/usr/share/perl5/Bio/Tools/Run/Bowtie/Config.pm is in libbio-perl-run-perl 1.6.9-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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#
# BioPerl module for Bio::Tools::Run::Bowtie::Config
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Dan Kortschak <dan.kortschak@adelaide.edu.au>
#
# Copyright Dan Kortschak and 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::Bowtie::Config - Configuration data for bowtie commands
=head1 SYNOPSIS
Used internally by L<Bio::Tools::Run::Bowtie>.
=head1 DESCRIPTION
This package exports information describing bowtie commands, parameters,
switches, and input and output filetypes for individual bowtie 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 - Dan Kortschak
Email dan.kortschak adelaide.edu.au
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::Bowtie::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_executables
%format_lookup
%command_prefixes
%composite_commands
@program_params
@program_switches
%incompat_params
%corequisite_switches
%param_translation
%command_files
%accepted_types
);
@EXPORT_OK = qw();
our @program_commands = qw(
single
paired
crossbow
build
inspect
);
our %command_executables = (
'single' => 'bowtie',
'paired' => 'bowtie',
'crossbow' => 'bowtie',
'build' => 'bowtie-build',
'inspect' => 'bowtie-inspect'
);
# These should be in clobbering order - more delicate formats first
our %format_lookup = (
'sam_format' => 'sam',
'refidx' => 'bowtie',
'concise' => undef,
'suppress_columns' => undef,
'refout' => undef
);
# 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 = (
);
# prefixes only for commands that take params/switches...
our %command_prefixes = (
'single' => 'one',
'paired' => 'par',
'crossbow' => 'crb',
'build' => 'bld',
'inspect' => 'ins'
);
our @program_params = qw(
command
one|qualities
one|skip
one|upto
one|trim5
one|trim3
one|max_seed_mismatches
one|max_qual_mismatch
one|max_quality_sum
one|snp_penalty
one|snp_frac
one|seed_length
one|max_mismatches
one|max_backtracks
one|max_search_ram
one|report_n_alignments
one|supress
one|supress_random
one|offset_base
one|defaul_mapq
one|sam_rg
one|suppress_columns
one|alignmed_file
one|unaligned_file
one|excess_file
one|threads
one|offrate
one|random_seed
par|qualities1
par|qualities2
par|min_insert_size
par|max_insert_size
par|max_mate_attempts
bld|max_bucket_block
bld|max_bucket_div
bld|diff_cover
bld|off_rate
bld|ftabchars
bld|seed
bld|cutoff
ins|seq_width
);
our @program_switches = qw(
one|fastq
one|fasta
one|raw
one|inline
one|color_space
one|phred33
one|phred64
one|solexa
one|solexa1_3
one|integer_qual
one|no_maq_rounding
one|no_forward_alignment
one|no_reverse_alignment
one|try_hard
one|all
one|best
one|strata
one|fix_strand_bias
one|print_color
one|color_quals
one|color_keep_ends
one|sam_format
one|sam_no_head
one|sam_no_sq
one|concise
one|time
one|be_quiet
one|ref_map
one|ref_index
one|full_ref_name
one|memory_mapped_io
one|shared_memory
par|forward_reverse
par|reverse_reverse
par|forward_forward
bld|fasta
bld|inline
bld|color_space
bld|both
bld|no_auto
bld|packed
bld|no_diff_cover
bld|no_ref
bld|just_ref
bld|NtoA
bld|big_endian
bld|little_endian
ins|names_only
ins|summary
ins|reconstruct
);
# be careful of collisions here - this could do with command specification
our %incompat_params = (
qualities => [qw( qualities1 qualities2 )],
qualities1 => [qw( qualities )],
qualities2 => [qw( qualities )],
max_seed_mismatches => [qw( max_mismatches )],
max_mismatches => [qw( max_seed_mismatches )],
fastq => [qw( fasta raw inline )],
fasta => [qw( fastq raw inline )],
raw => [qw( fastq fasta inline )],
inline => [qw( fastq fasta raw )],
phred33 => [qw( phred64 solexa solexa1_3 integer_qual )],
phred64 => [qw( phred33 solexa solexa1_3 integer_qual )],
solexa => [qw( phred33 phred64 solexa1_3 integer_qual )],
solexa1_3 => [qw( phred33 phred64 solexa integer_qual )],
integer_qual => [qw( phred33 phred64 solexa solexa1_3 )],
