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filling out cyoa with various utilities.
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@abelew
abelew committed Dec 18, 2015
1 parent 4c47fbc commit 8aa4ed1
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59 changes: 19 additions & 40 deletions bin/cyoa
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Original file line number Diff line number Diff line change
Expand Up @@ -51,23 +51,31 @@ my $menus = {
TNSeq => {
name => 'tnseq',
message => "You have enterred a world of jumping DNA, be ware and go to page 342.",
choices => ['Sort_Indexes','Biopieces_Graph','Cutadapt','Essentiality_TAs','BT_Multi'],},
choices => ['Sort_Indexes','Biopieces_Graph','Cutadapt','BT_Multi','Essentiality_TAs','Run_Essentiality',],},
RiboSeq => {
name => 'riboseq',
message => "Awake Awake Fear Fire Foes! Go to page 4",
choices => ['Biopieces_Graph','Cutadapt','BT_Multi','Calibrate','Count_States','Graph_Reads'],},
choices => ['Biopieces_Graph','Cutadapt','BT_Multi','Calibrate','Count_States','Graph_Reads',],},
Alignment => {
name => 'alignment',
message => "Hari Seldon once said violence is the last refuge of the incompetent. Go to page 128.",
choices => ['Blast_Parse','Split_Align','Split_Align_Blast','Split_Align_Fasta','Parse_Blast'],},
choices => ['Split_Align_Blast','Split_Align_Fasta','Concatenate_Searches','Parse_Fasta','Parse_Blast','Merge_Parse_Blast'],},
Conversion => {
name => 'convert',
message => qq"And it rained a fever.
And it rained a silence.
And it rained a sacrifice.
And it rained a miracle.
And it rained sorceries and saturnine eyes of the totem. Go to page 222.",
choices => ['Sam2Bam','Gb2Gff','TriTryp2Text','TriTryp_Download',],},
message => qq"And it rained a fever. And it rained a silence. And it rained a sacrifice. And it rained a miracle. And it rained sorceries and saturnine eyes of the totem. Go to page 222.",
choices => ['Sam2Bam','Gb2Gff','Gff2Fasta', 'TriTryp2Text','TriTryp_Download',],},
Assembly => {
name => 'assembly',
message => qq"The wise man fears the wrath of a gentle heart.",
choices => ['Trinity', 'Trinity_Post',]},
Pipeline => {
name => 'pipeline',
message => qq"When Mr. Bilbo Baggins announced he would shortly be celebrating his eleventyfirst birthday, there was much talk and excitement in Hobbiton.",
choices => ['Pipeline_Riboseq','Pipeline_TNseq','Pipline_RNAseq_Bowtie','Pipline_RNAseq_Bowtie2','Pipline_RNAseq_Tophat','Pipline_RNAseq_BWA','Pipline_RNAseq_Kallisto',]},
Test => {
name => 'test',
message => qq"All happy families are happy in the same way.",
choices => ['Test_Job',],},
};
## The general idea is to have a toplevel 'task' to perform
## Something like TNSeq, RNASeq, etc
Expand Down Expand Up @@ -145,39 +153,10 @@ sub Match_Method {
my $h = $args{hpgl};
my $m = '--' . $args{method};
my @method = ($m,);

my %todo = (
);
my %methods = %{$h->{methods}};
## This way, we can trivially make an array to pass to GetOptionsFromArray()
my %methods = (
"biopieces+" => \$todo{Biopieces_Graph},
"blastparse+" => \$todo{Blast_Parse},
"bowtierrna+" => \$todo{Bowtie_RRNA},
"btmulti+" => \$todo{BT_Multi},
"calibrate+" => \$todo{Calibrate},
"countstates+" => \$todo{Count_States},
"cutadapt+" => \$todo{Cutadapt},
"essentialitytas+" => \$todo{Essentiality_TAs},
"fastqc+" => \$todo{FastQC},
"gb2gff+" => \$todo{Gb2Gff},
"graphreads+" => \$todo{Graph_Reads},
"htmulti+" => \$todo{HT_Multi},
"kallisto+" => \$todo{Kallisto},
"parseblast+" => \$todo{Parse_Blast},
"sam2bam+" => \$todo{Sam2Bam},
"sortindexes+" => \$todo{Sort_Indexes},
"splitalign+" => \$todo{Split_Align},
"blastsplitalign+" => \$todo{Split_Align_Blast},
"fastasplitalign+" => \$todo{Split_Align_Fasta},
"tophat+" => \$todo{Tophat},
"trinity+" => \$todo{Trinity},
"tritrypdownload+" => \$todo{TriTryp_Download},
"tritryp2text+" => \$todo{TriTryp2Text},
"posttrinity+" => \$todo{Trinity_Post},
"trimomatic+" => \$todo{Trimomatic},
);

