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Bioscripts 1.3 - Bioperl scripts
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A list of the scripts in the Bioperl package
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These scripts have been contributed by the developers and users of
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Bioperl. They are organized into directories roughly mirroring those
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in the Bioperl Bio/ directory. There are 2 directories for these
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scripts, scripts/ and examples/. The scripts in scripts/ are
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production quality scripts that have POD documentation and accept
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command-line arguments, the scripts in examples/ are useful
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examples of Bioperl code.
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You can install the scripts in the scripts/ directory if you'd like,
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simply follow the instructions on 'make install'. The installation
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directory is specified by the INSTALLSCRIPT variable in the Makefile,
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the default directory is /usr/bin. Installation will copy the scripts
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to the specified directory, change the 'PLS' suffix to 'pl' and
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prepend 'bp_' to the script name if it isn't so named already.
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Please contact bioperl-l at bioperl.org if you are interested in
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contributing your own script.
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=head1 PRODUCTION SCRIPTS
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=head2 scripts/install_bioperl_scripts.PLS
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This script installs scripts from the scripts/ directory on
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A fully-featured script that uses Bio::Biblio, a module for
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accessing and querying bibliographic repositories like Medline.
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=head2 scripts/biblio/biblio.PLS
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A fully-featured script that uses Bio::Biblio, a module for
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accessing and querying bibliographic repositories like Medline.
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=head2 scripts/Bio-DB-GFF/bulk_load_gff.PLS
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This script loads a mySQL Bio::DB::GFF database with the features
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contained in a list of GFF files, it cannot do incremental loads.
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=head2 scripts/Bio-DB-GFF/bp_genbank2gff.PLS
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This script loads a Bio::DB::GFF database with the features contained
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in a either a local Genbank file or an accession that is fetched from
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=head2 scripts/Bio-DB-GFF/fast_load_gff.PLS
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This script does a rapid load of a mySQL Bio::DB::GFF database
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using files as source. Probably only works in Unix as it relies
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=head2 scripts/Bio-DB-GFF/generate_histogram.PLS
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Create a GFF-formatted histogram of the density of the indicated set
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=head2 scripts/Bio-DB-GFF/load_gff.PLS
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This script loads a mySQL Bio::DB::GFF database with the features
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contained in a list of GFF files. This script will work with all
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database adaptors supported by Bio::DB::GFF (mySQL, Oracle, Postgres).
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=head2 scripts/Bio-DB-GFF/pg_bulk_load_gff.PLS
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Bulk-load a PostgreSQL Bio::DB::GFF database from GFF files.
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=head2 scripts/Bio-DB-GFF/process_gadfly.PLS
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Transforms Gadfly GFF files into correct format.
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=head2 scripts/Bio-DB-GFF/process_ncbi_human.PLS
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Trnasforms NCBI's chromosome annotations into correct format.
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=head2 scripts/Bio-DB-GFF/process_sgd.PLS
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Transform SGD format annotations into GFF format.
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=head2 scripts/Bio-DB-GFF/process_wormbase.PLS
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Transforms Wormbase's GFF files into correct format. Requires Ace.pm.
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=head2 scripts/DB/bioflat_index.pl
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Create or update a biological sequence database indexed with the
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Bio::DB::Flat indexing scheme.
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=head2 scripts/DB/flanks.PLS
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Fetch a sequence, find the sequences flanking a variant or SNP in the
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sequence given its position.
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=head2 scripts/DB/biofetch_genbank_proxy.PLS
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A CGI scripts that queries NCBI's eutils to provide database access
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according to the BioFetch protocol. Requires Cache::FileCache.
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=head2 scripts/DB/biogetseq.PLS
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Sequence retrieval using the OBDA registry.
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=head2 scripts/graphics/feature_draw.PLS
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Script that accepts files in GFF or tab-delimited format and creates
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corresponding PNG image files. See L<Bio::Graphics> and
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L<Bio::Graphics::FeatureFile> for more information.
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=head2 scripts/graphics/frend.PLS
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Create a PNG file on the Web using Bio::Graphics - accepts a file
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containing sequence and feature coordinates.
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=head2 scripts/graphics/search_overview.PLS
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Create a simple overview graphic of the hits, color is based on the hit
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score much like the NCBI overview graphic in a BLAST report.
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=head2 scripts/index/bp_fetch.PLS
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Fetch sequences from local indexed database or over the network and
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reformat using Bio::Index* and Bio::DB*.
