Changeset 254

Show
Ignore:
Timestamp:
09/04/09 09:46:41 (3 months ago)
Author:
cholt
Message:

iprscan and gff3_merge and fastamerge update

Files:

Legend:

Unmodified
Added
Removed
Modified
Copied
Moved

  • bin/fasta_merge

    r213 r254  
    99Synopsis: 
    1010 
    11 fasta_merge --datastore /maker/datastore -o genome.all 
     11fasta_merge -d maker_datastore_index 
     12fasta_merge -o genome.all -i <fasta1> <fasta2> ... 
    1213 
    1314Descriptions: 
    1415 
    1516This script will take a MAKER datastore, extract all the relevant 
    16 fasta files and create fasta files with -o base name for all the 
    17 relevant categories of sequence (i.e. transcript, protein, GeneMark 
    18 protien, etc.). 
     17fasta files and create fasta files with relevant categories of 
     18sequence (i.e. transcript, protein, GeneMark protien, etc.). 
    1919 
    2020Options: 
    2121 
    22   -d The location of the MAKER datastore 
    23   -o The base name for the output files. 
     22  -d The location of the MAKER datastore. 
     23  -o Alternate base name for the output files. 
    2424  -i A optional list of files to process along with or instead of the 
    2525     datastore. 
    …… 
    3737            ); 
    3838 
    39 if((! $datastore && ! @files) || ! $outfile){ 
     39if(! $datastore){ 
    4040    print $usage; 
    4141    exit(); 
     42} 
     43    
     44if (! $outfile){ 
     45    ($outfile) = $datastore =~ /([^\/]+)$/; 
     46    $outfile =~ s/_master_datastore_index.log//; 
     47    $outfile = "genome" if(! defined $outfile); 
    4248} 
    4349 

  • bin/gff3_merge

    r205 r254  
    55use File::Temp qw(tempfile); 
    66 
    7 my $usage = ""; 
     7my $usage = " 
     8 
     9Synopsis: 
     10 
     11gff3_merge -d maker_datastore_index 
     12gff3_merge -o genome.all.gff <gff3_file1> <gff3_file2> ... 
     13 
     14Descriptions: 
     15 
     16This script will take a MAKER datastore, extract all the relevant 
     17GFF3 files and combined GFF3 file.  The script can also combine  
     18other correctly formated GFF3 files. 
     19 
     20Options: 
     21 
     22  -d The location of the MAKER datastore. 
     23  -o Alternate base name for the output files. 
     24 
     25"; 
    826 
    927my $datastore; 
    …… 
    2341    print $usage; 
    2442    exit(); 
     43} 
     44 
     45if (! $outfile){ 
     46    ($outfile) = $datastore =~ /([^\/]+)$/; 
     47    $outfile =~ s/_master_datastore_index.log// 
     48        $outfile .= ".gff"; 
     49    $outfile = "genome.all.gff" if(! defined $outfile); 
    2550} 
    2651 

  • lib/Process/IPRchunk.pm

    r225 r254  
    6363 
    6464   #handle case of calling as function rather than method 
    65    if (ref($self) ne "Process::IPRchunk") { 
     65   if ($self ne "Process::IPRchunk" && ref($self) ne "Process::IPRchunk") { 
    6666      $VARS = $self; 
    6767      $self = new Process::IPRchunk(); 
    …… 
    123123 
    124124   #handle case of calling as function rather than method 
    125    if (ref($self) ne "Process::IPRchunk") { 
     125   if ($self ne "Process::IPRchunk" && ref($self) ne "Process::IPRchunk") { 
    126126      $tID = $VARS; 
    127127      $VARS = $level; 
    …… 
    199199 
    200200   #handle case of calling as function rather than method 
    201    if (ref($self) ne "Process::IPRchunk") { 
     201   if ($self ne "Process::IPRchunk" && ref($self) ne "Process::IPRchunk") { 
    202202      $VARS = $level; 
    203203      $level = $self; 

  • lib/Process/IPRtiers.pm

    r228 r254  
    121121sub next_chunk { 
    122122   my $self = shift; 
    123    my $level = $self->{LEVEL}{CURRENT}; 
    124123 
    125124   return undef if ($self->terminated || $self->failed); 
    126125 
    127    $self->_next_level if($self->_level_finished); 
     126   #handle levels that have no chunks to run 
     127   while($self->_level_finished){ 
     128       $self->_next_level; 
     129       $self->_load_chunks; 
     130   } 
     131 
     132   #handle case where level needs to be initialized 
    128133   $self->_load_chunks if(! $self->_level_started); 
     134 
     135   #get level after doing any necessary moves to next level 
     136   my $level = $self->{LEVEL}{CURRENT}; 
    129137 
    130138   if (my $chunk = shift @{$self->{LEVEL}{$level}{CHUNKS}}) { 
    …… 
    167175 
    168176   return if ($self->terminated || $self->failed); 
    169    #return if ($self->_level_started && ! $self->_level_finished); 
     177   return if ($self->_level_started && ! $self->_level_finished); 
    170178 
    171179   $self->_next_level if ($self->_level_finished);