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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -11,7 +11,7 @@ | |
| # pipeline may fail upon custom modification of this script. | ||
| # In case of doubt, contact [email protected] | ||
| # | ||
| # Mario Stanke & Katharina Hoff, last modification on Feb 19th 2018 | ||
| # Mario Stanke & Katharina Hoff, last modification on May 31 2019 | ||
|
|
||
| use strict; | ||
| use Getopt::Long; | ||
|
|
@@ -30,8 +30,11 @@ | |
| # | ||
| my $max_percent_id = 0.8; | ||
| my $BLAST_PATH; | ||
| my $DIAMOND_PATH; | ||
| my $blast_path; | ||
| my $diamond_path; | ||
| my $CPU = 1; | ||
| my $diamond; | ||
| my $v = 0; | ||
| my $help; | ||
|
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||
|
|
@@ -40,17 +43,21 @@ | |
| $usage .= "In output.fa the percent identity value between each pair of \n"; | ||
| $usage .= "When removing redundant sequences, priority is given to the sequence occuring last.\n"; | ||
| $usage .= "Options:\n"; | ||
| $usage .= "--maxid=f maximum percent identity between to sequences\n"; | ||
| $usage .= " (#identical aa) / (length of shorter sequence) default: 0.8\n"; | ||
| $usage .= "--BLAST_PATH=s path to blast (only implemented for NCBI BLAST)\n"; | ||
| $usage .= "--cores=n number of cores to be used by NCBI BLAST\n"; | ||
| $usage .= "--verbosity=n verbosity level for information printed to stdout\n"; | ||
| $usage .= "--help print this help message\n"; | ||
| $usage .= "--maxid=f maximum percent identity between to sequences\n"; | ||
| $usage .= " (#identical aa) / (length of shorter sequence) default: 0.8\n"; | ||
| $usage .= "--BLAST_PATH=s path to blast (only implemented for NCBI BLAST)\n"; | ||
| $usage .= "--DIAMOND_PATH=s path to diamond\n"; | ||
| $usage .= "--cores=n number of cores to be used by NCBI BLAST or DIAMOND\n"; | ||
| $usage .= "--diamond use DIAMOND istead of NCBI BLAST\n"; | ||
| $usage .= "--verbosity=n verbosity level for information printed to stdout\n"; | ||
| $usage .= "--help print this help message\n"; | ||
|
|
||
| GetOptions( | ||
| 'maxid:f' => \$max_percent_id, | ||
| 'BLAST_PATH=s' => \$blast_path, | ||
| 'DIAMOND_PATH=s' => \$diamond_path, | ||
| 'cores=i' => \$CPU, | ||
| 'diamond!' => \$diamond, | ||
| 'verbosity=i' => \$v, | ||
| 'help!' => \$help | ||
| ); | ||
|
|
@@ -66,8 +73,11 @@ | |
| exit(1); | ||
| } | ||
|
|
||
|
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||
| set_BLAST_PATH(); | ||
| if($diamond){ | ||
| set_DIAMOND_PATH(); | ||
| }else{ | ||
| set_BLAST_PATH(); | ||
| } | ||
|
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||
|
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||
| my $inputfilename = $ARGV[0]; | ||
|
|
@@ -82,7 +92,7 @@ | |
| my $splitDir; # for parallelization | ||
| my @splitFiles; | ||
| my $SPLITF; | ||
| if ( $CPU > 1 ) { | ||
| if ( $CPU > 1 && not($diamond)) { | ||
|
|
||
| my $nFastaEntries = 0; | ||
| # counter number of fasta entries | ||
|
|
@@ -165,36 +175,56 @@ | |
|
|
||
| my $tempoutfile = "$inputfilename.blastout"; | ||
|
|
||
| ## NCBI blast | ||
| system("$BLAST_PATH/makeblastdb -in $tempdbname -dbtype prot -parse_seqids -out $tempdbname"); | ||
| if ( $CPU == 1 ) { | ||
| system("$BLAST_PATH/blastp -query $tempdbname -db $tempdbname > $tempoutfile"); | ||
| if($diamond){ | ||
| if($CPU > 1){ | ||
| system("$DIAMOND_PATH/diamond makedb --in $tempdbname -d $tempdbname --threads $CPU"); | ||
| }else{ | ||
| system("$DIAMOND_PATH/diamond makedb --in $tempdbname -d $tempdbname --threads 1"); | ||
| } | ||
| }else{ | ||
| my $pm = new Parallel::ForkManager($CPU); | ||
| foreach ( @splitFiles ) { | ||
| my $pid = $pm->start and next; | ||
| system("$BLAST_PATH/blastp -query $tempdbname -db $tempdbname > $_.blastout"); | ||
| $pm->finish; | ||