no_forward_alignment => [qw( no_reverse_alignment )],
no_reverse_alignment => [qw( no_forward_alignment )],
all => [qw( report_n_alignments )],
report_n_alignments => [qw( all )],
forward_reverse => [qw( reverse_reverse forward_forward )],
reverse_reverse => [qw( forward_reverse forward_forward )],
forward_forward => [qw( reverse_reverse forward_forward )],
color_space => [qw( both )],
both => [qw( color_space)]
);
our %corequisite_switches = (
qualities1 => [qw( qualities2 )],
qualities2 => [qw( qualities1 )],
strata => [qw( best )],
suppress_random => [qw( best )],
snp_penalty => [qw( color_space )],
snp_frac => [qw( color_space )],
print_color => [qw( color_space )],
color_quals => [qw( color_space )],
color_keep_ends => [qw( color_space )],
defaul_mapq => [qw( sam_format )],
sam_no_head => [qw( sam_format )],
sam_no_sq => [qw( sam_format )],
sam_rg => [qw( sam_format )]
);
our %param_translation = (
'one|fastq' => 'q',
'one|fasta' => 'f',
'one|raw' => 'r',
'one|inline' => 'c',
'one|color_space' => 'C',
'one|qualities' => 'Q',
'one|skip' => 's',
'one|upto' => 'u',
'one|trim5' => '5',
'one|trim3' => '3',
'one|phred33' => 'phred33-quals',
'one|phred64' => 'phred64-quals',
'one|solexa' => 'solexa-quals',
'one|solexa1_3' => 'solexa1.3-quals',
'one|integer_qual' => 'integer-quals',
'one|max_seed_mismatches' => 'n',
'one|max_qual_mismatch' => 'e',
'one|seed_length' => 'l',
'one|no_maq_rounding' => 'nomaqround',
'one|max_mismatches' => 'v',
'one|no_forward_alignment' => 'nofw',
'one|no_reverse_alignment' => 'norc',
'one|max_backtracks' => 'maxbts',
'one|try_hard' => 'y',
'one|max_search_ram' => 'chunkmbs',
'one|report_n_alignments' => 'k',
'one|all' => 'a',
'one|supress' => 'm',
'one|supress_random' => 'M',
'one|best' => 'best',
'one|strata' => 'strata',
'one|snp_penalty' => 'snpphred',
'one|snp_frac' => 'snpfrac',
'one|print_color' => 'col-cseq',
'one|color_quals' => 'colc-cqual',
'one|color_keep_ends' => 'col-keepends',
'one|sam_format' => 'S',
'one|defaul_mapq' => 'mapq',
'one|sam_no_head' => 'sam_nohead',
'one|sam_no_sq' => 'sam_nosq',
'one|sam_rg' => 'sam-RG',
'one|suppress_columns' => 'suppress',
'one|time' => 't',
'one|offset_base' => 'B',
'one|be_quiet' => 'quiet',
'one|ref_map' => 'refout',
'one|ref_index' => 'refidx',
'one|alignmed_file' => 'al',
'one|unaligned_file' => 'un',
'one|excess_file' => 'max',
'one|full_ref_name' => 'fullref',
'one|threads' => 'p',
'one|offrate' => 'o',
'one|memory_mapped_io' => 'mm',
'one|shared_memory' => 'shmem',
'one|random_seed' => 'seed',
'one|version' => 'version',
'par|fastq' => 'q',
'par|fasta' => 'f',
'par|raw' => 'r',
'par|inline' => 'c',
'par|color_space' => 'C',
'par|qualities' => 'Q', # Don't know if bowtie will accept this - won't break if left in
'par|qualities1' => 'Q1',
'par|qualities2' => 'Q2',
'par|skip' => 's',
'par|upto' => 'u',
'par|trim5' => '5',
'par|trim3' => '3',
'par|phred33' => 'phred33-quals',
'par|phred64' => 'phred64-quals',
'par|solexa' => 'solexa-quals',
'par|solexa1_3' => 'solexa1.3-quals',
'par|integer_qual' => 'integer-quals',
'par|max_seed_mismatches' => 'n',
'par|max_qual_mismatch' => 'e',
'par|seed_length' => 'l',
'par|no_maq_rounding' => 'nomaqround',
'par|max_mismatches' => 'v',
'par|min_insert_size' => 'I',
'par|max_insert_size' => 'X',
'par|forward_reverse' => 'fr',
'par|reverse_forward' => 'rf',
'par|forward_forward' => 'ff',
'par|no_forward_alignment' => 'nofw',
'par|no_reverse_alignment' => 'norc',
'par|max_backtracks' => 'maxbts',
'par|max_mate_attempts' => 'pairtries',
'par|try_hard' => 'y',
'par|max_search_ram' => 'chunkmbs',
'par|report_n_alignments' => 'k',
'par|all' => 'a',
'par|suppress' => 'm',
'par|suppress_random' => 'M',
'par|best' => 'best',
'par|strata' => 'strata',
'par|snp_penalty' => 'snpphred',
'par|snp_frac' => 'snpfrac',
'par|print_color' => 'col-cseq',
'par|color_quals' => 'colc-cqual',
'par|color_keep_ends' => 'col-keepends',
'par|sam_format' => 'S',
'par|defaul_mapq' => 'mapq',
