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Author: Andreas Tille <tille@debian.org>
Last-Update: Wed, 20 Jan 2016 09:10:18 +0100
Description: To run build time tests enable running the scripts
from build path
--- a/NAST-iEr/run_NAST-iEr.pl
+++ b/NAST-iEr/run_NAST-iEr.pl
@@ -8,6 +8,13 @@ use Getopt::Long;
#use FindBin;
##Hack needed because FindBin is braindead.
BEGIN{ $FindBin::Bin = "/usr/lib/NAST-iEr" };
+if ( ! -d $FindBin::Bin ) {
+ if ( -d "../../NAST-iEr" ) {
+ $FindBin::Bin = "../../NAST-iEr" ;
+ } else {
+ die("Directory $FindBin::Bin does not exist.");
+ }
+}
use lib ("$FindBin::Bin/PerlLib");
use Fasta_reader;
use CdbTools;
@@ -15,8 +22,21 @@ use Nuc_translator;
my $db_FASTA = "/usr/share/microbiomeutil-data/RESOURCES/rRNA16S.gold.fasta";
+if ( ! -e $db_FASTA ) {
+ if ( -e "../../RESOURCES/rRNA16S.gold.fasta" ) {
+ $db_FASTA = "../../RESOURCES/rRNA16S.gold.fasta" ;
+ } else {
+ die("File $db_FASTA does not exist.");
+ }
+}
my $db_NAST = "/usr/share/microbiomeutil-data/RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta";
-
+if ( ! -e $db_NAST ) {
+ if ( -e "../../RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta" ) {
+ $db_NAST = "../../RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta" ;
+ } else {
+ die("File $db_NAST does not exist.");
+ }
+}
my $usage = <<_EOUSAGE_;
--- a/NAST-iEr/sample_data/runMe.sh
+++ b/NAST-iEr/sample_data/runMe.sh
@@ -12,9 +12,9 @@ echo "../NAST-iEr -b template_seqs.NAST
echo "converting NAST mfasta to multi-alignment output highlighting differences"
echo "../show_malign_no_gap.pl --IGNOREGAPS tmp.both.NAST > tmp.both.NAST.malign\n\n"
-../util/show_malign_no_gap.pl --IGNOREGAPS tmp.both.NAST > tmp.both.NAST.malign
+perl -I../PerlLib ../util/show_malign_no_gap.pl --IGNOREGAPS tmp.both.NAST > tmp.both.NAST.malign
echo "Run via the megablast wrapper"
-../run_NAST-iEr.pl --query_FASTA query_seq.fasta > tmp.mb_select.NAST
+perl -I../PerlLib ../run_NAST-iEr.pl --query_FASTA query_seq.fasta > tmp.mb_select.NAST
--- a/ChimeraSlayer/sample_data/runMe.sh
+++ b/ChimeraSlayer/sample_data/runMe.sh
@@ -1,9 +1,9 @@
#!/bin/sh
# remove any preexisting outputs from an earlier run.
-rm chims.NAST.CPS*
-rm tmp.*
+rm -f chims.NAST.CPS*
+rm -f tmp.*
-../ChimeraSlayer.pl --query_NAST chims.NAST --printCSalignments --printFinalAlignments
+perl -I../PerlLib ../ChimeraSlayer.pl --query_NAST chims.NAST --printCSalignments --printFinalAlignments
--- a/ChimeraSlayer/ChimeraSlayer.pl
+++ b/ChimeraSlayer/ChimeraSlayer.pl
@@ -7,6 +7,13 @@ use Getopt::Long qw(:config no_ignore_ca
#use FindBin;
#Hack needed because FindBin is braindead.
BEGIN{ $FindBin::Bin = "/usr/lib/ChimeraSlayer" };
+if ( ! -d $FindBin::Bin ) {
+ if ( -d "../../ChimeraSlayer" ) {
+ $FindBin::Bin = "../../ChimeraSlayer" ;
+ } else {
+ die("Directory $FindBin::Bin does not exist.");
+ }
+}
use lib ("$FindBin::Bin/PerlLib");
use Fasta_reader;
@@ -14,7 +21,21 @@ use CdbTools;
use File::Basename;
my $db_NAST = "/usr/share/microbiomeutil-data/RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta";
+if ( ! -e $db_NAST ) {
+ if ( -e "../../RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta" ) {
+ $db_NAST = "../../RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta" ;
+ } else {
+ die("File $db_NAST does not exist.");
+ }
+}
my $db_FASTA = "/usr/share/microbiomeutil-data/RESOURCES/rRNA16S.gold.fasta";
+if ( ! -e $db_FASTA ) {
+ if ( -e "../../RESOURCES/rRNA16S.gold.fasta" ) {
+ $db_FASTA = "../../RESOURCES/rRNA16S.gold.fasta" ;
+ } else {
+ die("File $db_FASTA does not exist.");
+ }
+}
my $usage = <<_EOUSAGE_;
--- a/ChimeraSlayer/util/CS_add_taxonomy.pl
+++ b/ChimeraSlayer/util/CS_add_taxonomy.pl
@@ -13,7 +13,15 @@ use Fasta_reader;
my %acc_to_taxonomy;
{
- my $fasta_reader = new Fasta_reader("/usr/share/microbiomeutil-data/RESOURCES/rRNA16S.gold.fasta");
+ my $db_FASTA = "/usr/share/microbiomeutil-data/RESOURCES/rRNA16S.gold.fasta";
+ if ( ! -e $db_FASTA ) {
+ if ( -e "../../RESOURCES/rRNA16S.gold.fasta" ) {
+ $db_FASTA = "../../RESOURCES/rRNA16S.gold.fasta" ;
+ } else {
+ die("File $db_FASTA does not exist.");
+ }
+ }
+ my $fasta_reader = new Fasta_reader($db_FASTA);
while (my $seq_obj = $fasta_reader->next()) {
my $acc = $seq_obj->get_accession;
--- a/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl
+++ b/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl
@@ -655,7 +655,7 @@ sub report_alignment_trace {
}
#print( (" " x 26) . join ("", @$error_profile_aref) . "\n");
- printf("%-25s $align_region\n", substr("$alignment_counter $acc", 0, 25), $align_region);
+ printf("%-25s $align_region\n", substr("$alignment_counter $acc", 0, 25));
}
print "\n";
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