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=head2 scripts/index/bp_index.PLS
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Indexes local databases, partners with bp_fetch.pl.
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=head2 scripts/seq/extract_feature_seq.PLS
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Extract the sequence for a specified feature type.
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=head2 scripts/popgen/composite_LD.PLS
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An easy way to calculate composite linkage disequilibrium (LD).
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=head2 scripts/popgen/heterogeneity.PLS
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A test for distinguishing between selection and population
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=head2 scripts/searchio/filter_search.PLS
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Simple script to filter by SearchIO criteria and print.
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=head2 scripts/seq/seqconvert.PLS
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Bioperl sequence format converter.
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=head2 scripts/seq/split_seq.PLS
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Split a sequence in a file into chunks of equal size.
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=head2 scripts/seq/translate_seq.PLS
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A simple Bioperl translator.
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=head2 scripts/seqstats/aacomp.PLS
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Prints out the count of amino acids over all protein
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sequences in the input file.
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=head2 scripts/seqstats/chaos_plot.PLS
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Produce a PNG or JPEG chaos plot given a DNA sequence using GD.pm.
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=head2 scripts/seqstats/gccalc.PLS
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Prints out the GC content for every nucleotide sequence
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=head2 scripts/seqstats/oligo_count.PLS
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Use this script to determine what primers would be useful for
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frequent priming of nucleic acid for random labeling.
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=head2 scripts/taxa/local_taxonomydb_query.PLS
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Script that accesses a local Taxonomy database and retrieves
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species or taxon ids.
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=head2 scripts/taxa/taxid4species.PLS
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Retrieve the NCBI Tada ID for a given species.
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=head2 scripts/tree/blast2tree.PLS
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Builds a phylogenetic tree based on a sequence search (Fasta,
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=head2 scripts/utilities/bp_mrtrans.PLS
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Perl implementation of Bill Pearson's mrtrans to project protein
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alignment back into cDNA coordinates.
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=head2 scripts/utilities/bp_nrdb.PLS
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Make a non-redundant database based on sequence, not id.
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Requires Digest::MD5.
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=head2 scripts/utilities/bp_sreformat.PLS
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Perl implementation of Sean Eddy's sreformat, a sequence and
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=head2 scripts/utilities/dbsplit.PLS
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Splits one or more sequence files into subfiles with specified
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numbers of sequences, any sequence format.
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=head2 scripts/utilities/mask_by_search.PLS
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Masks parts of a sequence based on a significant matches to that
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sequence as contained in a SearchIO-compatible report file.
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=head2 scripts/utilities/mutate.PLS
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Randomly mutagenize a single protein or DNA sequence. Specify
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percentage mutated and number of resulting mutagenized sequences.
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=head2 scripts/utilities/pairwise_kaks.PLS
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Takes DNA sequences as input, aligns them as proteins,
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projects the alignment back into DNA and estimates
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the Ka (non-synonymous) and Ks (synonymous) substitutions.
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=head2 scripts/utilities/remote_blast.PLS
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This script executes a remote Blast search using RemoteBlast. See
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L<Bio::Tools::Run::RemoteBlast> for more information.
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=head2 scripts/utilities/search2BSML.PLS
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Turns SearchIO-compatible reports into a BSML report.
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=head2 scripts/utilities/search2alnblocks.PLS
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Turns SearchIO-compatible reports into alignments in formats supported
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=head2 scripts/utilities/search2tribe.PLS
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This script will turn a protein SearchIO-compatible report (BLASTP,
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FASTP, SSEARCH) into a Markov Matrix for TribeMCL clustering.
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=head2 scripts/utilities/search2gff.PLS
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Turn SearchIO parseable reports(s) into a GFF report.
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=head2 scripts/utilities/seq_length.PLS
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Reports the total number of residues and total number of individual
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sequences in a specified sequence database file.
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=head1 EXAMPLE SCRIPTS
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=head2 examples/align/align_on_codons.pl
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Aligns nucleotide sequences based on codons in a specified reading frame.
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=head2 examples/align/aligntutorial.pl
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Examples using EMBOSS, pSW, Clustalw, TCoffee, and Blast to align sequences.
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=head2 examples/align/clustalw.pl
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A demonstration of the various uses of Alignment::Clustalw. See
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L<Bio::Tools::Run::Alignment::Clustalw> for more.
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=head2 examples/align/simplealign.pl
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A script that demonstrates some uses of AlignIO. Please see
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L<Bio::AlignIO> for more information.
