Mercurial > repos > edward-kirton > velvet_toolsuite
changeset 0:4afe13ac23b6 default tip
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
| author | edward-kirton |
|---|---|
| date | Tue, 07 Jun 2011 17:52:16 -0400 |
| parents | |
| children | |
| files | velvet/jgi_assembly.py velvet/suite_config.xml velvet/velvetg_jgi.xml velvet/velvetg_jgi_wrapper.pl velvet/velveth_jgi.xml velvet/velveth_jgi_wrapper.pl |
| diffstat | 6 files changed, 633 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/velvet/jgi_assembly.py Tue Jun 07 17:52:16 2011 -0400 @@ -0,0 +1,117 @@ +""" +Assembly classes +""" + +import data +import logging +import re +import string +from cgi import escape +from galaxy.datatypes.metadata import MetadataElement +from galaxy.datatypes import metadata +import galaxy.model +from galaxy import util +from sniff import * + +log = logging.getLogger(__name__) + +class Assembly( data.Text ): + """Class describing an assembly""" + + """Add metadata elements""" + MetadataElement( name="contigs", default=0, desc="Number of contigs", readonly=True, visible=False, optional=True, no_value=0 ) + MetadataElement( name="reads", default=0, desc="Number of reads", readonly=True, visible=False, optional=True, no_value=0 ) + + +class Ace(Assembly): + """Class describing an assembly Ace file""" + + file_ext = "ace" + +# def init_meta( self, dataset, copy_from=None ): +# Assembly.init_meta( self, dataset, copy_from=copy_from ) + + def set_meta( self, dataset, overwrite=True, **kwd ): + """ + Set the number of assembled contigs and read sequences and the number of data lines in dataset. + """ + contigs = 0 + reads = 0 + for line in file( dataset.file_name ): + line = line.strip() + if line and line.startswith( '#' ): + # Don't count comment lines + continue + if line and line.startswith( 'CO' ): + contigs += 1 + if line and line.startswith( 'RD' ): + reads += 1 + dataset.metadata.contigs = contigs + dataset.metadata.reads = reads + + def set_peek( self, dataset, is_multi_byte=False ): + if not dataset.dataset.purged: + dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte ) + if dataset.metadata.contigs: + dataset.blurb = "%s contigs" % util.commaify( str( dataset.metadata.contigs ) ) + else: + dataset.blurb = data.nice_size( dataset.get_size() ) + else: + dataset.peek = 'file does not exist' + dataset.blurb = 'file purged from disk' + + def sniff( self, filename ): + """ + Determines whether the file is in ace format + + An ace file contains these sections + AS \d+ \d+ + + CO \S+ \d+ \d+ \d+ \w + [atcgATCGN\*]+ + + BQ + [\d\s]+ + + AF \S+ [CU] \-?\d+ + + BS \d+ \d+ \S+ + + RD \S+ \d+ \d+ \d+ + [ATCGN\*]+ + + QA \d+ \d+ \d+ \d+ + DS .* + + Currently we only check if file begins with AS + + >>> fname = get_test_fname( 'genome.ace' ) + >>> Ace().sniff( fname ) + True + >>> fname = get_test_fname( 'genome.fasta' ) + >>> Ace().sniff( fname ) + False + """ + + try: + fh = open( filename ) + line = fh.readline() + line = line.strip() + if line: + if line.startswith( 'AS ' ): + fh.close() + return True + fh.close() + return False + except: + pass + return False + +class Velveth(Assembly): + composite_type='basic' + file_ext = "txt" + + def __init__(self,**kwd): + Assembly.__init__(self,**kwd) + self.add_composite_file('Roadmap') + self.add_composite_file('Sequences')
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/velvet/suite_config.xml Tue Jun 07 17:52:16 2011 -0400 @@ -0,0 +1,9 @@ +<suite id='velvet_toolsuite' name='Suite of Velvet assembler tools' version="1.0.0"> + <description>Velvet assembler (a different version than in galaxy-central)</description> + <tool id="velveth_jgi" name="velveth" version="1.0.0"> + <description>Hash reads</description> + </tool> + <tool id="velvetg_jgi" name="velvetg" version="1.0.0"> + <description>Generate contigs</description> + </tool> +</suite>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/velvet/velvetg_jgi.xml Tue Jun 07 17:52:16 2011 -0400 @@ -0,0 +1,134 @@ +<tool