trends in Genetics, 15:276-278.

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.

CATHPARSE documentation

CONTENTS

1.0 SUMMARY

2.0 INPUTS & OUTPUTS

3.0 INPUT FILE FORMAT

Input files for usage example

File: caths.list.small

File: domlist.small

File: CAT.names.all.small

4.0 OUTPUT FILE FORMAT

Output files for usage example

File: Ecath.dat

File: cathparse.log

5.0 DATA FILES

6.0 USAGE

6.1 COMMAND LINE ARGUMENTS

6.2 EXAMPLE SESSION

7.0 KNOWN BUGS & WARNINGS

8.0 NOTES

8.1 GLOSSARY OF FILE TYPES

9.0 DESCRIPTION

10.0 ALGORITHM

11.0 RELATED APPLICATIONS

See also

12.0 DIAGNOSTIC ERROR MESSAGES

13.0 AUTHORS

14.0 REFERENCES

14.1 Other useful references