my $array_result = GetOptionsFromArray(\@method, %methods);
my %todo = %{$h->{todo}};
## Now some portions of $todo should be filled in with 1s
foreach my $job (keys %todo) {
if ($todo{$job}) {
Expand Down
186 changes: 175 additions & 11 deletions lib/HPGL.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -170,7 +170,7 @@ sub new {
## The base directory when invoking various shell commands
$me->{basedir} = cwd() if (!defined($me->{basedir}));
$me->{blast_params} = ' -e 10 ' if (!defined($me->{blast_params}));
$me->{blast_program} = 'blastn' if (!defined($me->{blast_program}));
$me->{blast_tool} = undef;
$me->{blast_peptide} = 'F' if (!defined($me->{blast_peptide}));

## A series of default bowtie1 arguments
Expand All @@ -193,29 +193,30 @@ sub new {
## A default feature type when examining gff files
$me->{feature_type} = 'CDS' if (!defined($me->{feature_type}));
## A default gff file!
$me->{gff} = 'default.gff' if (!defined($me->{gff}));
$me->{genome} = undef;
$me->{gff} = undef;
## Ask for help?
$me->{help} = undef if (!defined($me->{help}));
$me->{help} = undef;
## An hpgl identifier
$me->{hpgl} = undef if (!defined($me->{hpgl}));
$me->{hpgl} = undef;
## The identifier flag passed to htseq (probably should be moved to feature_type)
$me->{htseq_identifier} = 'ID' if (!defined($me->{htseq_identifier}));
## Use htseq stranded options?
$me->{htseq_stranded} = 'no' if (!defined($me->{htseq_stranded}));
## An index file for tnseq (change this variable to tnseq_index I think)
$me->{index_file} = 'indexes.txt' if (!defined($me->{index_file}));
## The default input file
$me->{input} = undef if (!defined($me->{input}));
$me->{input} = undef;
## A list of jobs
$me->{jobs} = [] if (!defined($me->{jobs}));
## And a hash of jobids
$me->{jobids} = {} if (!defined($me->{jobids}));
## Minimum length for good reads (riboseq): FIXME rename this
$me->{len_min} = 21 if (!defined($me->{len_min}));
$me->{len_min} = 16 if (!defined($me->{len_min}));
## Maximum length for good reads (riboseq): FIXME rename this
$me->{len_max} = 40 if (!defined($me->{len_max}));
$me->{len_max} = 42 if (!defined($me->{len_max}));
## The default directory for gff/fasta/genbank/indexes
$me->{library} = undef if (!defined($me->{library}));
$me->{library} = undef;
$me->{libdir} = "$ENV{HOME}/libraries" if (!defined($me->{libdir}));
## What type of library are we going to search for?
$me->{libtype} = 'genome' if (!defined($me->{libtype}));
Expand All @@ -238,7 +239,8 @@ sub new {
$me->{qsub_cpus} = '4' if (!defined($me->{qsub_cpus}));
$me->{qsub_depends} = 'depend=afterok:' if (!defined($me->{qsub_depends}));
$me->{qsub_loghost} = 'localhost' if (!defined($me->{qsub_loghost}));
$me->{query} = undef if (!defined($me->{query}));
$me->{qual} = undef;
$me->{query} = undef;