| ## NCBI blast | ||
| system("$BLAST_PATH/makeblastdb -in $tempdbname -dbtype prot -parse_seqids -out $tempdbname"); | ||
| } | ||
|
|
||
| if ( $CPU == 1 ) { | ||
| if($diamond){ | ||
| system("$DIAMOND_PATH/diamond blastp --db $tempdbname --outfmt 0 --query $tempdbname --out $tempoutfile") | ||
|
|
||
| }else{ | ||
| system("$BLAST_PATH/blastp -query $tempdbname -db $tempdbname > $tempoutfile"); | ||
| } | ||
| $pm->wait_all_children; | ||
| foreach ( @splitFiles ) { | ||
| system("cat $_.blastout >> $tempoutfile"); | ||
| }else{ | ||
| if($diamond){ | ||
| system("$DIAMOND_PATH/diamond blastp --db $tempdbname --outfmt 0 --query $tempdbname --threads $CPU --out $tempoutfile"); | ||
| }else{ | ||
| my $pm = new Parallel::ForkManager($CPU); | ||
| foreach ( @splitFiles ) { | ||
| my $pid = $pm->start and next; | ||
| system("$BLAST_PATH/blastp -query $tempdbname -db $tempdbname > $_.blastout"); | ||
| $pm->finish; | ||
| } | ||
| $pm->wait_all_children; | ||
| foreach ( @splitFiles ) { | ||
| system("cat $_.blastout >> $tempoutfile"); | ||
| } | ||
| } | ||
| } | ||
|
|
||
|
|
||
| ########################################################################################### | ||
| # | ||
| # parse the blast output | ||
| # parse the blast/diamond output | ||
| # | ||
| ########################################################################################### | ||
|
|
||
| open( BLASTOUT, "<$tempoutfile" ) or die("ERROR in file " . __FILE__ ." at line ". __LINE__ ."\nCould not open $tempoutfile!\n"); | ||
| $/ = "\nQuery= "; | ||
| my ( $query, $target, $qlen, $tlen, $numid, $minlen ); | ||
| while (<BLASTOUT>) { | ||
| next unless / producing /; | ||
| $_ =~ m/(\S+)\n\nLength=(\d+)/; | ||
| if(not($diamond)){ | ||
| next unless / producing /; | ||
| } | ||
| $_ =~ m/(\S+)\n+Length=(\d+)/; | ||
| $query = $1; | ||
| $qlen = $2; | ||
| print STDOUT "query=$query, qlen=$qlen\n" if ($v>0); | ||
|
|
@@ -217,6 +247,7 @@ | |
| } | ||
| } | ||
| } | ||
|
|
||
| } | ||
| close (BLASTOUT) or die("ERROR in file " . __FILE__ ." at line ". __LINE__ ."\nCould not close $tempoutfile!\n"); | ||
|
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||
|
|
@@ -238,14 +269,18 @@ | |
| # | ||
| ########################################################################################### | ||
| unlink ( rel2abs($tempdbname) ); | ||
| unlink ( rel2abs($tempdbname).".phr" ); | ||
| unlink ( rel2abs($tempdbname).".pin" ); | ||
| unlink ( rel2abs($tempdbname).".pog" ); | ||
| unlink ( rel2abs($tempdbname).".psd" ); | ||
| unlink ( rel2abs($tempdbname).".psi" ); | ||
| unlink ( rel2abs($tempdbname).".psq" ); | ||
| if(not($diamond)){ | ||
| unlink ( rel2abs($tempdbname).".phr" ); | ||
| unlink ( rel2abs($tempdbname).".pin" ); | ||
| unlink ( rel2abs($tempdbname).".pog" ); | ||
| unlink ( rel2abs($tempdbname).".psd" ); | ||
| unlink ( rel2abs($tempdbname).".psi" ); | ||
| unlink ( rel2abs($tempdbname).".psq" ); | ||
| }else{ | ||
| unlink (rel2abs($tempdbname).".dmnd" ); | ||
| } | ||
| unlink ( rel2abs($tempoutfile) ); | ||
| if ($CPU > 1) { | ||
| if ($CPU > 1 && not($diamond)) { | ||
| rmtree( ["$splitDir"] ); | ||
| } | ||
|
|
||
|
|
@@ -369,3 +404,121 @@ sub set_BLAST_PATH { | |
| exit(1); | ||
| } | ||
| } | ||
|
|
||
| ########################################################################################### | ||
| # | ||
| # finding diamond executable | ||
| # | ||
| ########################################################################################### | ||
| sub set_DIAMOND_PATH { | ||
| my $prtStr; | ||
| # try to get path from ENV | ||
| if ( defined( $ENV{'DIAMOND_PATH'} ) ) { | ||
| if ( -e $ENV{'DIAMOND_PATH'} ) { | ||
| $prtStr | ||
| = "\# " | ||
| . (localtime) | ||
| . ": Found environment variable \$DIAMOND_PATH.\n"; | ||
