void show_help(FILE * ofp)
{
fprintf(ofp,"%s (%s)\n",program_name,VERSION_NUMBER);
fprintf(ofp,"cdnawise <cdna-file> <genomic-dna-file> in fasta format\n");
show_help_GeneModelParam(ofp);
show_help_DPRunImpl(ofp);
show_standard_options(ofp);
}
void show_help(FILE * ofp)
{
fprintf(ofp,"%s sequence-as-fasta\n",program_name);
show_help_GeneModelParam(ofp);
show_help_DPRunImpl(ofp);
show_standard_options(ofp);
}
void show_help(FILE * ofp)
{
fprintf(ofp,"%s pairwise-alignment-as-fasta\n",program_name);
show_help_GeneModelParam(ofp);
show_help_ShowGenomicRegionOptions(ofp);
show_help_DPRunImpl(ofp);
show_help_StandardOutputOptions(ofp);
show_standard_options(ofp);
}
void show_help(FILE * ofp)
{
fprintf(ofp,"%s (%s)\n",program_name,VERSION_NUMBER);
fprintf(ofp,"genewise <protein-file> <dna-file> in fasta format\n");
/* program specific help */
fprintf(ofp,"Dna sequence options\n");
fprintf(ofp," -u start position in dna\n");
fprintf(ofp," -v end position in dna\n");
fprintf(ofp," -trev Compare on the reverse strand\n");
fprintf(ofp," -tfor [default] Compare on the forward strand\n");
fprintf(ofp," -both Both strands\n");
fprintf(ofp," -tabs Report positions as absolute to truncated/reverse sequence\n");
fprintf(ofp," -fembl File is an EMBL file native format\n");
fprintf(ofp,"Protein comparison options\n");
fprintf(ofp," -s start position in protein\n");
fprintf(ofp," -t end position in protein\n");
fprintf(ofp," -[g]ap [%3d] gap penalty\n",gap);
fprintf(ofp," -[e]xt [%3d] extension penalty\n",ext);
fprintf(ofp," -[m]atrix [%s] Comparison matrix\n",matrix_file);
fprintf(ofp,"HMM options\n");
fprintf(ofp," -hmmer Protein file is HMMer file (version 2 compatible)\n");
fprintf(ofp," -hname Use this as the name of the HMM, not filename\n");
show_help_GeneModelParam(ofp);
fprintf(ofp," -splice [model/flat] [LEGACY only for -splice flat. use -splice_gtag]\n");
show_help_PhasedProteinPara(ofp);
fprintf(ofp,"Other model options\n");
fprintf(ofp," -[no]newgene use new gene stats (default), no for reverting to old system\n");
fprintf(ofp," -init [%s] [default/global/local/wing/endbias] startend policy for the HMM/protein\n",startend_string);
fprintf(ofp," -codon [%s] Codon file\n",codon_file);
fprintf(ofp," -subs [%2.2g] Substitution error rate\n",subs_error);
fprintf(ofp," -indel [%2.2g] Insertion/deletion error rate\n",indel_error);
fprintf(ofp," -null [syn/flat] Random Model as synchronous or flat [default syn]\n");
fprintf(ofp," -alln [%s] Probability of matching a NNN codon\n",allN_string);
fprintf(ofp," -insert [model/flat] Use protein insert model [default flat]\n");
fprintf(ofp,"Algorithm options\n");
fprintf(ofp," -alg [623/623L/623S/623P/2193/2193L] Algorithm used [default 623/623L]\n");
fprintf(ofp," (normally use 623 for proteins, 623L for HMMs and 623P for Phased Proteins)\n");
fprintf(ofp,"Output options [default -pretty -para]\n");
fprintf(ofp," -pretty show pretty ascii output\n");
fprintf(ofp," -pseudo Mark genes with frameshifts as pseudogenes\n");
fprintf(ofp," -genes show gene structure\n");
fprintf(ofp," -genesf show gene structure with supporting evidence\n");
fprintf(ofp," -embl show EMBL feature format with CDS key\n");
fprintf(ofp," -diana show EMBL feature format with misc_feature key (for diana)\n");
fprintf(ofp," -para show parameters\n");
fprintf(ofp," -sum show summary output\n");
/* lets not bring trouble on ourselves ;) */
/* fprintf(ofp," -over show EMBL overlap (only with EMBL format)\n"); */
fprintf(ofp," -cdna show cDNA\n");
fprintf(ofp," -trans show protein translation, breaking at frameshifts\n");
fprintf(ofp," -pep show protein translation, splicing frameshifts\n");
fprintf(ofp," -ace ace file gene structure\n");
fprintf(ofp," -gff Gene Feature Format file\n");
fprintf(ofp," -gener raw gene structure\n");
fprintf(ofp," -alb show logical AlnBlock alignment\n");
fprintf(ofp," -pal show raw matrix alignment\n");
fprintf(ofp," -block [%s] Length of main block in pretty output\n",main_block_str);
fprintf(ofp," -divide [%s] divide string for multiple outputs\n",divide_str);
show_help_GeneWiseRunPara(ofp);
show_help_DPRunImpl(ofp);
show_standard_options(ofp);
exit(63);
}