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Fixing POD documentation. Empty line before =cut to avoid problems wi…

…th pod2X tools
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1 parent 9f20929 commit 9bc9b0208dd9a60dde4584ab4ddf1367f9fc2a13 @carandraug carandraug committed Jan 28, 2013
Showing with 18 additions and 0 deletions.
  1. +18 −0 scripts/Bio-DB-EUtilities/bp_genbank_ref_extractor.pl
@@ -49,13 +49,15 @@ =head1 OPTIONS
See the section bugs for problems when using default values of options.
=over
+
=cut
=item B<--assembly>
When retrieving the sequence, a specific assemly can be defined. The value expected
is a regex that will be case-insensitive. If it matches more than one assembly, it will
use the first match. It defauls to C<(primary|reference) assembly>.
+
=cut
my $assembly_regex = '(primary|reference) assembly';
@@ -64,20 +66,23 @@ =head1 OPTIONS
If set, even more output will be printed that may help on debugging. Unlike the messages
from B<--verbose> and B<--very-verbose>, these will not appear on the log file
unless this option is selected. This option also sets B<--very-verbose>.
+
=cut
my $debug = 0;
=item B<--downstream>, B<--down>
Specifies the number of extra base pairs to be retrieved downstream of the gene.
This extra base pairs will only affect the gene sequence, not the transcript or proteins.
+
=cut
my $downstream = 0;
=item B<--format>
Specifies the format that the sequences will be saved. Defaults to I<genbank> format.
Valid formats are 'genbank' or 'fasta'.
+
=cut
my $format = 'genbank';
@@ -86,6 +91,7 @@ =head1 OPTIONS
Specifies the name for gene file. By default, they are not saved. If no value is given
defaults to its UID. Possible values are 'uid', 'name', 'symbol' (the official symbol or
nomenclature).
+
=cut
my $genes = '';
sub genes_option_parsing {
@@ -105,13 +111,15 @@ sub genes_option_parsing {
prevent the use of specially unspecific queries and a warning will be given if a
query returns more results than the limit. The default value is 200. Note that
this limit is for I<each> search.
+
=cut
my $limit = 200;
=item B<--non-coding>, B<--nonon-coding>
Some protein coding genes have transcripts that are non-coding. By default, these sequences are
saved as well. B<--nonon-coding> can be used to ignore those transcripts.
+
=cut
my $get_noncoding = 1;
@@ -123,6 +131,7 @@ sub genes_option_parsing {
Note that if not using 'accession' is possible for files to be overwritten. It is possible for the same gene
to encode more than one protein or different proteins to have the same description.
+
=cut
my $proteins = '';
sub proteins_option_parsing {
@@ -140,6 +149,7 @@ sub proteins_option_parsing {
=item B<--pseudo>, B<--nopseudo>
By default, sequences of pseudo genes will be saved. B<--nopseudo> can be used to ignore those genes.
+
=cut
my $get_pseudo = 1;
@@ -149,6 +159,7 @@ sub proteins_option_parsing {
directory does not exist it will be created altough the path to it must exist. Files on the
directory may be rewritten if necessary. If unspecified, a directory named F<extracted sequences>
on the current directory will be used.
+
=cut
my $save = File::Spec->catfile (getcwd, 'extracted sequences');
@@ -160,6 +171,7 @@ sub proteins_option_parsing {
Currently only CSV is supported.
Saving the data structure as a CSV file, requires the installation of the Text::CSV module.
+
=cut
my $save_data = '';
sub save_data_option_parsing {
@@ -179,6 +191,7 @@ sub save_data_option_parsing {
Note that if not using 'accession' is possible for files to be overwritten. It is possible for the same gene
to have more than one transcript or different transcripts to have the same description. Also, non-coding
transcripts will create problems if using 'protein'.
+
=cut
my $transcripts = '';
sub transcripts_option_parsing {
@@ -197,19 +210,22 @@ sub transcripts_option_parsing {
Specifies the number of extra base pairs to be extracted upstream of the gene.
This extra base pairs will only affect the gene sequence, not the transcript or proteins.
+
=cut
my $upstream = 0;
=item B<--verbose>, B<--v>
If set, program becomes verbose. For an extremely verbose program, use B<--very-verbose> instead.
+
=cut
my $verbose = '';
=item B<--very-verbose>, B<--vv>
If set, program becomes extremely verbose. Setting this option, automatically sets B<--verbose> as well.
For help in debugging, consider using B<--debug>
+
=cut
my $very_verbose = '';
@@ -761,6 +777,7 @@ sub get_products {
When creating the directories to save the files, if the directory already exists it will be used and no error
or warning will be issued unless B<--debug> as been set. If a non-directory file already exists with that name
bp_genbank_ref_extractor exits with an error.
+
=cut
## checks if directories exist and creates them as needed
@@ -781,6 +798,7 @@ sub check_dir {
B<--verbose> and B<--very-verbose> only affect their printing to standard
output. Debug messages are different as they will only show up (and be logged)
if requested with B<--debug>.
+
=cut
sub log_it {

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