$me->{riboasite} = 1 if (!defined($me->{riboasite}));
$me->{ribopsite} = 1 if (!defined($me->{ribopsite}));
$me->{riboesite} = 1 if (!defined($me->{riboesite}));
Expand All @@ -249,8 +251,8 @@ sub new {
$me->{ribocorrect} = 1 if (!defined($me->{ribocorrect}));
$me->{riboanchor} = 'start' if (!defined($me->{rioanchor}));
$me->{ribosizes} = '25,26,27,28,29,30,31,32,33,34' if (!defined($me->{ribosizes}));
$me->{species} = undef if (!defined($me->{species}));
$me->{suffixes} = ['.fastq', '.gz', '.xz', '.fasta', '.sam', '.bam', '.count'] if (!defined($me->{suffixes}));
$me->{species} = undef;
$me->{suffixes} = ['.fastq', '.gz', '.xz', '.fasta', '.sam', '.bam', '.count', '.csfasta', '.qual'] if (!defined($me->{suffixes}));
$me->{task} = undef;
$me->{taxid} = '353153' if (!defined($me->{taxid}));
$me->{tnseq_trim} = 0 if (!defined($me->{tnseq_trim}));
Expand Down Expand Up @@ -355,6 +357,47 @@ sub new {
if ($failed) {
warn("HPGL.pm requires external programs, of which $failed were missing.");
}
$me->{todo} = ();
$me->{methods} = {
"biopieces+" => \$me->{todo}{Biopieces_Graph},
"blastparse+" => \$me->{todo}{Blast_Parse},
"blastsplitalign+" => \$me->{todo}{Split_Align_Blast},
"bowtierrna+" => \$me->{todo}{Bowtie_RRNA},
"btmulti+" => \$me->{todo}{BT_Multi},
"calibrate+" => \$me->{todo}{Calibrate},
"countstates+" => \$me->{todo}{Count_States},
"concat+" => \$me->{todo}{Concatenate_Searches},
"cutadapt+" => \$me->{todo}{Cutadapt},
"essentialitytas+" => \$me->{todo}{Essentiality_TAs},
"fastasplitalign+" => \$me->{todo}{Split_Align_Fasta},
"fastqc+" => \$me->{todo}{FastQC},
"gb2gff+" => \$me->{todo}{Gb2Gff},
"gff2fasta+" => \$me->{todo}{Gff2Fasta},
"graphreads+" => \$me->{todo}{Graph_Reads},
"htmulti+" => \$me->{todo}{HT_Multi},
"kallisto+" => \$me->{todo}{Kallisto},
"mergeparse+" => \$me->{todo}{Merge_Parse_Blast},
"pbt1+" => \$me->{todo}{RNAseq_Pipeline_Bowtie},
"pbt2+" => \$me->{todo}{RNAseq_Pipeline_Bowtie2},
"pbwa+" => \$me->{todo}{RNAseq_Pipeline_BWA},
"pkallisto+" => \$me->{todo}{RNAseq_Pipeline_Kallisto},
"ptophat+" => \$me->{todo}{RNAseq_Pipeline_Tophat},
"ptnseq+" => \$me->{todo}{TNseq_Pipeline},
"priboseq+" => \$me->{todo}{Riboseq_Pipeline},
"parseblast+" => \$me->{todo}{Parse_Blast},
"posttrinity+" => \$me->{todo}{Trinity_Post},
"runessentiality+" => \$me->{todo}{Run_Essentiality},
"sam2bam+" => \$me->{todo}{Sam2Bam},
"sortindexes+" => \$me->{todo}{Sort_Indexes},
"splitalign+" => \$me->{todo}{Split_Align},
"test+" => \$me->{todo}{Test_Job},
"tophat+" => \$me->{todo}{Tophat},
"trimomatic+" => \$me->{todo}{Trimomatic},
"trinity+" => \$me->{todo}{Trinity},
"tritrypdownload+" => \$me->{todo}{TriTryp_Download},
"tritryp2text+" => \$me->{todo}{TriTryp2Text},
"helpme+" => \$me->{todo}{CYOA_Help},
};
return($me);
}

