bioscripts.PL

   1 #!/usr/bin/perl
   2 use strict;
   3 use LocalConfig;
   4 use File::Basename qw(basename dirname);
   5 my $file;
   6 ($file = basename($0)) =~ s/\.PL$/\.pod/;
   7 open OUT,">$file" or die "Can't create $file: $!";
   8
   9 print OUT<<"THEEND";
  10 =head1 NAME
  11
  12 Bioscripts v$Local{VERSION} - Bioperl scripts
  13
  14 =head1 SYNOPSIS
  15
  16 A list of the scripts in the Bioperl package
  17
  18 =head1 DESCRIPTION
  19
  20 These scripts have been contributed by the developers and users of
  21 Bioperl. They are organized into directories roughly mirroring those
  22 in the Bioperl Bio/ directory. There are 2 directories for these
  23 scripts, scripts/ and examples/. The scripts in scripts/ are
  24 production quality scripts that have POD documentation and accept
  25 command-line arguments, the scripts in examples/ are useful
  26 examples of Bioperl code.
  27
  28 Please contact bioperl-l at bioperl.org if you are interested in
  29 contributing your own script.
  30
  31 =head1 PRODUCTION SCRIPTS
  32
  33 =head2 scripts/Bio-DB-GFF/generate_histogram.PLS
  34
  35 Create a GFF-formatted histogram of the density of the indicated set
  36 of feature types.
  37
  38 =head2 scripts/Bio-DB-GFF/process_gadfly.PLS
  39
  40 Transforms Gadfly GFF files into correct format.
  41
  42 =head2 scripts/Bio-DB-GFF/process_ncbi_human.PLS
  43
  44 Trnasforms NCBI's chromosome annotations into correct format.
  45
  46 =head2 scripts/Bio-DB-GFF/process_sgd.PLS
  47
  48 Transform SGD format annotations into GFF format.
  49
  50 =head2 scripts/Bio-DB-GFF/process_wormbase.PLS
  51
  52 Transforms Wormbase's GFF files into correct format. Requires Ace.pm.
  53
  54 =head2 scripts/DB/flanks.PLS
  55
  56 Fetch a sequence, find the sequences flanking a variant or SNP in the
  57 sequence given its position.
  58
  59 =head2 scripts/DB/biofetch_genbank_proxy.PLS
  60
  61 A CGI scripts that queries NCBI's eutils to provide database access
  62 according to the BioFetch protocol. Requires Cache::FileCache.
  63
  64 =head2 scripts/DB/biogetseq.PLS
  65
  66 Sequence retrieval the OBDA registry.
  67
  68 =head2 scripts/graphics/feature_draw.PLS
  69
  70 Script that accepts files in GFF or tab-delimited format and creates
  71 corresponding PNG image files. See L<Bio::Graphics> and
  72 L<Bio::Graphics::FeatureFile> for more information.
  73
  74 =head2 scripts/index/bpfetch.PLS
  75
  76 Fetch sequences from local indexed database or over the network and
  77 reformat using Bio::Index* and Bio::DB*.
  78
  79 =head2 scripts/index/bpindex.PLS
  80
  81 Indexes local databases, partners with bpfetch.pl.
  82
  83 =head2 scripts/seq/extract_feature_seq.PLS
  84
  85 Extract the sequence for a specified feature type.
  86
  87 =head2 scripts/seqstats/chaos_plot.pl
  88
  89 Produce a PNG or JPEG chaos plot given a DNA sequence using GD.pm.
  90
  91 =head2 scripts/taxa/taxid4species.PLS
  92
  93 Retrieve the NCBI Tada ID for a given species.
  94
  95 =head2 scripts/tree/blast2tree.PLS
  96
  97 Builds a phylogenetic tree based on a sequence search (Fasta,
  98 BLAST, HMMER).
  99
 100 =head2 scripts/utilities/remote_blast.PLS
 101
 102 This script executes a remote Blast search using RemoteBlast. See
 103 L<Bio::Tools::Run::RemoteBlast> for more information.
 104
 105 =head2 scripts/utilities/bp_mrtrans.PLS
 106
 107 Perl implementation of Bill Pearson's mrtrans to project protein
 108 alignment back into cDNA coordinates.
 109
 110 =head2 scripts/utilities/bp_nrdb.PLS
 111
 112 Make a non-redundant database based on sequence, not id.
 113 Requires Digest::MD5.
 114
 115 =head2 scripts/utilities/bp_sreformat.PLS
 116
 117 Perl implementation of Sean Eddy's sreformat, a sequence and
 118 alignment converter.
 119
 120 =head2 scripts/utilities/pairwise_kaks.PLS
 121
 122 Takes cDNA sequences as input, aligns them as proteins,
 123 projects the alignment back into cDNA and estimates
 124 the Ka (non-synonymous) and Ks (synonymous) substitutions.