'par|sam_no_head' => 'sam_nohead',
'par|sam_no_sq' => 'sam_nosq',
'par|sam_rg' => 'sam-RG',
'par|suppress_columns' => 'suppress',
'par|time' => 't',
'par|offset_base' => 'B',
'par|be_quiet' => 'quiet',
'par|ref_map' => 'refout',
'par|ref_index' => 'refidx',
'par|alignmed_file' => 'al',
'par|unaligned_file' => 'un',
'par|excess_file' => 'max',
'par|full_ref_name' => 'fullref',
'par|threads' => 'p',
'par|offrate' => 'o',
'par|memory_mapped_io' => 'mm',
'par|shared_memory' => 'shmem',
'par|random_seed' => 'seed',
'par|version' => 'version',
'crb|fastq' => 'q',
'crb|fasta' => 'f',
'crb|raw' => 'r',
'crb|inline' => 'c',
'crb|color_space' => 'C',
'crb|qualities' => 'Q',
'crb|skip' => 's',
'crb|upto' => 'u',
'crb|trim5' => '5',
'crb|trim3' => '3',
'crb|phred33' => 'phred33-quals',
'crb|phred64' => 'phred64-quals',
'crb|solexa' => 'solexa-quals',
'crb|solexa1_3' => 'solexa1.3-quals',
'crb|integer_qual' => 'integer-quals',
'crb|max_seed_mismatches' => 'n',
'crb|max_qual_mismatch' => 'e',
'crb|seed_length' => 'l',
'crb|no_maq_rounding' => 'nomaqround',
'crb|max_mismatches' => 'v',
'crb|min_insert_size' => 'I',
'crb|max_insert_size' => 'X',
'crb|forward_reverse' => 'fr',
'crb|reverse_forward' => 'rf',
'crb|forward_forward' => 'ff',
'crb|no_forward_alignment' => 'nofw',
'crb|no_reverse_alignment' => 'norc',
'crb|max_backtracks' => 'maxbts',
'crb|max_mate_attempts' => 'pairtries',
'crb|try_hard' => 'y',
'crb|max_search_ram' => 'chunkmbs',
'crb|report_n_alignments' => 'k',
'crb|all' => 'a',
'crb|suppress' => 'm',
'crb|suppress_random' => 'M',
'crb|best' => 'best',
'crb|strata' => 'strata',
'crb|snp_penalty' => 'snpphred',
'crb|snp_frac' => 'snpfrac',
'crb|print_color' => 'col-cseq',
'crb|color_quals' => 'colc-cqual',
'crb|color_keep_ends' => 'col-keepends',
'crb|sam_format' => 'S',
'crb|defaul_mapq' => 'mapq',
'crb|sam_no_head' => 'sam_nohead',
'crb|sam_no_sq' => 'sam_nosq',
'crb|sam_rg' => 'sam-RG',
'crb|suppress_columns' => 'suppress',
'crb|time' => 't',
'crb|offset_base' => 'B',
'crb|be_quiet' => 'quiet',
'crb|ref_map' => 'refout',
'crb|ref_index' => 'refidx',
'crb|alignmed_file' => 'al',
'crb|unaligned_file' => 'un',
'crb|excess_file' => 'max',
'crb|full_ref_name' => 'fullref',
'crb|threads' => 'p',
'crb|offrate' => 'o',
'crb|memory_mapped_io' => 'mm',
'crb|shared_memory' => 'shmem',
'crb|random_seed' => 'seed',
'crb|version' => 'version',
'bld|fasta' => 'f',
'bld|inline' => 'c',
'bld|color_space' => 'C',
'bld|both' => 'B',
'bld|no_auto' => 'a',
'bld|packed' => 'p',
'bld|max_bucket_block' => 'bmax',
'bld|max_bucket_div' => 'bmaxdivn',
'bld|diff_cover' => 'dcv',
'bld|no_diff_cover' => 'nodc',
'bld|no_ref' => 'r',
'bld|just_ref' => '3',
'bld|off_rate' => 'o',
'bld|ftabchars' => 't',
'bld|NtoA' => 'ntoa',
'bld|big_endian' => 'big',
'bld|little_endian' => 'little',
'bld|seed' => 'seed',
'bld|cutoff' => 'cutoff',
'bld|version' => 'version',
'ins|seq_width' => 'a',
'ins|names_only' => 'n',
'ins|summary' => 's',
'ins|reconstruct' => 'e',
'ins|version' => 'version'
);
#
# 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_bowtie
#
# special chars:
#
# '#' implies optional
# '*' implies variable number of this type
# <|> implies stdin/stdout redirect
#
our %command_files = (
'single' => [qw( ind seq #out )],
'paired' => [qw( ind -1|seq -2|seq2 #out )],
'crossbow' => [qw( ind -12|seq #out )],
'build' => [qw( ref #out )],
'inspect' => [qw( ind >#out )]
);
our %accepted_types = ( # ind is not a single file, so not included here
'seq' => [qw( fasta fastq raw crossbow )],
'seq2' => [qw( fasta fastq raw )],
'ref' => [qw( fasta )]
);
foreach (@program_params) {
push @program_params, "par\|".$1 if (m/^one\|(.*)/);
push @program_params, "crb\|".$1 if (m/^par\|(.*)/) && !(m/^par\|(?:fasta|fastq|raw|qualities[12])/);
}
foreach (@program_switches) {
push @program_switches, "par\|".$1 if (m/^one\|(.*)/);
push @program_switches, "crb\|".$1 if (m/^par\|(.*)/) && !(m/^par\|(?:fasta|fastq|raw)/);
}
1;
|