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hetparse |
This package is still being developed.
Please ignore this program until further details can be documented.
All further queries should go to Jon Ison. (Jon Ison)
% hetparse
Mandatory qualifiers (* if not always prompted): [-inf] infile Name of input file (raw dictionary of heterogen groups) -dogrep boolean Search a directory of files with keywords? * -path string Directory to search with keywords * -extn string Exension of files to search in above directory [-outf] outfile Name of output file (embl format) Optional qualifiers: (none) Advanced qualifiers: (none) General qualifiers: -help boolean Report command line options. More information on associated and general qualifiers can be found with -help -verbose |
Mandatory qualifiers | Allowed values | Default | |
---|---|---|---|
[-inf] (Parameter 1) |
Name of input file (raw dictionary of heterogen groups) | Input file | Required |
-dogrep | Search a directory of files with keywords? | Yes/No | No |
-path | Directory to search with keywords | Any string is accepted | ./ |
-extn | Exension of files to search in above directory | Any string is accepted | .ent |
[-outf] (Parameter 2) |
Name of output file (embl format) | Output file | <sequence>.hetparse |
Optional qualifiers | Allowed values | Default | |
(none) | |||
Advanced qualifiers | Allowed values | Default | |
(none) |
Program name | Description |
---|---|
aaindexextract | Extract data from AAINDEX |
cutgextract | Extract data from CUTG |
domainer | Reads protein coordinate files and writes domains coordinate files |
funky | Reads clean coordinate files and writes file of protein-heterogen contact data |
groups | Removes redundant hits from a scop families file |
nrscope | Converts redundant EMBL-format SCOP file to non-redundant one |
pdbparse | Parses pdb files and writes cleaned-up protein coordinate files |
pdbtosp | Convert raw swissprot:pdb equivalence file to embl-like format |
printsextract | Extract data from PRINTS |
prosextract | Builds the PROSITE motif database for patmatmotifs to search |
rebaseextract | Extract data from REBASE |
scope | Convert raw scop classification file to embl-like format |
scopnr | Removes redundant domains from a scop classification file |
scopparse | Converts raw scop classification files to a file in embl-like format |
scopseqs | Adds pdb and swissprot sequence records to a scop classification file |
tfextract | Extract data from TRANSFAC |