void show_help(FILE * ofp)
{
show_help_DPRunImpl(ofp);
show_standard_options(ofp);
exit(63);
}
void show_help(FILE * ofp)
{
fprintf(ofp,"%s query_sequence_file_fasta\n",program_name);
fprintf(ofp," -dbsize [number] effective db size for Evalue calculation [300000]\n");
fprintf(ofp," -[no]mott use Mott's statistics or not (default yes)\n");
show_help_ScanWiseHSPImpl(ofp);
show_help_HSPScanInterfacePara(ofp);
show_help_HSP2HitList(ofp);
show_help_HSPset2HitPairPara(ofp);
show_help_HitListOutputImpl(ofp);
show_help_DPRunImpl(ofp);
show_standard_options(ofp);
fprintf(ofp,"The following options are only applicable to the -seqdb case\n");
show_help_SeqLookupLoadPara(ofp);
show_help_ProteinIndexConstructor(ofp);
}
void show_help(FILE * ofp)
{
fprintf(ofp,"%s query_sequence target_sequence\n",program_name);
fprintf(ofp,"Seed restriction\n");
fprintf(ofp," -align [normal/motif] use normal DBA or motif alignment [normal]\n");
fprintf(ofp," -s query start position restriction\n");
fprintf(ofp," -t query end position restriction\n");
fprintf(ofp," -u target start position restriction\n");
fprintf(ofp," -v target end position restriction\n");
show_help_LocalCisHitSetPara(ofp);
fprintf(ofp,"Motif Matching and TransFactor matches only for motif alignment\n");
fprintf(ofp," ie, when the -align motif option is used\n");
fprintf(ofp," -lr motif library is in Laurence's format (default is Ewan's)\n");
fprintf(ofp," -ben motif library is in Ben's IUPAC format (default is Ewan's)\n");
fprintf(ofp," -motiflib [filename] motif library file name\n");
show_help_MotifMatrixPara(ofp);
show_help_TransFactorBuildPara(ofp);
show_help_TransFactorMatchPara(ofp);
show_help_HitListOutputImpl(ofp);
show_help_DPRunImpl(ofp);
show_standard_options(ofp);
}
void show_help(FILE * ofp)
{
fprintf(ofp,"%s align_cds_pair hmm_set\n",program_name);
show_help_DPRunImpl(ofp);
show_standard_options(ofp);
}
void show_help(FILE * ofp)
{
fprintf(ofp,"%s fasta-file-for-promoter-set\n",program_name);
show_help_DnaProfileEnginePara(ofp);
show_standard_options(ofp);
}
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 (%s)\n",program_name,VERSION_NUMBER);
fprintf(ofp,"%s <protein-input> <dna-input>\n",program_name);
/* program specific help */
fprintf(ofp,"Protein input type\n");
fprintf(ofp," -protein [default] single protein\n");
fprintf(ofp," -prodb protein fasta format db\n");
fprintf(ofp," -pfam pfam hmm library \n");
fprintf(ofp," -pfam2 pfam style model directory (2.1) \n");
fprintf(ofp," -hmmer single hmmer 1.x HMM\n");
fprintf(ofp,"DNA input type\n");
fprintf(ofp," -dnadb [default] dna fasta database\n");
fprintf(ofp," -dnas a single dna fasta sequence\n");
fprintf(ofp,"DNA sequence options\n");
fprintf(ofp," -tfor search forward strands only\n");
fprintf(ofp,"Protein comparison options\n");
fprintf(ofp," -gap [%3d] gap penalty\n",gap);
fprintf(ofp," -ext [%3d] extension penalty\n",ext);
fprintf(ofp," -matrix [%s] Comparison matrix\n",matrix_file);
fprintf(ofp,"HMM options\n");
fprintf(ofp," -hname For single hmms, use this as the name, not filename\n");
fprintf(ofp,"Model options\n");
fprintf(ofp," -init [%s] [default/global/local/wing] start-end policy\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," -flati Flat insert probabilities\n");
fprintf(ofp,"Algorithm options\n");
fprintf(ofp," -alg [333/312] Algorithm used for searching [default %s]\n",string_from_alg_estwrap(alg));
fprintf(ofp," -aalg [312/333/333L] Algorithm used for alignment [default %s]\n",string_from_alg_estwrap(aln_alg));
fprintf(ofp," -cut [%.2f] Bits cutoff for reporting in search algorithm\n",search_cutoff);
fprintf(ofp," -ecut [n/a] Evalue cutoff for single protein vs DNA searches.\n");
fprintf(ofp," -aln [%d] Max number of alignments (even if above cut)\n",aln_number);
fprintf(ofp," -nohis Don't show histogram on single protein/hmm vs DNA search\n");
fprintf(ofp," -report [0] Issue a report every x comparisons (default 0 comparisons)\n");
fprintf(ofp,"Output options for each alignment [default -pretty -para]\n");
