[Bioperl-l] scripts

[Lincoln Stein]

I'll fix the Bio-DB-GFF ones that I'm responsible for.

Lincoln

On Tuesday 25 February 2003 10:18 am, Brian Osborne wrote:
> 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.
>
>
>
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-- 
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Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein at cshl.org			                  Cold Spring Harbor, NY
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