 125
 126 =head2 scripts/utilities/seq_length.PLS
 127
 128 Reports the total number of residues and total number of individual
 129 sequences in a specified sequence database file.
 130
 131 =head1 EXAMPLE SCRIPTS
 132
 133 =head2 examples/align/align_on_codons.pl
 134
 135 Aligns nucleotide sequences based on codons in a specified reading frame.
 136
 137 =head2 examples/align/aligntutorial.pl
 138
 139 Examples using EMBOSS, pSW, Clustalw, TCoffee, and Blast to align sequences.
 140
 141 =head2 examples/align/clustalw.pl
 142
 143 A demonstration of the various uses of Alignment::Clustalw. See
 144 L<Bio::Tools::Run::Alignment::Clustalw> for more.
 145
 146 =head2 examples/align/simplealign.pl
 147
 148 A script that demonstrates some uses of AlignIO. Please see
 149 L<Bio::AlignIO> for more information.
 150
 151 =head2 examples/biblio/biblio.pl
 152
 153 A script that shows how to query bibliographic databases, such as
 154 Medline, using ids, keywords, and other fields. See L<Bio::Biblio> for
 155 details.
 156
 157 =head2 examples/biblio/biblio_soap.pl
 158
 159 Connect to and test a SOAP server using a Bio::Biblio object.
 160
 161 =head2 examples/bioperl.pl
 162
 163 A Bioperl shell!
 164
 165 =head2 examples/cluster/dbsnp.pl
 166
 167 How to parse a dbsnp XML file. See L<Bio::ClusterIO> for details.
 168
 169 =head2 examples/contributed/nmrpdb_parse.pl
 170
 171 Extracts individual conformers from an NMR-derived PDB file.
 172
 173 =head2 examples/contributed/prosite2perl.pl
 174
 175 Convert Prosite motifs to Perl regular expressions.
 176
 177 =head2 examples/contributed/rebase2list.pl
 178
 179 Script to convert rebase file to format compatible with
 180 Bio::Tools::RestrictionEnzyme.
 181
 182 =head2 examples/das/das_server.pl
 183
 184 Sets up a minimal DAS annotation server, requires Apache::DBI and
 185 Bio::DB::GFF. See L<Bio::DB::GFF> for details.
 186
 187 =head2 examples/db/dbfetch
 188
 189 Creates a Web page to query a local SRS server and fetch sequences.
 190
 191 =head2 examples/db/est_tissue_query.pl
 192
 193 Fetch EST sequences from local files or Genbank filtered by tissue
 194 using Bio::DB* or Bio::Index*.
 195
 196 =head2 examples/db/gb2features.pl
 197
 198 Shows how to extract all the features from a Genbank file. See
 199 L<Bio::Seq> for more information on features.
 200
 201 =head2 examples/db/getGenBank.pl
 202
 203 Retrieving Genbank entries over the Web using DB::GenBank. See
 204 L<Bio::DB::GenBank> for more information.
 205
 206 =head2 examples/db/get_seqs.pl
 207
 208 Fetches and formats sequences from GenBank, EMBL, or SwissProt over
 209 the network using Bio::DB*.
 210
 211 =head2 examples/db/gff/*
 212
 213 Scripts that reformat sequence to GFF and load GFF format files into
 214 an indexed database - see L<Bio::DB::GFF> for more information.
 215
 216 =head2 examples/db/rfetch.pl
 217
 218 A script that uses Bio::DB::Registry to retrieve sequences from EMBL,
 219 reformat them, and print them. See L<Bio::DB::Registry>.
 220
 221 =head2 examples/db/use_registry.pl
 222
 223 Script that shows how to use Bio::DB::Registry, part of Bioperl's
 224 integration with OBDA, the Open Bio Database Access registry
 225 scheme. See L<Bio::DB::Registry> for more information.
 226
 227 =head2 examples/exceptions/*
 228
 229 Scripts that demonstrate how to throw and catch Error.pm objects.
 230
 231 =head2 examples/generate_random_seq.pl
 232
 233 Writes random RNA, DNA, or protein sequence of given length.
 234
 235 =head2 examples/graphics/render_sequence.pl
 236
 237 This scripts fetchs a sequence from a remote database, extracts its
 238 features (CDS, gene, tRNA), and creates a graphic representation of
 239 the sequence in PNG or GIF format. See L<Bio::DB::BioFetch>
 240 and L<Bio::Graphics>.
 241
 242 =head2 examples/liveseq/change_gene.pl
 243
 244 A script showing how to use LiveSeq::Mutator and
 245 LiveSeq::Mutation. Please see L<Bio::LiveSeq::Mutator> and
 246 L<Bio::LiveSeq::Mutation> for more information.
 247
 248 =head2 examples/longorf.pl
 249
 250 A script that finds the longest ORF in one or more nucleotide sequences.
 251
 252 =head2 examples/make_mrna_protein.pl
 253
 254 Translate a cDNA or ORF to protein using Bio::Seq's translate() method.
 255
 256 =head2 examples/make_primers.pl
 257
 258 Design PCR primers given a sequence and the positions of the start and
 259 stop codons in the sequence's ORF.
