Merge pull request #17 from carandraug/master

prefix scripts with bp_.  Will possibly run another pull request to change file extension to .pl, depending on feedback.

scripts/Bio-DB-EUtilities/einfo.PLS → scripts/Bio-DB-EUtilities/bp_einfo.PLS

@@ -1,17 +1,17 @@
 #!perl
-# $Id: einfo.PLS 15088 2008-12-04 02:49:09Z bosborne $
+# $Id: bp_einfo.PLS 15088 2008-12-04 02:49:09Z bosborne $
 use strict;
 use warnings;
 
 =head1 NAME 
 
-einfo.pl - query einfo to find all available databases or information about a
+bp_einfo.pl - query einfo to find all available databases or information about a
             specific database (field information or links to other NCBI
             databases)
 
 =head1 SYNOPSIS
 
- einfo [-d database] [-f Field Code] [-l Link Name] [-o outfile]
+ bp_einfo [-d database] [-f Field Code] [-l Link Name] [-o outfile]
 
 =head1 DESCRIPTION
 

scripts/Bio-DB-GFF/bulk_load_gff.PLS → scripts/Bio-DB-GFF/bp_bulk_load_gff.PLS

@@ -19,11 +19,11 @@ use constant FATTRIBUTE_TO_FEATURE => 'fattribute_to_feature';
 
 =head1 NAME
 
-bulk_load_gff.pl - Bulk-load a Bio::DB::GFF database from GFF files.
+bp_bulk_load_gff.pl - Bulk-load a Bio::DB::GFF database from GFF files.
 
 =head1 SYNOPSIS
 
-  % bulk_load_gff.pl -d testdb dna1.fa dna2.fa features1.gff features2.gff ...
+  % bp_bulk_load_gff.pl -d testdb dna1.fa dna2.fa features1.gff features2.gff ...
 
 =head1 DESCRIPTION
 

scripts/Bio-DB-GFF/genbank2gff3.PLS → scripts/Bio-DB-GFF/bp_genbank2gff3.PLS

@@ -6,24 +6,24 @@
 
 =head1 NAME 
 
-genbank2gff3.pl -- Genbank-E<gt>gbrowse-friendly GFF3
+bp_genbank2gff3.pl -- Genbank-E<gt>gbrowse-friendly GFF3
 
 =head1 SYNOPSIS
 
-  genbank2gff3.pl [options] filename(s)
+  bp_genbank2gff3.pl [options] filename(s)
 
   # process a directory containing GenBank flatfiles
-  perl genbank2gff3.pl --dir path_to_files --zip
+  perl bp_genbank2gff3.pl --dir path_to_files --zip
 
   # process a single file, ignore explicit exons and introns
-  perl genbank2gff3.pl --filter exon --filter intron file.gbk.gz
+  perl bp_genbank2gff3.pl --filter exon --filter intron file.gbk.gz
 
   # process a list of files 
-  perl genbank2gff3.pl *gbk.gz
+  perl bp_genbank2gff3.pl *gbk.gz
 
   # process data from URL, with Chado GFF model (-noCDS), and pipe to database loader
   curl ftp://ftp.ncbi.nih.gov/genomes/Saccharomyces_cerevisiae/CHR_X/NC_001142.gbk \
-  | perl genbank2gff3.pl -noCDS -in stdin -out stdout \
+  | perl bp_genbank2gff3.pl -noCDS -in stdin -out stdout \
   | perl gmod_bulk_load_gff3.pl -dbname mychado -organism fromdata
 
     Options:
@@ -132,7 +132,7 @@ model features remain the same.
 Several other improvements and bugfixes, minor but useful are included
 
   * IO pipes now work:
-    curl ftp://ncbigenomes/... | genbank2gff3 --in stdin --out stdout | gff2chado ...
+    curl ftp://ncbigenomes/... | bp_genbank2gff3 --in stdin --out stdout | gff2chado ...
 
   * GenBank main record fields are added to source feature, e.g. organism, date,
     and the sourcetype, commonly chromosome for  genomes, is used.
@@ -172,7 +172,7 @@ errors), and found corrected:
    -- unspecified errors (sample data works now).
 
  From: Eric Just <e-just <at> northwestern.edu>
- Subject: bp_genbank2gff3.pl
+ Subject: genbank2gff3.pl
  Date: 2007-01-26 17:08:49 GMT
    -- bug fixed in genbank2gff3 for multi-record handling
 

scripts/Bio-DB-GFF/generate_histogram.PLS → scripts/Bio-DB-GFF/bp_generate_histogram.PLS

@@ -89,11 +89,11 @@ __END__
 
 =head1 NAME
 
-generate_histogram.pl -- Generate a histogram of Bio::DB::GFF features
+bp_generate_histogram.pl -- Generate a histogram of Bio::DB::GFF features
 
 =head1 SYNOPSIS
 
-  generate_histogram.pl -d gadfly variation gene:curated
+  bp_generate_histogram.pl -d gadfly variation gene:curated
 
 =head1 DESCRIPTION
 

scripts/Bio-DB-GFF/load_gff.PLS → scripts/Bio-DB-GFF/bp_load_gff.PLS

@@ -73,7 +73,7 @@ e.g. -d instead of --database.
 