id="velvetg_jgi" name="velvetg" version="1.0.0"> +<description>Assemble preprocessed reads</description> +<command interpreter='perl'>velvetg_jgi_wrapper.pl +$velveth.extra_files_path +$velvetg_outfile.extra_files_path +$velvetg_outfile +$contigs_outfile +$stats_outfile +$lastgraph_outfile +$unused_reads_outfile +$amos_outfile +velvetg $velvetg_outfile.extra_files_path +-very_clean yes +#if $ins_length != '': +-ins_length $ins_length + #if $ins_length_sd != '': + -ins_length_sd $ins_length_sd + #end if +#end if +#if $ins_length2 != '': +-ins_length2 $ins_length2 + #if $ins_length2_sd != '': + -ins_length2_sd $ins_length2_sd + #end if +#end if +#if $ins_length3 != '': +-ins_length3 $ins_length3 + #if $ins_length3_sd != '': + -ins_length3_sd $ins_length3_sd + #end if +#end if +#if $ins_length4 != '': +-ins_length4 $ins_length4 + #if $ins_length4_sd != '': + -ins_length4_sd $ins_length4_sd + #end if +#end if +#if $ins_length5 != '': +-ins_length5 $ins_length5 + #if $ins_length5_sd != '': + -ins_length5_sd $ins_length5_sd + #end if +#end if +#if $ins_length_long != '': +-ins_length_long $ins_length_long + #if $ins_length_long_sd != '': + -ins_length_long_sd $ins_length_long_sd + #end if +#end if +-exp_cov $exp_cov +-cov_cutoff $cov_cutoff +-long_cov_cutoff $long_cov_cutoff +-max_coverage $max_coverage +-min_contig_lgth $min_contig_lgth +-read_trkg $read_trkg +-amos_file $amos_file +-unused_reads $unused_reads +-max_branch_length $max_branch_length +-max_divergence $max_divergence +-max_gap_count $max_gap_count +-scaffolding $scaffolding +-long_mult_cutoff $long_mult_cutoff +-min_pair_count $min_pair_count +-alignments $alignments +-exportFiltered $exportFiltered +</command> +<inputs> + <param name="velveth" type="data" format="velveth" label="velvet hash"/> + + <param name="ins_length" type="text" value='auto' label="[-ins_length] Insert length (bp) of short library" help="blank=no read pairing; auto=infer; or supply value (integer)" /> + <param name="ins_length_sd" type="text" value='auto' label="[ins_length_sd] Insert length standard deviation (bp) of short library; requires above" help="blank=default of 10% of corresponding length; auto=infer; or supply value (integer)" /> + <param name="ins_length2" type="text" value='auto' label="[ins_length2] Insert length (bp) of short2 library" help="blank=no read pairing; auto=infer; or supply value (integer)" /> + <param name="ins_length2_sd" type="text" value='auto' label="[-ins_length2_sd] Insert length standard deviation (bp) of short2 library; requires above" help="blank=default of 10% of corresponding length; auto=infer; or supply value (integer)" /> + <param name="ins_length3" type="text" value='auto' label="[ins_length3] Insert length (bp) of short3 library" help="blank=no read pairing; auto=infer; or supply value (integer)" /> + <param name="ins_length3_sd" type="text" value='auto' label="[-ins_length3_sd] Insert length standard deviation (bp) of short3 library; requires above" help="blank=default of 10% of corresponding length; auto=infer; or supply value (integer)" /> + <param name="ins_length4" type="text" value='auto' label="[ins_length4] Insert length (bp) of short4 library" help="blank=no read pairing; auto=infer; or supply value (integer)" /> + <param name="ins_length4_sd" type="text" value='auto' label="[-ins_length4_sd] Insert length standard deviation (bp) of short4 library; requires above" help="blank=default of 10% of corresponding length; auto=infer; or supply value (integer)" /> + <param name="ins_length5" type="text" value='auto' label="[ins_length5] Insert length (bp) of short5 library" help="blank=no read pairing; auto=infer; or supply value (integer)" /> + <param name="ins_length5_sd" type="text" value='auto' label="[-ins_length5_sd] Insert length standard deviation (bp) of short5 library; requires above" help="blank=default of 10% of corresponding length; auto=infer; or supply value (integer)" /> + <param name="ins_length_long" type="text" value='auto' label="[ins_length_long] Insert