 260
 261 =head2 examples/rev_and_trans.pl
 262
 263 Examples using Bio::Seq.pm for reversing and translating
 264 sequences. See L<Bio::Seq> for more information.
 265
 266 =head2 examples/revcom_dir.pl
 267
 268 Eeturn reverse complement sequences of all sequences in the current
 269 directory and save them in the same directory.
 270
 271 =head2 examples/root_object/*
 272
 273 Scripts that demonstrate uses of the Bio::Root modules.
 274
 275 =head2 examples/root_object/vector/vector.pl
 276
 277 Script to test Bio::Root::Vector.
 278
 279 =head2 examples/searchio/*
 280
 281 A number of scripts illustrating the use of Bio::SearchIO for parsing
 282 Blast and PSI-Blast results. See L<Bio::SearchIO> for more information.
 283
 284 =head2 examples/searchio/waba2gff.pl
 285
 286 Convert raw WABA output to one type of GFF.
 287
 288 =head2 examples/seq/*
 289
 290 Example code for working with multiple sequence files, including
 291 formatting, printing, and filtering based on length or description or ID.
 292
 293 =head2 examples/seqstats/aacomp.pl
 294
 295 Calculate amino acid composition of a protein using Tools::CodonTable
 296 and Tools::IUPAC. See L<Bio::Tools::IUPAC> and
 297 L<Bio::Tools::CodonTable> for more information.
 298
 299 =head2 examples/seqstats/gccalc.pl
 300
 301 Calculate %GC given a DNA sequence using Tools::SeqStats. See
 302 L<Bio::Tools::SeqStats> for more information.
 303
 304 =head2 examples/seqstats/oligo_count.pl
 305
 306 Calculates oligomer frequencies given an oligomer length and a sequence.
 307
 308 =head2 examples/structure/struct_example*
 309
 310 Scripts that show how to examine details of the 3D structure of a
 311 protein by parsing a PDB file. See L<Bio::Structure::IO> for more information.
 312
 313 =head2 examples/subsequence.cgi
 314
 315 CGI script to fetch a sequence from Genbank and extract a subsequence
 316 using DB::GenBank. See L<Bio::DB::GenBank>.
 317
 318 =head2 examples/tk/gsequence
 319
 320 Create a Protein Sequence Control Panel GUI with Gtk.
 321
 322 =head2 examples/tk/hitdisplay.pl
 323
 324 Create a GUI for displaying Blast results using Tk::HitDisplay.
 325 Please see L<Bio::Tk::HitDisplay> for more information.
 326
 327 =head2 examples/tools/gb_to_gff.pl
 328
 329 Extracts top-level sequence features from Genbank-formatted sequence
 330 files using Tools::GFF. See L<Bio::Tools::GFF>.
 331
 332 =head2 examples/tools/gff2ps.pl
 333
 334 Takes an input file in GFF format and draws its genes and features as
 335 Postscript using Tools::GFF. See L<Bio::Tools::GFF>.
 336
 337 =head2 examples/tools/parse_codeml.pl
 338
 339 Script that parses output from codeml, one of the PAML programs. See
 340 L<Bio::Tools::Phylo::PAML>.
 341
 342 =head2 examples/tools/psw.pl
 343
 344 Example code for using the XS extensions for comparing proteins
 345 using Smith-Waterman.
 346
 347 =head2 examples/tools/restriction.pl
 348
 349 Example code for using the RestrictionEnzyme module. See
 350 L<Bio::Tools::RestrictionEnzyme> for more information.
 351
 352 =head2 examples/tools/run_genscan.pl
 353
 354 Run GENSCAN on multiple sequences and create output sequence files
 355 using Tools::Genscan. Please see L<Bio::Tools::Genscan> for more information.
 356
 357 =head2 examples/tools/seq_pattern.pl
 358
 359 A script that shows how to use sequences as regular expressions using
 360 Tools::SeqPattern. Please see L<Bio::Tools::SeqPattern> for more information.
 361
 362 =head2 examples/tools/state-machine.pl
 363
 364 A demonstration of how to create a state machine using
 365 StateMachine::AbstractStateMachine. Please see
 366 L<Bio::Tools::StateMachine::AbstractStateMachine> for more information.
 367
 368 =head2 examples/tools/test-genscan.pl
 369
 370 Script for testing and demonstrating Bio::Tools::Genscan.
 371
 372 =head2 examples/tree/paup2phylip.pl
 373
 374 Convert a PAUP tree block to Phylip format.
 375
 376 =cut
 377 THEEND