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=head2 examples/biblio/biblio.pl
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A script that shows how to query bibliographic databases, such as
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Medline, using ids, keywords, and other fields. See L<Bio::Biblio> for
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=head2 examples/biblio/biblio_soap.pl
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Connect to and test a SOAP server using a Bio::Biblio object.
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=head2 examples/biographics/all_glyphs.pl
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Creates an image showing all possible glyphs.
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=head2 examples/biographics/dynamic_glyphs.pl
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Creates a complex image of a gene with confirmed and predicted exons,
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transcripts, and text labels.
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=head2 examples/biographics/lots_of_glyphs.pl
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Creates a complex image of a gene with confirmed and predicted exons,
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transcripts, and text labels.
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=head2 examples/bioperl.pl
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=head2 examples/cluster/dbsnp.pl
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How to parse a dbsnp XML file. See L<Bio::ClusterIO> for details.
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=head2 examples/contributed/nmrpdb_parse.pl
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Extracts individual conformers from an NMR-derived PDB file.
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=head2 examples/contributed/prosite2perl.pl
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Convert Prosite motifs to Perl regular expressions.
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=head2 examples/contributed/rebase2list.pl
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Script to convert rebase file to format compatible with
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Bio::Tools::RestrictionEnzyme.
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=head2 examples/contributed/expression_analysis*
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A set of scripts that accept microarray data as input and perform
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statistical analyses, including t test, U test, Mann-Whitney,
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and Pearson correlation coefficent.
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=head2 examples/db/dbfetch
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Creates a Web page to query a local SRS server and fetch sequences.
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=head2 examples/db/est_tissue_query.pl
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Fetch EST sequences from local files or Genbank filtered by tissue
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using Bio::DB* or Bio::Index*.
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=head2 examples/db/gb2features.pl
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Shows how to extract all the features from a Genbank file. See
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L<Bio::Seq> for more information on features.
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=head2 examples/db/getGenBank.pl
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Retrieving Genbank entries over the Web using DB::GenBank. See
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L<Bio::DB::GenBank> for more information.
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=head2 examples/db/get_seqs.pl
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Fetches and formats sequences from GenBank, EMBL, or SwissProt over
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the network using Bio::DB*.
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=head2 examples/db/gff/*
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Scripts that reformat sequence to GFF and load GFF format files into
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an indexed database - see L<Bio::DB::GFF> for more information.
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=head2 examples/db/rfetch.pl
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A script that uses Bio::DB::Registry to retrieve sequences from EMBL,
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reformat them, and print them. See L<Bio::DB::Registry>.
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=head2 examples/db/use_registry.pl
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Script that shows how to use Bio::DB::Registry, part of Bioperl's
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integration with OBDA, the Open Bio Database Access registry
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scheme. See L<Bio::DB::Registry> for more information.
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=head2 examples/exceptions/*
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Scripts that demonstrate how to throw and catch Error.pm objects.
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=head2 examples/generate_random_seq.pl
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Writes random RNA, DNA, or protein sequence of given length.
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=head2 examples/biographics/render_sequence.pl
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This scripts fetchs a sequence from a remote database, extracts its
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features (CDS, gene, tRNA), and creates a graphic representation of
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the sequence in PNG or GIF format. See L<Bio::DB::BioFetch>
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and L<Bio::Graphics>.
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=head2 examples/liveseq/change_gene.pl
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A script showing how to use LiveSeq::Mutator and
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LiveSeq::Mutation. Please see L<Bio::LiveSeq::Mutator> and
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L<Bio::LiveSeq::Mutation> for more information.
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=head2 examples/longorf.pl
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A script that finds the longest ORF in one or more nucleotide sequences.
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=head2 examples/make_mrna_protein.pl
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Translate a cDNA or ORF to protein using Bio::Seq's translate() method.
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=head2 examples/make_primers.pl
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Design PCR primers given a sequence and the positions of the start and
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stop codons in the sequence's ORF.
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=head2 examples/popgen/parse_calc_stats.pl
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Shows how to read data from a Bio::PopGen::IO object.
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=head2 examples/rev_and_trans.pl
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Examples using Bio::Seq.pm for reversing and translating
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sequences. See L<Bio::Seq> for more information.
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=head2 examples/revcom_dir.pl
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Eeturn reverse complement sequences of all sequences in the current
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directory and save them in the same directory.
