[Bioperl-l] scripts

[Heikki Lehvaslaiho]

Great job Brian!

Not it is up to everyone who has written scrips to check them, and if
necessary, add POD, rename xxx.PLS and to move them into scripts.

Please check the list of .pl files in Brian's message below. 

	-Heikki




On Tue, 2003-02-25 at 15:18, 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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-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho          heikki at ebi.ac.uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
___ _/_/_/_/_/________________________________________________________