 =head1 SEE ALSO
 
-L<Bio::DB::GFF>, L<bulk_load_gff.pl>, L<load_gff.pl>
+L<Bio::DB::GFF>, L<bulk_load_gff.pl>, L<bp_load_gff.pl>
 
 =head1 AUTHOR
 

scripts/Bio-DB-GFF/process_gadfly.PLS → scripts/Bio-DB-GFF/bp_process_gadfly.PLS

@@ -122,11 +122,11 @@ __END__
 
 =head1 NAME
 
-process_gadfly.pl - Massage Gadfly/FlyBase GFF files into a version suitable for the Generic Genome Browser
+bp_process_gadfly.pl - Massage Gadfly/FlyBase GFF files into a version suitable for the Generic Genome Browser
 
 =head1 SYNOPSIS
 
-  % process_gadfly.pl ./RELEASE2 > gadfly.gff
+  % bp_process_gadfly.pl ./RELEASE2 > gadfly.gff
 
 =head1 DESCRIPTION
 
@@ -145,7 +145,7 @@ you wish you can download the ZIP compressed versions of these files.
 Next run this script on the two files, indicating the name of the
 downloaded FASTA file first, followed by the gff file:
 
- % process_gadfly.pl na_whole-genome_genomic_dmel_RELEASE3.FASTA whole-genome_annotation-feature-region_dmel_RELEASE3.GFF > fly.gff
+ % bp_process_gadfly.pl na_whole-genome_genomic_dmel_RELEASE3.FASTA whole-genome_annotation-feature-region_dmel_RELEASE3.GFF > fly.gff
 
 The gadfly.gff file and the fasta file can now be loaded into a Bio::DB::GFF database
 using the following command:

scripts/Bio-DB-GFF/process_sgd.PLS → scripts/Bio-DB-GFF/bp_process_sgd.PLS

@@ -83,11 +83,11 @@ __END__
 
 =head1 NAME
 
-process_sgd.pl - Massage SGD annotation flat files into a version suitable for the Generic Genome Browser
+bp_process_sgd.pl - Massage SGD annotation flat files into a version suitable for the Generic Genome Browser
 
 =head1 SYNOPSIS
 
-  % process_sgd.pl chromosomal_features.tab > yeast.gff
+  % bp_process_sgd.pl chromosomal_features.tab > yeast.gff
 
 =head1 DESCRIPTION
 
@@ -99,7 +99,7 @@ genome browser.
 To use this script, get the SGD chromosomal_features.tab file from the
 FTP site listed above, and run the following command:
 
-  % process_sgd.pl chromosomal_features.tab > yeast.gff
+  % bp_process_sgd.pl chromosomal_features.tab > yeast.gff
 
 The yeast.gff file can then be loaded into a Bio::DB::GFF database
 using the following command:

scripts/Bio-DB-GFF/process_wormbase.PLS → scripts/Bio-DB-GFF/bp_process_wormbase.PLS

@@ -172,11 +172,11 @@ __END__
 
 =head1 NAME
 
-process_wormbase.pl - Massage WormBase GFF files into a version suitable for the Generic Genome Browser
+bp_process_wormbase.pl - Massage WormBase GFF files into a version suitable for the Generic Genome Browser
 
 =head1 SYNOPSIS
 
-  % process_wormbase.pl ./WS61 > wormbase.gff
+  % bp_process_wormbase.pl ./WS61 > wormbase.gff
 
 =head1 DESCRIPTION
 
@@ -197,7 +197,7 @@ not need to uncompress the files.
 Then give that directory as the argument to this script and capture
 the script's output to a file:
 
-  % process_wormbase.pl ./WS61 > wormbase.gff
+  % bp_process_wormbase.pl ./WS61 > wormbase.gff
 
 It may take a while before you see output from this script, since it
 must first fetch gene and protein database from the remote AceDB

scripts/DB-HIV/hivq.PLS → scripts/DB-HIV/bp_hivq.PLS

@@ -1,16 +1,16 @@
 #!perl
-#$Id: hivq.PL 362 2009-01-23 22:45:51Z maj $#
+#$Id: bp_hivq.PL 362 2009-01-23 22:45:51Z maj $#
 
 # command-line script for HIV sequence queries
 # using HIV.pm and HIVQuery.pm
 
 =head1 NAME
 
-hivq.PL - an interactive command-line interface to L<Bio::DB::HIV> and L<Bio::DB::Query::HIVQuery>
+bp_hivq.PL - an interactive command-line interface to L<Bio::DB::HIV> and L<Bio::DB::Query::HIVQuery>
 
