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# $Id$
#
# BioPerl module for Bio::Tools::Run::Maq::Config
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Mark A. Jensen <maj@fortinbras.us>
#
# Copyright Mark A. Jensen
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Tools::Run::Maq::Config - Configuration data for maq commands
=head1 SYNOPSIS
Used internally by L<Bio::Tools::Run::Maq>.
=head1 DESCRIPTION
This package exports information describing maq commands, parameters,
switches, and input and output filetypes for individual maq commands.
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
L<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
the web:
http://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR - Mark A. Jensen
Email maj@fortinbras.us
Describe contact details here
=head1 CONTRIBUTORS
Additional contributors names and emails here
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Tools::Run::Maq::Config;
use strict;
use warnings;
no warnings qw(qw);
use Bio::Root::Root;
use Exporter;
use base qw(Bio::Root::Root );
our (@ISA, @EXPORT, @EXPORT_OK);
push @ISA, 'Exporter';
@EXPORT = qw(
@program_commands
%command_prefixes
%composite_commands
@program_params
@program_switches
%param_translation
%command_files
);
@EXPORT_OK = qw();
our @program_commands = qw(
run
fasta2bfa
fastq2bfq
map
mapmerge
rmdup
assemble
indelpe
indelsoa
sol2sanger
bfq2fastq
mapass2maq
mapview
mapcheck
pileup
cns2fq
cns2snp
cns2view
cns2ref
cns2win
fasta2csfa
csmap2nt
submap
eland2maq
export2maq
);
# composite commands: pseudo-commands that run a
# sequence of commands
# composite command prefix => list of prefixes of commands this
# composite command runs
#
our %composite_commands = (
'run' => [qw( map asm c2q )]
);
# prefixes only for commands that take params/switches...
our %command_prefixes = (
'fastq2bfq' => 'q2q',
'map' => 'map',
'assemble' => 'asm',
'mapview' => 'mv',
'mapcheck' => 'mck',
'pileup' => 'pup',
'cns2fq' => 'c2q',
'cns2win' => 'c2w',
'submap' => 'sub',
'eland2maq' => 'l2m',
'export2maq' => 'x2m',
'run' => 'run'
);
our @program_params = qw(
command
q2q|n
map|adaptor_file
map|first_read_length
map|max_hits
map|max_mismatches
map|max_outer_distance
map|max_outer_distance_rf
map|mismatch_dump
map|mismatch_posn_dump
map|mismatch_thr
map|mutation_rate
map|second_read_length
map|unmapped_dump
asm|error_dep_coeff
asm|het_fraction
asm|max_mismatches
asm|max_quality_sum
asm|min_map_quality
asm|num_haplotypes
mck|max_mismatches
mck|min_map_quality
pup|max_mismatches
pup|max_quality_vals
pup|min_map_quality
pup|site_input_file
c2q|min_map_quality
c2q|min_read_depth
c2q|min_nbr_quality
c2q|max_read_depth
c2w|window_size
c2w|ref_seq
c2w|start_posn
c2w|end_posn
c2w|min_cons_quality
sub|max_mismatches
sub|max_quality_sum
sub|min_map_quality
l2q|def_qual
x2m|max_outer_distance
x2m|first_read_length
x2m|second_read_length
);
our @program_switches = qw(
asm|single_end_quality
asm|discard_wrong_pairs
mv|omit_seq_qual
mv|show_mismatch_posns
mck|single_end_quality
pup|single_end_quality
pup|discard_wrong_pairs
pup|verbose
pup|show_base_posn
sub|discard_wrong_pairs
x2m|retain_filt_reads
);
our %param_translation = (
'q2q|n' => 'n',
'map|max_mismatches' => 'n',
'map|max_outer_distance' => 'a',
'map|max_outer_distance_rf' => 'A',