length (bp) of long library" help="blank=no read pairing; auto=infer; or supply value (integer)" /> + <param name="ins_length_long_sd" type="text" value='auto' label="[-ins_length_sd_long] Insert length standard deviation (bp) of long library; requires above" help="blank=default of 10% of corresponding length; auto=infer; or supply value (integer)" /> + + <param name='exp_cov' type='text' value='-1' label='[-exp_cov] Expected short read k-mer coverage' help='-1=no long or paired-end read resolution; auto=infer it; or supply value (real number)' /> + <param name="cov_cutoff" type="text" value='-1' label="[-cov_cutoff] Removal of low coverage nodes AFTER tour bus" help="-1=no removal; auto=infer cutoff; or specify cutoff (real number)" /> + <param name="long_cov_cutoff" type="float" value='-1' label="[-long_cov_cutoff] Removal of low long-read coverage nodes AFTER tour bus" help="-1=no removal; or specify cutoff (real number)" /> + <param name='max_coverage' type='float' value='-1' label="[-max_coverage] Exclude highly covered data from your assembly (e.g. plasmid, mitochondrial, and chloroplast sequences)" help='-1 for default: no removal' /> + <param name="min_contig_lgth" type="integer" value='-1' label="Minimum contig length" help="-1 for default: hash length *2" /> + <param name="scaffolding" type="boolean" checked='true' label="Scaffolding" truevalue='yes' falsevalue='no'/> + + <!-- Tour Bus Parameters --> + <param name="max_branch_length" type="integer" value='100' label="Maximum branch length" help="Default recommended"/> + <param name="max_divergence" type="float" value='0.20' label="Maximum divergence rate" help="Default recommended"/> + <param name="max_gap_count" type="integer" value='3' label="Maximum gap count" help="Default recommended"/> + + <!-- Rock Band Parameters --> + <param name='long_mult_cutoff' type="integer" value='2' label="Minimum long read connection cutoff"/> + + <!-- Pebble Parameters --> + <param name="min_pair_count" type="integer" value='10' label="Minimum Read-Pair Validation"/> + + <!-- Output Parameters --> + <param name='unused_reads' type='boolean' truevalue='yes' falsevalue='no' checked='true' label='Export unused reads' /> + <param name='read_trkg' type='boolean' truevalue='yes' falsevalue='no' checked='false' label="[-read_trkg] tracking of short read positions in assembly" help="This will cost slightly more memory and calculation time, but will have the advantage of producing in the end a more detailed description of the assembly. The additional information will be included in the LastGraph file and optionally the Amos assembly file (below)." /> + <param name='amos_file' type='boolean' truevalue='yes' falsevalue='no' checked='false' label="[-amos_file] export assembly to AMOS file" help="If selecting this option, you may also want to select -read_trkg (above)" /> + <param name="alignments" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="[-alignments] export a summary of contig alignment to the reference sequences" /> + <param name="exportFiltered" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="[-exportFiltered] export the long nodes which were eliminated by the coverage filters" /> +</inputs> + +<outputs> + <data name="velvetg_outfile" format="txt" /> + <data name="contigs_outfile" format="fasta" label='Contigs' /> + <data name="stats_outfile" format="tabular" label='Contig Stats' /> + <data name="lastgraph_outfile" format="txt" label="LastGraph" /> + <data name='unused_reads_outfile' format='fasta' label='Unused Reads'> + <filter>unused_reads is True</filter> + </data> + <data name='amos_outfile' format='txt' label='Amos Assembly'> + <filter>amos_file is True</filter> + </data> +</outputs> + +<help> + +**What it does** + +This tool assembles contigous sequences from preprocessed reads by constructing a de Bruijn graph. + +Sequences must be preprocessed by the velveth tool. + +**Manual** + +http://www.ebi.ac.uk/~zerbino/velvet/Manual.pdf +</help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/velvet/velvetg_jgi_wrapper.pl Tue Jun 07 17:52:16 2011 -0400 @@ -0,0 +1,66 @@ +#!