| print STDOUT $prtStr; | ||
| $DIAMOND_PATH = $ENV{'DIAMOND_PATH'}; | ||
| } | ||
| } | ||
| else { | ||
| $prtStr | ||
| = "\# " | ||
| . (localtime) | ||
| . ": Did not find environment variable \$DIAMOND_PATH\n"; | ||
| print STDOUT $prtStr; | ||
| } | ||
|
|
||
| # try to get path from command line | ||
| if ( defined($diamond_path) ) { | ||
| my $last_char = substr( $diamond_path, -1 ); | ||
| if ( $last_char eq "\/" ) { | ||
| chop($diamond_path); | ||
| } | ||
| if ( -d $diamond_path ) { | ||
| $prtStr | ||
| = "\# " | ||
| . (localtime) | ||
| . ": Setting \$DIAMOND_PATH to command line argument "; | ||
| $prtStr .= "--DIAMOND_PATH value $diamond_path.\n"; | ||
| print STDOUT $prtStr; | ||
| $DIAMOND_PATH = $diamond_path; | ||
| } | ||
| else { | ||
| $prtStr | ||
| = "\# " | ||
| . (localtime) | ||
| . ": WARNING: Command line argument --DIAMOND_PATH was "; | ||
| $prtStr | ||
| .= "supplied but value $diamond_path is not a directory. Will not set "; | ||
| $prtStr .= "\$DIAMOND_PATH to $diamond_path!\n"; | ||
| print STDOUT $prtStr; | ||
| } | ||
| } | ||
|
|
||
| # try to guess | ||
| if ( not( defined($DIAMOND_PATH) ) | ||
| || length($DIAMOND_PATH) == 0 ) | ||
| { | ||
| $prtStr | ||
| = "\# " | ||
| . (localtime) | ||
| . ": Trying to guess \$DIAMOND_PATH from location of diamond"; | ||
| $prtStr .= " executable that is available in your \$PATH.\n"; | ||
| print STDOUT $prtStr; | ||
| my $epath = which 'diamond'; | ||
| if ( -d dirname($epath) ) { | ||
| $prtStr | ||
| = "\# " | ||
| . (localtime) | ||
| . ": Setting \$DIAMOND_PATH to " | ||
| . dirname($epath) . "\n"; | ||
| print STDOUT $prtStr; | ||
| $DIAMOND_PATH = dirname($epath); | ||
| } | ||
| else { | ||
| $prtStr | ||
| = "\# " | ||
| . (localtime) | ||
| . ": WARNING: Guessing the location of \$DIAMOND_PATH "; | ||
| $prtStr | ||
| .= "failed. " . dirname($epath) . " is not a directory!\n"; | ||
| print STDOUT $prtStr; | ||
| } | ||
| } | ||
|
|
||
| if ( not( defined($DIAMOND_PATH) ) ) { | ||
| my $diamond_err; | ||
| $diamond_err .= "There are 3 alternative ways to set this variable for " | ||
| . " aa2nonred.pl:\n" | ||
| . " a) provide command-line argument " | ||
| . "--DIAMOND_PATH=/your/path\n" | ||
| . " b) use an existing environment variable " | ||
| . "\$DIAMOND_PATH\n" | ||
| . " for setting the environment variable, run\n" | ||
| . " export DIAMOND_PATH=/your/path\n" | ||
| . " in your shell. You may append this to your " | ||
| . ".bashrc or .profile file in\n" | ||
| . " order to make the variable available to all your " | ||
| . "bash sessions.\n" | ||
| . " c) aa2nonred.pl can try guessing the location of " | ||
| . "\$DIAMOND_PATH from the\n" | ||
| . " location of a diamond executable that is " | ||
| . "available in your \$PATH variable.\n" | ||
| . " If you try to rely on this option, you can check " | ||
| . "by typing\n" | ||
| . " which diamond\n" | ||
| . " in your shell, whether there is a diamond " | ||
| . "executable in your \$PATH\n"; | ||
| $prtStr = "\# " . (localtime) . " ERROR in file " . __FILE__ ." at line ". __LINE__ ."\n\$DIAMOND_PATH not set!\n"; | ||
| print STDERR $prtStr; | ||
| print STDERR $diamond_err; | ||
| exit(1); | ||
| } | ||
| if ( not ( -x "$DIAMOND_PATH/diamond" ) ) { | ||
| print STDERR "\# " . (localtime) . " ERROR in file " . __FILE__ ." at line ". __LINE__ ."\n$DIAMOND_PATH/diamond is not an executable file!\n"; | ||
| exit(1); | ||
| } | ||
| } | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,4 +1,4 @@ | ||
| #!/usr/bin/perl | ||
| #!/usr/bin/env perl | ||
| # convert AUGUSTUS output to Gbrowse format GFF file | ||
| # Mario Stanke | ||
|
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|
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