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Commit message:
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository |
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added:
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 |
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| diff -r 000000000000 -r 4afe13ac23b6 velvet/jgi_assembly.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/velvet/jgi_assembly.py Tue Jun 07 17:52:16 2011 -0400 |
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| @@ -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') |
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| diff -r 000000000000 -r 4afe13ac23b6 velvet/suite_config.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/velvet/suite_config.xml Tue Jun 07 17:52:16 2011 -0400 |
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| @@ -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> |
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| diff -r 000000000000 -r 4afe13ac23b6 velvet/velvetg_jgi.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/velvet/velvetg_jgi.xml Tue Jun 07 17:52:16 2011 -0400 |
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| b'@@ -0,0 +1,134 @@\n+<tool id="velvetg_jgi" name="velvetg" version="1.0.0">\n+<description>Assemble preprocessed reads</description>\n+<command interpreter=\'perl\'>velvetg_jgi_wrapper.pl\n+$velveth.extra_files_path\n+$velvetg_outfile.extra_files_path\n+$velvetg_outfile\n+$contigs_outfile\n+$stats_outfile\n+$lastgraph_outfile\n+$unused_reads_outfile\n+$amos_outfile\n+velvetg $velvetg_outfile.extra_files_path\n+-very_clean yes\n+#if $ins_length != \'\':\n+-ins_length $ins_length\n+ #if $ins_length_sd != \'\':\n+ -ins_length_sd $ins_length_sd\n+ #end if\n+#end if\n+#if $ins_length2 != \'\':\n+-ins_length2 $ins_length2\n+ #if $ins_length2_sd != \'\':\n+ -ins_length2_sd $ins_length2_sd\n+ #end if\n+#end if\n+#if $ins_length3 != \'\':\n+-ins_length3 $ins_length3\n+ #if $ins_length3_sd != \'\':\n+ -ins_length3_sd $ins_length3_sd\n+ #end if\n+#end if\n+#if $ins_length4 != \'\':\n+-ins_length4 $ins_length4\n+ #if $ins_length4_sd != \'\':\n+ -ins_length4_sd $ins_length4_sd\n+ #end if\n+#end if\n+#if $ins_length5 != \'\':\n+-ins_length5 $ins_length5\n+ #if $ins_length5_sd != \'\':\n+ -ins_length5_sd $ins_length5_sd\n+ #end if\n+#end if\n+#if $ins_length_long != \'\':\n+-ins_length_long $ins_length_long\n+ #if $ins_length_long_sd != \'\':\n+ -ins_length_long_sd $ins_length_long_sd\n+ #end if\n+#end if\n+-exp_cov $exp_cov\n+-cov_cutoff $cov_cutoff\n+-long_cov_cutoff $long_cov_cutoff\n+-max_coverage $max_coverage\n+-min_contig_lgth $min_contig_lgth\n+-read_trkg $read_trkg\n+-amos_file $amos_file\n+-unused_reads $unused_reads\n+-max_branch_length $max_branch_length\n+-max_divergence $max_divergence\n+-max_gap_count $max_gap_count\n+-scaffolding $scaffolding\n+-long_mult_cutoff $long_mult_cutoff\n+-min_pair_count $min_pair_count\n+-alignments $alignments\n+-exportFiltered $exportFiltered\n+</command>\n+<inputs>\n+ <param name="velveth" type="data" format="velveth" label="velvet hash"/>\n+\n+ <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)" />\n+ <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)" />\n+ <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)" />\n+ <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)" />\n+ <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)" />\n+ <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)" />\n+ <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)" />\n+ <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)" />\n+ <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)" />\n+ <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 le'..b'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)" />\n+\n+ <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)\' />\n+ <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)" />\n+ <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)" />\n+ <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\' />\n+ <param name="min_contig_lgth" type="integer" value=\'-1\' label="Minimum contig length" help="-1 for default: hash length *2" />\n+ <param name="scaffolding" type="boolean" checked=\'true\' label="Scaffolding" truevalue=\'yes\' falsevalue=\'no\'/>\n+\n+ <!