/usr/bin/env perl + +# Conventience wrapper for velvetg; copies outfiles to galaxy-specified destinations. +# Please email bugs/feature requests to Edward Kirton (ESKirton@LBL.gov) +# +# History: +# - 2010/03/04 : file created +# - 2001/02/05 : added new options, outfiles; renamed to velvetg_jgi to avoid collision with the other velvetg tool + +use strict; +use warnings; +use File::Copy; + +# shift wrapper args +my $velveth_path=shift @ARGV or die; +my $velvetg_path=shift @ARGV or die; +my $velvetg_outfile=shift @ARGV or die; +my $contigs_outfile=shift @ARGV or die; +my $stats_outfile=shift @ARGV or die; +my $lastgraph_outfile=shift @ARGV or die; +my $unused_reads_outfile=shift @ARGV or die; +my $amos_outfile=shift @ARGV or die; + +# setup velvetg folder +die("Velveth folder does not exist: $velveth_path\n") unless -d $velveth_path; +-d $velvetg_path or mkdir($velvetg_path) or die("Unable to create output folder, $velvetg_path: $!\n"); +die("velveth Sequences file does not exist: $velveth_path/Sequences") unless -f "$velveth_path/Sequences"; +symlink("$velveth_path/Sequences", "$velvetg_path/Sequences"); +die("velveth Roadmaps file does not exist: $velveth_path/Roadmaps") unless -f "$velveth_path/Roadmaps"; +symlink("$velveth_path/Roadmaps", "$velvetg_path/Roadmaps"); +die("velveth Log file does not exist: $velveth_path/Log") unless -f "$velveth_path/Log"; +copy("$velveth_path/Log", "$velvetg_path/Log"); + +# run command (remaining args, starting with exe path) +open (VELVETG, "@ARGV|") or die("Unable to run velvetg\n"); +open (OUT, ">$velvetg_outfile") or die("Unable to open outfile, $velvetg_outfile: $!\n"); +while (<VELVETG>) { + print OUT $_; + print if /^Final graph/; +} +close VELVETG; +close OUT; + +# process output +unlink($contigs_outfile); +move("$velvetg_path/contigs.fa", $contigs_outfile); +unlink($stats_outfile); +move("$velvetg_path/stats.txt", $stats_outfile); + +unlink($lastgraph_outfile); +if ( -f "$velvetg_path/LastGraph") { + move("$velvetg_path/LastGraph", $lastgraph_outfile); +} elsif ( -f "$velvetg_path/Graph2") { + move("$velvetg_path/Graph2", $lastgraph_outfile); +} else { + open(OUT, ">$lastgraph_outfile") or die($!); + print OUT "ERROR: $velvetg_path/LastGraph not found!\n"; + close OUT; +} +unlink($unused_reads_outfile); +move("$velvetg_path/UnusedReads.fa", $unused_reads_outfile); +if ( $amos_outfile ne 'None' ) { + unlink($amos_outfile); + move("$velvetg_path/velvet_asm.afg", $amos_outfile); +} +exit;
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/velvet/velveth_jgi.xml Tue Jun 07 17:52:16 2011 -0400 @@ -0,0 +1,276 @@ +<tool id="velveth_jgi" name="velveth" version="1.0.0"> +<description>Preprocess sequences for velvet assembly</description> +<command interpreter='perl'>velveth_jgi_wrapper.pl $output $output.extra_files_path +velveth $output.extra_files_path $hash_length $strand_specific +#for $i in $short.files +$short.libtype $i.filetype.select $i.filetype.file +#end for +#for $i in $short2.files +$short2.libtype $i.filetype.select $i.filetype.file +#end for +#for $i in $short3.files +$short3.libtype $i.filetype.select $i.filetype.file +#end for +#for $i in $short4.files +$short4.libtype $i.filetype.select $i.filetype.file +#end for +#for $i in $short5.files +$short5.libtype $i.filetype.select $i.filetype.file +#end for +#for $i in $long.files +$long.libtype $i.filetype.select $i.filetype.file +#end for +</command> +<inputs> + <param name="hash_length" type="integer" value='21' label="Hash length. Odd numbers only. Maximum 75."