[Bioperl-l] scripts

[Brian Osborne]

Bioperl-l,

I've rearranged the scripts into 2 directories, scripts/ and examples/. Some
people didn't remember what this was about, so I'll review. Scripts in
scripts/ have *PLS suffixes, and they can be installed on 'make install',
but this isn't implemented yet. These scripts are different from the scripts
in examples/, they:

Do something useful and non-trivial
Accept command-line arguments well, if necessary
Have POD documentation

Here's a list of these production scripts:

scripts/graphics/feature_draw.PLS
scripts/index/bpfetch.PLS
scripts/index/bpindex.PLS
scripts/taxa/taxid4species.PLS
scripts/seq/extract_feature_seq.PLS no -h
scripts/utilities/bp_mrtrans.PLS
scripts/utilities/bp_nrdb.PLS no -h
scripts/utilities/bp_sreformat.PLS
scripts/utilities/pairwise_kaks.PLS
scripts/utilities/remote_blast.PLS
scripts/utilities/seq_length.PLS
scripts/Bio-DB-GFF/generate_histogram.PLS
scripts/Bio-DB-GFF/process_gadfly.PLS
scripts/Bio-DB-GFF/process_ncbi_human.PLS
scripts/Bio-DB-GFF/process_sgd.PLS
scripts/Bio-DB-GFF/process_wormbase.PLS s
cripts/tree/blast2tree.PLS deprecated methods, no -h
scripts/DB/flanks.PLS
scripts/DB/biofetch_genbank_proxy.PLS
scripts/DB/biogetseq.PLS

These scripts could be production scripts, except that they have no POD:

make_mrna_protein.pl
Bio-DB-GFF/bulk_load_gff
Bio-DB-GFF/fast_load_gff
Bio-DB-GFF/load_gff
Bio-DB-GFF/ucsc2gff
DB/blast_fetch.pl
DB/blast_fetch_local.pl
DB/get_seqs.pl
align/align_on_codons.pl
align/clustalw.pl
biblio/biblio.pl

I don't claim to be an authority here, just doing what needed to be done.

Brian O.