fprintf(ofp," -pretty show pretty ascii output\n");
fprintf(ofp," -para show parameters\n");
fprintf(ofp," -pep show protein translation, splicing frameshifts\n");
fprintf(ofp," -mul protein mul format alignments [only for one HMM vs DNA db]\n");
fprintf(ofp," -sum show summary output\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_DBSearchImpl(ofp);
show_help_DPRunImpl(ofp);
show_standard_options(ofp);
fprintf(ofp,"\nSee WWW help at http://www.sanger.ac.uk/Software/Wise2/\n");
exit(63);
}
void show_help(FILE * ofp)
{
fprintf(ofp,"%s target-fasta-file amplimer-fasta-file\n",program_name);
show_help_DnaMatchPara(ofp);
show_help_HitListOutputImpl(ofp);
show_standard_options(ofp);
}
void show_help(FILE * ofp)
{
fprintf(ofp,"%s string1 string2\n",program_name);
fprintf(ofp,"-pretty show pretty alignment\n");
show_help_StandardOutputOptions(ofp);
show_help_DPRunImpl(ofp);
show_standard_options(ofp);
}
void show_help(FILE * ofp)
{
fprintf(ofp,"%s fivestar-directory protein-file-fasta\n",program_name);
fprintf(ofp," -ga gathering cutoff (bits)");
show_help_DBSearchImpl(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 trusted-clone-path weak-clone-path\n",program_name);
fprintf(ofp,"Algorithm\n");
/* fprintf(ofp," -spread smell area to use in comparing clones\n"); */
fprintf(ofp," -match [%d] clone match score\n",match_score);
fprintf(ofp," -mismatch [%d] clone mismatch score\n",mismatch_score);
fprintf(ofp," -wgap [%d] weak gap start cost\n",query_gap_start);
fprintf(ofp," -wext [%d] weak gap extension\n",query_gap_extend);
fprintf(ofp," -wswitch [%d] weak switch cost\n",query_switch_cost);
fprintf(ofp," -tgap [%d] trusted gap start cost\n",target_gap_start);
fprintf(ofp," -text [%d] trusted gap extension\n",target_gap_extend);
fprintf(ofp,"Output\n");
fprintf(ofp," -[no]path show path format (default no)\n");
fprintf(ofp," -[no]zip show zip format (default yes)\n");
fprintf(ofp," -[no]alb show aln block format (default no)\n");
fprintf(ofp," -[no]pal show packaln format (default no)\n");
show_standard_options(ofp);
}
void show_help(FILE * ofp)
{
fprintf(ofp,"%s genomic-fasta-file evidence-file\n",program_name);
fprintf(ofp," ** Genomewise is designed to work with the Ensembl EST build system\n");
fprintf(ofp," ** Although you can reuse it directly, alot of the magic occurs in \n");
fprintf(ofp," ** the Ensembl Runnable/RunnableDB system behind this. see www.ensembl.org \n\n");
fprintf(ofp," evidence file should have exon,cds and indel lines separated by //\n");
fprintf(ofp," between predictions (multiple predictions ok)\n");
fprintf(ofp," exon start end -- means exon prediction, no phase restriction\n");
fprintf(ofp," cds start end phase -- means exon prediction, only in that phase\n");
fprintf(ofp," indel start end -- allow frameshifting in this area\n");
fprintf(ofp,"eg - \n");
fprintf(ofp,"exon 120 340\n");
fprintf(ofp,"exon 560 591\n");
fprintf(ofp,"//\n");
fprintf(ofp,"cds 12 56 0\n");
fprintf(ofp,"cds 70 80 1\n");
fprintf(ofp,"\n\nOPTIONS (can occur anywhere on the command line\n");
fprintf(ofp,"Scoring\n");
fprintf(ofp," -start <number> no start codon penalty 30\n");
fprintf(ofp," -stop <number> no stop codon penalty 200\n");
fprintf(ofp," -gene <number> new gene cost 5000\n");
fprintf(ofp," -switch <number> evidence switch cost 100\n");
fprintf(ofp," -smell <number> smell space used for out-phase splice sites 8\n");
fprintf(ofp,"Output\n");
fprintf(ofp," -[no]genes show gene structure (default yes)\n");
fprintf(ofp," -[no]geneutr show gene structure with utrs (default yes)\n");
fprintf(ofp," -[no]trans show protein translation (default yes)\n");
fprintf(ofp," -[no]gff show gff (default yes)\n");
fprintf(ofp," -[no]alb show aln block format (default no)\n");
fprintf(ofp," -[no]debug show debug format (default no)\n");
fprintf(ofp," -kbyte <number> number of kbytes available for main memory build (10,000 default)\n");
show_help_DPRunImpl(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);
}