 =head1 SYNOPSIS
 
- $ perl hivq.PL
+ $ perl bp_hivq.PL
  hivq> query C[subtype] SI[phenotype]
  hivq> prerun
  80 sequences returned
@@ -32,7 +32,7 @@ hivq.PL - an interactive command-line interface to L<Bio::DB::HIV> and L<Bio::DB
 The BioPerl modules L<Bio::DB::HIV> and L<Bio::DB::Query::HIVQuery>
 together allow batch queries against the Los Alamos National
 Laboratories' HIV Sequence Database using a simple query
-language. C<hivq.PL> provides both an example of the use of these
+language. C<bp_hivq.PL> provides both an example of the use of these
 modules, and a standalone interactive command-line interface to the
 LANL HIV DB. Simple commands allow the user to retrieve HIV sequences
 and annotations using the query language implemented in
@@ -41,7 +41,7 @@ more details.
 
 =head1 USAGE
 
-Run the script using C<perl hivq.PL> or, in Unix, C<./hivq.PL>. You will see
+Run the script using C<perl bp_hivq.PL> or, in Unix, C<./bp_hivq.PL>. You will see
 the
 
  hivq>
@@ -81,11 +81,11 @@ sequence hits for a query without retrieving the data. Use C<run> or
 C<do> to perform a complete query, retrieving sequence data into the
 currently set output files.
 
-To process C<hivq.PL> commands in batch, create a text file
-(C<hivq.cmd>, for example) containing desired commands one per
+To process C<bp_hivq.PL> commands in batch, create a text file
+(C<bp_hivq.cmd>, for example) containing desired commands one per
 line. Then execute the following from the shell:
 
- $ cat hivq.cmd | perl hivq.PL
+ $ cat bp_hivq.cmd | perl bp_hivq.PL
 
 =head1 COMMANDS
 

scripts/DB/biofetch_genbank_proxy.PLS → scripts/DB/bp_biofetch_genbank_proxy.PLS

@@ -222,7 +222,7 @@ __END__
 
 =head1 NAME
 
-biofetch_genbank_proxy.pl - Caching BioFetch-compatible web proxy for GenBank
+bp_biofetch_genbank_proxy.pl - Caching BioFetch-compatible web proxy for GenBank
 
 =head1 SYNOPSIS
 

scripts/DB/bioflat_index.PLS → scripts/DB/bp_bioflat_index.PLS

@@ -3,7 +3,7 @@
 
 =head1 NAME
 
-bioflat_index.pl - index sequence files using Bio::DB::Flat
+bp_bioflat_index.pl - index sequence files using Bio::DB::Flat
 
 =head1 DESCRIPTION
 
@@ -13,7 +13,7 @@ bioflat_index.pl - index sequence files using Bio::DB::Flat
 
 =head1 USAGE
 
- bioflat_index.pl <options> file1 file2 file3...
+ bp_bioflat_index.pl <options> file1 file2 file3...
 
  Options:
 

scripts/DB/biogetseq.PLS → scripts/DB/bp_biogetseq.PLS

@@ -36,7 +36,7 @@ while (my $id = shift) {
 
 =head1 NAME
 
-biogetseq - sequence retrieval using OBDA registry
+bp_biogetseq - sequence retrieval using OBDA registry
 
 =head1 DESCRIPTION
 
@@ -46,7 +46,7 @@ file, sql database or over the web.
 
 =head1 USAGE
 
-  Usage: biogetseq --dbname embl --format embl
+  Usage: bp_biogetseq --dbname embl --format embl
                    --namespace acc id [ ids... ]
          * dbname defaults to embl
          * format defaults to embl

scripts/DB/flanks.PLS → scripts/DB/bp_flanks.PLS

@@ -183,11 +183,11 @@ sub extract {
 
 =head1 NAME
 
-flanks - finding flanking sequences for a variant in a sequence position
+bp_flanks - finding flanking sequences for a variant in a sequence position
 
 =head1 SYNOPSIS
 
-  flanks --position POS [-p POS ...]  [--flanklen INT]
+  bp_flanks --position POS [-p POS ...]  [--flanklen INT]
          accession | filename
 
 =head1 DESCRIPTION
@@ -271,7 +271,7 @@ upper case and rest of the sequence in lower case characters.
 
 =head1 EXAMPLE
 
-  % flanks ~/seq/ar.embl
+  % bp_flanks ~/seq/ar.embl
 
   >1_/HOME/HEIKKI/SEQ/AR.EMBL oripos=100 strand=1 allelepos=100
   taataactcagttcttatttgcacctacttcagtggacactgaatttggaaggtggagga