/> + <param name="strand_specific" type='boolean' label="All libraries strand-specific?" truevalue='-strand_specific' falsevalue=''/> + + <conditional name="short"> + <param name="libtype" type="select" label="Short Library Type"> + <option value="-shortPaired">Paired</option> + <option value="-short">Unpaired</option> + </param> + <when value="-shortPaired"> + <repeat name="files" title="Files"> + <conditional name="filetype"> + <param name='select' type='select' label='File Type'> + <option value='-fastq'>Fastq</option> + <option value='-fasta'>Fasta</option> + </param> + <when value="-fasta"> + <param name="file" type="data" format="fasta" label="File"/> + </when> + <when value="-fastq"> + <param name="file" type="data" format="fastq" label="File"/> + </when> + </conditional> + </repeat> + </when> + <when value="-short"> + <repeat name="files" title="Files"> + <conditional name="filetype"> + <param name='select' type='select' label='File Type'> + <option value='-fastq'>Fastq</option> + <option value='-fasta'>Fasta</option> + </param> + <when value="-fasta"> + <param name="file" type="data" format="fasta" label="File"/> + </when> + <when value="-fastq"> + <param name="file" type="data" format="fastq" label="File"/> + </when> + </conditional> + </repeat> + </when> + </conditional> + + <conditional name="short2"> + <param name="libtype" type="select" label="Short2 Library Type"> + <option value="-shortPaired2">Paired</option> + <option value="-short2">Unpaired</option> + </param> + <when value="-shortPaired2"> + <repeat name="files" title="Files"> + <conditional name="filetype"> + <param name='select' type='select' label='File Type'> + <option value='-fastq'>Fastq</option> + <option value='-fasta'>Fasta</option> + </param> + <when value="-fasta"> + <param name="file" type="data" format="fasta" label="File"/> + </when> + <when value="-fastq"> + <param name="file" type="data" format="fastq" label="File"/> + </when> + </conditional> + </repeat> + </when> + <when value="-short2"> + <repeat name="files" title="Files"> + <conditional name="filetype"> + <param name='select' type='select' label='File Type'> + <option value='-fastq'>Fastq</option> + <option value='-fasta'>Fasta</option> + </param> + <when value="-fasta"> + <param name="file" type="data" format="fasta" label="File"/> + </when> + <when value="-fastq"> + <param name="file" type="data" format="fastq" label="File"/> + </when> + </conditional> + </repeat> + </when> + </conditional> + + <conditional name="short3"> + <param name="libtype" type="select" label="Short3 Library Type"> + <option value="-shortPaired3">Paired</option> + <option value="-short3">Unpaired</option> + </param> + <when value="-shortPaired3"> + <repeat name="files" title="Files"> + <conditional name="filetype"> + <param name='select' type='select' label='File Type'> + <option value='-fastq'>Fastq</option> + <option value='-fasta'>Fasta</option> + </param> + <when value="-fasta"> + <param name="file" type="data" format="fasta" label="File"/> + </when> + <when value="-fastq"> + <param name="file" type="data" format="fastq" label="File"/> + </when> + </conditional> + </repeat> + </when> + <when value="-short3"> + <repeat name="files" title="Files"> + <conditional name="filetype"> + <param name='select' type='select' label='File Type'> + <option value='-fastq'>Fastq</option> + <option value='-fasta'>Fasta</option> + </param> + <when value="-fasta"> + <param name="file" type="data" format="fasta" label="File"/> + </when> + <when value="-fastq"> + <param name="file" type="data" format="fastq" label="File"/> + </when> + </conditional> + </repeat> + </when> + </conditional> + + <conditional name="short4"> + <param name="libtype" type="select" label="Short4 Library Type"> + <option value="-shortPaired4">Paired</option> + <option value="-short4">Unpaired</option> + </param> + <when value="-shortPaired4"> + <repeat name="files" title="Files"> + <conditional name="filetype"> + <param name='select' type='select' label='File Type'> + <option value='-fastq'>Fastq</option> + <option value='-fasta'>Fasta</option> + </param> + <when value="-fasta"> + <param name="file" type="data" format="fasta" label="File"/> + </when> + <when value="-fastq"> + <param name="file" type="data" format="fastq" label="File"/> + </when> + </conditional> + </repeat> + </when> + <when value="-short4"> + <repeat