-- Tour Bus Parameters -->\n+ <param name="max_branch_length" type="integer" value=\'100\' label="Maximum branch length" help="Default recommended"/>\n+ <param name="max_divergence" type="float" value=\'0.20\' label="Maximum divergence rate" help="Default recommended"/>\n+ <param name="max_gap_count" type="integer" value=\'3\' label="Maximum gap count" help="Default recommended"/>\n+\n+ <!-- Rock Band Parameters -->\n+ <param name=\'long_mult_cutoff\' type="integer" value=\'2\' label="Minimum long read connection cutoff"/> \n+\n+ <!-- Pebble Parameters -->\n+ <param name="min_pair_count" type="integer" value=\'10\' label="Minimum Read-Pair Validation"/>\n+\n+ <!-- Output Parameters -->\n+ <param name=\'unused_reads\' type=\'boolean\' truevalue=\'yes\' falsevalue=\'no\' checked=\'true\' label=\'Export unused reads\' />\n+ <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)." />\n+ <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)" />\n+ <param name="alignments" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="[-alignments] export a summary of contig alignment to the reference sequences" />\n+ <param name="exportFiltered" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="[-exportFiltered] export the long nodes which were eliminated by the coverage filters" />\n+</inputs>\n+\n+<outputs>\n+ <data name="velvetg_outfile" format="txt" />\n+ <data name="contigs_outfile" format="fasta" label=\'Contigs\' />\n+ <data name="stats_outfile" format="tabular" label=\'Contig Stats\' />\n+ <data name="lastgraph_outfile" format="txt" label="LastGraph" />\n+ <data name=\'unused_reads_outfile\' format=\'fasta\' label=\'Unused Reads\'>\n+ <filter>unused_reads is True</filter>\n+ </data>\n+ <data name=\'amos_outfile\' format=\'txt\' label=\'Amos Assembly\'>\n+ <filter>amos_file is True</filter>\n+ </data>\n+</outputs>\n+\n+<help>\n+\n+**What it does**\n+\n+This tool assembles contigous sequences from preprocessed reads by constructing a de Bruijn graph.\n+\n+Sequences must be preprocessed by the velveth tool.\n+\n+**Manual**\n+\n+http://www.ebi.ac.uk/~zerbino/velvet/Manual.pdf\n+</help>\n+</tool>\n' |
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| diff -r 000000000000 -r 4afe13ac23b6 velvet/velvetg_jgi_wrapper.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/velvet/velvetg_jgi_wrapper.pl Tue Jun 07 17:52:16 2011 -0400 |
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| @@ -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; |
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| diff -r 000000000000 -r 4afe13ac23b6 velvet/velveth_jgi.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/velvet/velveth_jgi.xml Tue Jun 07 17:52:16 2011 -0400 |
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| b'@@ -0,0 +1,276 @@\n+<tool id="velveth_jgi" name="velveth" version="1.0.0">\n+<description>Preprocess sequences for velvet assembly</description>\n+<command interpreter=\'perl\'>velveth_jgi_wrapper.pl $output $output.extra_files_path\n+velveth $output.extra_files_path $hash_length $strand_specific\n+#for $i in $short.files\n+$short.libtype $i.filetype.select $i.filetype.file\n+#end for\n+#for $i in $short2.files\n+$short2.libtype $i.filetype.select $i.filetype.file\n+#end for\n+#for $i in $short3.files\n+$short3.libtype $i.filetype.select $i.filetype.file\n+#end for\n+#for $i in $short4.files\n+$short4.libtype $i.filetype.select $i.filetype.file\n+#end for\n+#for $i in $short5.files\n+$short5.libtype $i.filetype.select $i.filetype.file\n+#end for\n+#for $i in $long.files\n+$long.libtype $i.filetype.select $i.filetype.file\n+#end for\n+</command>\n+<inputs>\n+ <param name="hash_length" type="integer" value=\'21\' label="Hash length. Odd numbers only. Maximum 75."/>\n+ <param name="strand_specific" type=\'boolean\' label="All libraries strand-specific?" truevalue=\'-strand_specific\' falsevalue=\'\'/>\n+\n+ <conditional name="short">\n+ <param name="libtype" type="select" label="Short Library Type">\n+ <option value="-shortPaired">Paired</option>\n+ <option value="-short">Unpaired</option>\n+ </param>\n+ <when value="-shortPaired">\n+ <repeat name="files" title="Files">\n+ <conditional name="filetype">\n+ <param name=\'select\' type=\'select\' label=\'File Type\'>\n+ <option value=\'-fastq\'>Fastq</option>\n+ <option value=\'-fasta\'>Fasta</option>\n+ </param>\n+ <when value="-fasta">\n+ <param name="file" type="data" format="fasta" label="File"/>\n+ </when>\n+ <when value="-fastq">\n+ <param name="file" type="data" format="fastq" label="File"/>\n+ </when>\n+ </conditional>\n+ </repeat>\n+ </when>\n+ <when value="-short">\n+ <repeat name="files" title="Files">\n+ <conditional name="filetype">\n+ <param