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=head2 examples/sirna/rnai_finder.cgi
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CGI script for RNAi reagent design. See L<Bio::Tools::SiRNA> for more
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=head2 examples/root_object/*
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Scripts that demonstrate uses of the Bio::Root modules.
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=head2 examples/searchio/blast_example.pl
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Print out all parsed values from a BLAST report.
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=head2 examples/searchio/custom_writer.pl
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Demonstrates how to extract data from BLAST reports and output as
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=head2 examples/searchio/hitwriter.pl
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Demonstrates how to extract data from BLAST reports and output as
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=head2 examples/searchio/hspwriter.pl
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Demonstrates how to extract data from BLAST reports and output as
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=head2 examples/searchio/htmlwriter.pl
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Demonstrates how to extract data from BLAST reports and output as
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=head2 examples/searchio/psiblast_features.pl
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Illustrates how to grab a set of SeqFeatures from a Psiblast report.
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=head2 examples/searchio/psiblast_iterations.pl
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Demonstrates the use of a SearchIO parser for processing the
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iterations within a PSI-BLAST report.
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=head2 examples/searchio/rawwriter.pl
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Shows how to print out raw BLAST alignment data for each HSP.
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=head2 examples/searchio/resultwriter.pl
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Demonstrates how to extract data from BLAST reports and output as
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=head2 examples/searchio/waba2gff.pl
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Convert raw WABA output to one type of GFF.
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=head2 examples/seq/*
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Example code for working with multiple sequence files, including
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formatting, printing, and filtering based on length or description or ID.
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=head2 examples/seq/extract_cds.pl
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Extract the CDS features from a Genbank file.
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=head2 examples/seqstats/aacomp.pl
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Calculate amino acid composition of a protein using Tools::CodonTable
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and Tools::IUPAC. See L<Bio::Tools::IUPAC> and
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L<Bio::Tools::CodonTable> for more information.
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=head2 examples/structure/struct_example*
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Scripts that show how to examine details of the 3D structure of a
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protein by parsing a PDB file. See L<Bio::Structure::IO> for more information.
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=head2 examples/subsequence.cgi
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CGI script to fetch a sequence from Genbank and extract a subsequence
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using DB::GenBank. See L<Bio::DB::GenBank>.
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=head2 examples/tk/gsequence.pl
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Create a Protein Sequence Control Panel GUI with Gtk.
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=head2 examples/tk/hitdisplay.pl
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Create a GUI for displaying Blast results using Tk::HitDisplay.
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Please see L<Bio::Tk::HitDisplay> for more information.
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=head2 examples/tools/gb_to_gff.pl
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Extracts top-level sequence features from Genbank-formatted sequence
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files using Tools::GFF. See L<Bio::Tools::GFF>.
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=head2 examples/tools/gff2ps.pl
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Takes an input file in GFF format and draws its genes and features as
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Postscript using Tools::GFF. See L<Bio::Tools::GFF>.
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=head2 examples/tools/parse_codeml.pl
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Script that parses output from codeml, one of the PAML programs. See
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L<Bio::Tools::Phylo::PAML>.
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=head2 examples/tools/psw.pl
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Example code for using the XS extensions for comparing proteins
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using Smith-Waterman.
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=head2 examples/tools/restriction.pl
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Example code for using the RestrictionEnzyme module. See
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L<Bio::Tools::RestrictionEnzyme> for more information (note that
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Bio::Tools::RestrictionEnzyme has been superceded by
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Bio::Restriction::*).
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=head2 examples/tools/run_genscan.pl
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Run GENSCAN on multiple sequences and create output sequence files
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using Tools::Genscan. Please see L<Bio::Tools::Genscan> for more information.
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=head2 examples/tools/seq_pattern.pl
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A script that shows how to use sequences as regular expressions using
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Tools::SeqPattern. Please see L<Bio::Tools::SeqPattern> for more information.
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=head2 examples/tools/standaloneblast.pl
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The many uses of StandAloneBlast, including BLAST and PSIBLAST.
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=head2 examples/tools/state-machine.pl
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A demonstration of how to create a state machine using
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StateMachine::AbstractStateMachine. Please see
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L<Bio::Tools::StateMachine::AbstractStateMachine> for more information.
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=head2 examples/tools/test-genscan.pl
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Script for testing and demonstrating Bio::Tools::Genscan.
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=head2 examples/tree/paup2phylip.pl
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Convert a PAUP tree block to Phylip format.
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bioscripts.pod