Expand Down Expand Up @@ -615,6 +658,127 @@ sub Read_Genome_GFF {
return($gff_out);
}

sub Pipeline_Riboseq {
my $me = shift;
my %args = @_;
$me->Fastqc(%args);
my $cutadapt_job = $me->Cutadapt(%args);
$args{depends} = $cutadapt_job->{pbs_id};
$me->Biopieces_Graph(%args);
my $rrna_job = $me->Bowtie_RRNA(%args);
$args{depends} = $rrna_job->{pbs_id};
my $bt_jobs = $me->Bowtie(%args);
}

sub Pipeline_RNAseq_Bowtie {
my $me = shift;
my %args = @_;
$args{aligner} = 'bowtie';
$me->Pipeline_RNAseq(%args);
return($me);
}

sub Pipeline_RNAseq_Bowtie2 {
my $me = shift;
my %args = @_;
$args{aligner} = 'bowtie2';
$me->Pipeline_RNAseq(%args);
return($me);
}


sub Pipeline_RNAseq_Tophat {
my $me = shift;
my %args = @_;
$args{aligner} = 'tophat';
$me->Pipeline_RNAseq(%args);
return($me);
}

sub Pipeline_RNAseq_BWA {
my $me = shift;
my %args = @_;
$args{aligner} = 'bwa';
$me->Pipeline_RNAseq(%args);
return($me);
}

sub Pipeline_RNAseq_Kallisto {
my $me = shift;
my %args = @_;
$args{aligner} = 'kallisto';
$me->Pipeline_RNAseq(%args);
return($me);
}

sub Pipeline_RNAseq {
my $me = shift;
my %args = @_;
$me->Fastqc(%args);
my $trim_job = $me->Trimomatic(%args);
$args{depends} = $trim_job->{pbs_id};
$me->Biopieces_Graph(%args);
my $rrna_job = $me->Bowtie_RRNA(%args);
$args{depends} = $rrna_job->{pbs_id};
my $align_jobs;
if ($args{aligner} eq 'bowtie') {
$align_jobs = $me->Bowtie(%args);
} elsif ($args{aligner} eq 'bowtie2') {
$align_jobs = $me->Bowtie2(%args);
} elsif ($args{aligner} eq 'tophat') {
$align_jobs = $me->Tophat(%args);
} elsif ($args{aligner} eq 'bwa') {
$align_jobs = $me->BWA(%args);
} elsif ($args{aligner} eq 'kallisto') {
$align_jobs = $me->Kallisto(%args);
} else {
$align_jobs = $me->Tophat(%args);
}
return($me);
}

sub Pipeline_TNseq {
my $me = shift;
my %args = @_;
$me->Fastqc(%args);
$args{type} = 'tnseq';
my $cutadapt_job = $me->Cutadapt(%args);
$args{depends} = $cutadapt_job->{pbs_id};
$me->Biopieces_Graph(%args);
my $bt_jobs = $me->Bowtie(%args);
}

sub CYOA_Help {
my $me = shift;
my %args = @_;
my %methods = %{$me->{methods}};
print qq"The command line program 'cyoa' has a series of shortcuts intended to make it easy to use and flexible.
The following comprises the set of strings you may feed it as 'methods':\n";
my $c = 0;
for my $k (sort keys %methods) {
my $sep = '\t';
if (($c % 3) == 0) {
$sep = '\n';
} else {
$sep = '\t';
}
$c++;
print "${k}${sep}";
}
print "\n";
print qq"cyoa uses GetOptions, so you can shortcut all the 'methods', so:
'cyoa --task ri --method cut --input test.fastq' calls the cutadapt with
options suitable for ribosome profiling data. Conversely:
'cyoa --task rna --method top --input test.fastq' calls tophat assuming
rnaseq data.
'cyoa --method blastsplt --query test.fasta --library nr --blast_tool blastp'
Splits the test.fasta into a bunch of pieces (settable with --number), calls
blastp on them, merges the outputs, and parses the result into a table of hits.
You get the idea, the following is the HPGL pod documentation:
";
$me->Help();
}

=back
=head1 AUTHOR - atb
Expand Down
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