'map|first_read_length' => '1',
'map|second_read_length' => '2',
'map|mutation_rate' => 'm',
'map|adaptor_file' => 'd',
'map|unmapped_dump' => 'u',
'map|mismatch_thr' => 'e',
'map|mismatch_dump' => 'H',
'map|max_hits' => 'C',
'map|mismatch_posn_dump' => 'N',
'asm|error_dep_coeff' => 't',
'asm|het_fraction' => 'r',
'asm|max_mismatches' => 'm',
'asm|max_quality_sum' => 'Q',
'asm|min_map_quality' => 'q',
'asm|num_haplotypes' => 'N',
'mck|max_mismatches' => 'm',
'mck|min_map_quality' => 'q',
'pup|max_mismatches' => 'm',
'pup|max_quality_vals' => 'Q',
'pup|min_map_quality' => 'q',
'pup|site_input_file' => 'l',
'c2q|min_map_quality' => 'Q',
'c2q|min_read_depth' => 'd',
'c2q|min_nbr_quality' => 'n',
'c2q|max_read_depth' => 'D',
'c2w|window_size' => 'w',
'c2w|ref_seq' => 'c',
'c2w|start_posn' => 'b',
'c2w|end_posn' => 'e',
'c2w|min_cons_quality' => 'q',
'sub|max_mismatches' => 'm',
'sub|max_quality_sum' => 'Q',
'sub|min_map_quality' => 'q',
'l2q|def_qual' => 'q',
'x2m|max_outer_distance' => 'a',
'x2m|first_read_length' => '1',
'x2m|second_read_length' => '2',
'asm|single_end_quality' => 's',
'asm|discard_wrong_pairs' => 'p',
'mv|omit_seq_qual' => 'b',
'mv|show_mismatch_posns' => 'N',
'mck|single_end_quality' => 's',
'pup|single_end_quality' => 's',
'pup|discard_wrong_pairs' => 'p',
'pup|verbose' => 'v',
'pup|show_base_posn' => 'P',
'sub|discard_wrong_pairs' => 'p',
'x2m|retain_filt_reads' => 'n'
);
#
# the order in the arrayrefs is the order required
# on the command line
#
# the strings in the arrayrefs (less special chars)
# become the keys for named parameters to run_maq
#
# special chars:
#
# '#' implies optional
# '*' implies variable number of this type
# <|> implies stdin/stdout redirect
#
our %command_files = (
'run' => [qw( faq fas faq )],
'fastq2bfq' => [qw( faq bfq )],
'fasta2bfa' => [qw( fas bfa )],
'map' => [qw( map bfa bfq1 #bfq2 2>#log )],
'mapmerge' => [qw( out_map *in_map )],
'rmdup' => [qw( out_map in_map )],
'assemble' => [qw( cns bfa map 2>#log )],
'indelpe' => [qw( bfa map >txt )],
'indelsoa' => [qw( bfa map >txt )],
'sol2sanger' => [qw( in_faq out_faq )],
'bfq2fastq' => [qw( bfq faq )],
'mapass2maq' => [qw( in_map out_map )],
'mapview' => [qw( map >txt )],
'mapcheck' => [qw( bfa map >txt )],
'pileup' => [qw( bfa map >txt )],
'cns2fq' => [qw( cns >faq )],
'cns2snp' => [qw( cns >txt )],
'cns2view' => [qw( cns >txt )],
'cns2ref' => [qw( cns >fas )],
'cns2win' => [qw( cns >txt )],
'fasta2csfa' => [qw( in_fas >out_fas )],
'csmap2nt' => [qw( out_map bfa in_map )],
'submap' => [qw( out_map in_map )],
'eland2maq' => [qw( map lis eld )],
'export2maq' => [qw( map lis xpt )]
);
INIT {
# add subcommand params and switches for
# composite commands
my @sub_params;
my @sub_switches;
foreach my $cmd (keys %composite_commands) {
foreach my $subcmd ( @{$composite_commands{$cmd}} ) {
my @sub_program_params = grep /^$subcmd\|/, @program_params;
my @sub_program_switches = grep /^$subcmd\|/, @program_switches;
for (@sub_program_params) {
m/^$subcmd\|(.*)/;
push @sub_params, "$cmd\|${subcmd}_".$1;
}
for (@sub_program_switches) {
m/^$subcmd\|(.*)/;
push @sub_switches, "$cmd\|${subcmd}_".$1;
}
}
}
push @program_params, @sub_params;
push @program_switches, @sub_switches;
# translations for subcmd params/switches not necessary
}
1;