name=\'select\' type=\'select\' label=\'File Type\'>\n+ <option value=\'-fastq\'>Fastq</option>\n+ <option value=\'-fasta\'>Fasta</option>\n+ </param>\n+ <when value="-fasta">\n+ <param name="file" type="data" format="fasta" label="File"/>\n+ </when>\n+ <when value="-fastq">\n+ <param name="file" type="data" format="fastq" label="File"/>\n+ </when>\n+ </conditional>\n+ </repeat>\n+ </when>\n+ </conditional>\n+\n+ <conditional name="short2">\n+ <param name="libtype" type="select" label="Short2 Library Type">\n+ <option value="-shortPaired2">Paired</option>\n+ <option value="-short2">Unpaired</option>\n+ </param>\n+ <when value="-shortPaired2">\n+ <repeat name="files" title="Files">\n+ <conditional name="filetype">\n+ <param name=\'select\' type=\'select\' label=\'File Type\'>\n+ <option value=\'-fastq\'>Fastq</option>\n+ <option value=\'-fasta\'>Fasta</option>\n+ </param>\n+ <when value="-fasta">\n+ <param name="file" type="data" format="fasta" label="File"/>\n+ </when>\n+ <when value="-fastq">\n+ <param name="file" type="data" format="fastq" label="File"/>\n+ </when>\n+ </conditional>\n+ </repeat>\n+ </when>\n+ <when value="-short2">\n+ <repeat name="files" title="Files">\n+ <conditional name="filetype">\n+ <param name=\'se'..b'at="fastq" label="File"/>\n+ </when>\n+ </conditional>\n+ </repeat>\n+ </when>\n+ </conditional>\n+\n+ <conditional name="short5">\n+ <param name="libtype" type="select" label="Short5 Library Type">\n+ <option value="-shortPaired5">Paired</option>\n+ <option value="-short5">Unpaired</option>\n+ </param>\n+ <when value="-shortPaired5">\n+ <repeat name="files" title="Files">\n+ <conditional name="filetype">\n+ <param name=\'select\' type=\'select\' label=\'File Type\'>\n+ <option value=\'-fastq\'>Fastq</option>\n+ <option value=\'-fasta\'>Fasta</option>\n+ </param>\n+ <when value="-fasta">\n+ <param name="file" type="data" format="fasta" label="File"/>\n+ </when>\n+ <when value="-fastq">\n+ <param name="file" type="data" format="fastq" label="File"/>\n+ </when>\n+ </conditional>\n+ </repeat>\n+ </when>\n+ <when value="-short5">\n+ <repeat name="files" title="Files">\n+ <conditional name="filetype">\n+ <param name=\'select\' type=\'select\' label=\'File Type\'>\n+ <option value=\'-fastq\'>Fastq</option>\n+ <option value=\'-fasta\'>Fasta</option>\n+ </param>\n+ <when value="-fasta">\n+ <param name="file" type="data" format="fasta" label="File"/>\n+ </when>\n+ <when value="-fastq">\n+ <param name="file" type="data" format="fastq" label="File"/>\n+ </when>\n+ </conditional>\n+ </repeat>\n+ </when>\n+ </conditional>\n+\n+ <conditional name="long">\n+ <param name="libtype" type="select" label="Long Library Type">\n+ <option value="-longPaired">Paired</option>\n+ <option value="-long">Unpaired</option>\n+ </param>\n+ <when value="-longPaired">\n+ <repeat name="files" title="Files">\n+ <conditional name="filetype">\n+ <param name=\'select\' type=\'select\' label=\'File Type\'>\n+ <option value=\'-fastq\'>Fastq</option>\n+ <option value=\'-fasta\'>Fasta</option>\n+ </param>\n+ <when value="-fasta">\n+ <param name="file" type="data" format="fasta" label="File"/>\n+ </when>\n+ <when value="-fastq">\n+ <param name="file" type="data" format="fastq" label="File"/>\n+ </when>\n+ </conditional>\n+ </repeat>\n+ </when>\n+ <when value="-long">\n+ <repeat name="files" title="Files">\n+ <conditional name="filetype">\n+ <param name=\'select\' type=\'select\' label=\'File Type\'>\n+ <option value=\'-fastq\'>Fastq</option>\n+ <option value=\'-fasta\'>Fasta</option>\n+ </param>\n+ <when value="-fasta">\n+ <param name="file" type="data" format="fasta" label="File"/>\n+ </when>\n+ <when value="-fastq">\n+ <param name="file" type="data" format="fastq" label="File"/>\n+ </when>\n+ </conditional>\n+ </repeat>\n+ </when>\n+ </conditional>\n+</inputs>\n+<outputs>\n+ <data name="output" format="velveth"/>\n+</outputs>\n+\n+<help>\n+\n+**What it does**\n+\n+This tool preprocesses the sequence data using the specified hash length. A larger hash length increases sensitivity at the expense of read depth.\n+\n+**Manual**\n+\n+http://www.ebi.ac.uk/~zerbino/velvet/Manual.pdf\n+</help>\n+</tool>\n' |
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| diff -r 000000000000 -r 4afe13ac23b6 velvet/velveth_jgi_wrapper.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/velvet/velveth_jgi_wrapper.pl Tue Jun 07 17:52:16 2011 -0400 |
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| @@ -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 |