Public Attributes

gotoh_arguments Struct Reference

Contains all command line arguments. More...

#include <structs.h>

List of all members.

Public Attributes

char * cfg_file
char * db_file
char * q_file
char * res_file
char * stat_file
char * m1_file
char * m2_file
int mD
double e
int p
int out
int split
int help
int version
int verbose
float m1_seqT
float m2_seqT
float m2_strucT
float m2T

Detailed Description

Contains all command line arguments.

gotoh_arguments contains all command line arguments or their initialized values if not set by the user. It can be initialized by gotoh_initArguments() and freed by gotoh_freeArguments().


Member Data Documentation

Filename of configuration file. Format see examples/Configuration.dat.

Filename of database file containing FASTA formatted sequences.

Evalue - only candidate alignments with lower or equal Evalue than this value are returned. Default: 1e-3

Print usage information.

Filename of query file containing a motif as frequency matrix reformatted using scripts/reformatFasta.pl

Sequence threshold to be a matching pattern for single motifs. Default: 0.7

Filename of query file containing a 2-sided motif as frequency matrices reformatted using scripts/reformatFasta.pl

Sequence threshold to be a matching pattern for 2-sided motifs. Default: 0.5

Structure threshold to be a matching pattern for 2-sided motifs. Default: 0.8

Complete Threshold for 2-sided motifs. Default: 0.6

Maximal distance between the 2 sides of the 2-sided motif

Output format. Values are:

  • 0 - Blast tabular output
  • 1 - Blast tabular output + aligned sequences
  • 2 - FASTA format. NOTE: Hit sequence only, without gaps !
  • 3 - MAF format. NOTE: Header truncated to 30 characters!
  • 4 - BED + aligned sequences
  • 5 - GFF + aligned sequences

Default: 0

Percent identity - only candidate alignments with higher or equal percent identity than this value are returned. Default: 60

Filename of query file conatining FASTA formatted (ungapped) sequences.

filenmae of output file.

Splits value - the database is split into pieces to enhance memory usage. Default: 10000

Filename of file where to statistics on the E-value calculation, i.e. the data of the histogram, the fit parameters and the final fitted curve

Print Verbose output.

Print version information.


The documentation for this struct was generated from the following file:
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