name="files" title="Files"> + <conditional name="filetype"> + <param name='select' type='select' label='File Type'> + <option value='-fastq'>Fastq</option> + <option value='-fasta'>Fasta</option> + </param> + <when value="-fasta"> + <param name="file" type="data" format="fasta" label="File"/> + </when> + <when value="-fastq"> + <param name="file" type="data" format="fastq" label="File"/> + </when> + </conditional> + </repeat> + </when> + </conditional> + + <conditional name="short5"> + <param name="libtype" type="select" label="Short5 Library Type"> + <option value="-shortPaired5">Paired</option> + <option value="-short5">Unpaired</option> + </param> + <when value="-shortPaired5"> + <repeat name="files" title="Files"> + <conditional name="filetype"> + <param name='select' type='select' label='File Type'> + <option value='-fastq'>Fastq</option> + <option value='-fasta'>Fasta</option> + </param> + <when value="-fasta"> + <param name="file" type="data" format="fasta" label="File"/> + </when> + <when value="-fastq"> + <param name="file" type="data" format="fastq" label="File"/> + </when> + </conditional> + </repeat> + </when> + <when value="-short5"> + <repeat name="files" title="Files"> + <conditional name="filetype"> + <param name='select' type='select' label='File Type'> + <option value='-fastq'>Fastq</option> + <option value='-fasta'>Fasta</option> + </param> + <when value="-fasta"> + <param name="file" type="data" format="fasta" label="File"/> + </when> + <when value="-fastq"> + <param name="file" type="data" format="fastq" label="File"/> + </when> + </conditional> + </repeat> + </when> + </conditional> + + <conditional name="long"> + <param name="libtype" type="select" label="Long Library Type"> + <option value="-longPaired">Paired</option> + <option value="-long">Unpaired</option> + </param> + <when value="-longPaired"> + <repeat name="files" title="Files"> + <conditional name="filetype"> + <param name='select' type='select' label='File Type'> + <option value='-fastq'>Fastq</option> + <option value='-fasta'>Fasta</option> + </param> + <when value="-fasta"> + <param name="file" type="data" format="fasta" label="File"/> + </when> + <when value="-fastq"> + <param name="file" type="data" format="fastq" label="File"/> + </when> + </conditional> + </repeat> + </when> + <when value="-long"> + <repeat name="files" title="Files"> + <conditional name="filetype"> + <param name='select' type='select' label='File Type'> + <option value='-fastq'>Fastq</option> + <option value='-fasta'>Fasta</option> + </param> + <when value="-fasta"> + <param name="file" type="data" format="fasta" label="File"/> + </when> + <when value="-fastq"> + <param name="file" type="data" format="fastq" label="File"/> + </when> + </conditional> + </repeat> + </when> + </conditional> +</inputs> +<outputs> + <data name="output" format="velveth"/> +</outputs> + +<help> + +**What it does** + +This tool preprocesses the sequence data using the specified hash length. A larger hash length increases sensitivity at the expense of read depth. + +**Manual** + +http://www.ebi.ac.uk/~zerbino/velvet/Manual.pdf +</help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/velvet/velveth_jgi_wrapper.pl Tue Jun 07 17:52:16 2011 -0400 @@ -0,0 +1,31 @@ +#!/usr/bin/env perl + +use strict; +use warnings; +my $start=time; +my $outfile=shift @ARGV; +my $outdir=shift @ARGV; +my $kmer=$ARGV[2]; +die ("USER ERROR: Hash length (kmer) must be odd!\n") unless $kmer % 2; +my $tot_reads=0; +open (VELVETH, "@ARGV 2>&1|") or die("Unable to run velveth: $!\n"); +open(OUT, ">$outfile") or die($!); +while (<VELVETH>) { + print OUT $_; + if (/^\[\d+\.\d+\] (\d+) sequences found/) { + $tot_reads += $1; + } +} +close VELVETH; +close OUT; +die("No reads found\n") unless $tot_reads; +my $sec=time-$start; +my $min=int($sec/60); +$sec -= ($min*60); +my $hr=int($min/60); +$min -= ($hr*60); +print "$tot_reads processed in"; +print " $hr hr" if $hr; +print " $min min" if $min; +print " $sec sec\n"; +exit