[med-svn] [sprai] 01/04: Imported Upstream version 0.9.9.19+dfsg

[Afif Elghraoui]

This is an automated email from the git hooks/post-receive script.

afif pushed a commit to branch master
in repository sprai.

commit 15589027e10f624b605790aceb363ae6f9ec196e
Author: Afif Elghraoui <afif at debian.org>
Date:   Sat Aug 13 23:28:21 2016 -0700

    Imported Upstream version 0.9.9.19+dfsg
---
 doc/_build/html/_sources/README.txt |  2 +-
 ezez_vx1.pl                         | 16 +++++++++++++++-
 makefile                            |  2 +-
 wscript                             |  2 +-
 4 files changed, 18 insertions(+), 4 deletions(-)

diff --git a/doc/_build/html/_sources/README.txt b/doc/_build/html/_sources/README.txt
index 65b3500..56e0eab 100644
--- a/doc/_build/html/_sources/README.txt
+++ b/doc/_build/html/_sources/README.txt
@@ -244,7 +244,7 @@ If you only want to error correction only, do as below
 
 The file result/c_l${libi}.1.fin.v$valid_voters.idfq.gz (eg. c_l0.1.fin.v30.idfq.gz) is the corrected read file.
 
-After error correction, if you want to assemble the corrected reads, do as below
+After error correction using ezez4makefile_v4.pl, if you want to assemble the corrected reads, do as below
 
 ::
 
diff --git a/ezez_vx1.pl b/ezez_vx1.pl
index a4abbd3..98341cd 100755
--- a/ezez_vx1.pl
+++ b/ezez_vx1.pl
@@ -10,6 +10,7 @@ my $opt_dryrun;
 my $opt_ec_only;
 my $opt_foobar;
 my $sprai_path="";
+my $blast_path="";
 
 my $now = `date +%Y%m%d_%H%M%S`;
 chomp $now;
@@ -167,6 +168,9 @@ if(defined($params{sprai_path})){
     die "there is no $sprai_path/nss2v_v3 or $sprai_path/fq2idfq.pl.\nset right sprai_path in ec.spec\n";
   }
 }
+if(defined($params{blast_path})){
+  $blast_path = $params{blast_path};
+}
 if(defined($params{word_size})){
   $word_size = $params{word_size};
 }
@@ -207,6 +211,9 @@ if($ca_path){
 if($sprai_path){
   printf STDERR ("sprai_path %s\n",$sprai_path);
 }
+if($blast_path){
+  printf STDERR ("blast_path %s\n",$blast_path);
+}
 if($word_size){
   printf STDERR ("word_size %d\n",$word_size);
 }
@@ -365,8 +372,12 @@ for(my $index=$from; $index<$to; ++$index){
       my $f_do=1;
       $f_do = &do_or_not(\@parents,\$child);
       my $parent = $parents[0];
+      my $MAKEBLASTDB = "makeblastdb";
+      if($blast_path){
+        $MAKEBLASTDB = "$blast_path/$MAKEBLASTDB";
+      }
       if($f_do){
-        $com1 = sprintf("$pipefail time gzip -d -c $parent | $PG1 -f - | makeblastdb -in - -dbtype nucl -out $tmp_dir/$preprefix%02d -title $preprefix%02d 1>$child.tmp && mv $child.tmp $child",$index,$index);
+        $com1 = sprintf("$pipefail time gzip -d -c $parent | $PG1 -f - | $MAKEBLASTDB -in - -dbtype nucl -out $tmp_dir/$preprefix%02d -title $preprefix%02d 1>$child.tmp && mv $child.tmp $child",$index,$index);
       }
       else{
         $com1 = "sleep 0";
@@ -416,6 +427,9 @@ for(my $index=$from; $index<$to; ++$index){
         $PG4 = "$sprai_path/$PG4";
       }
       my $BLASTN = "blastn -dbsize 1 -num_threads $num_threads";
+      if($blast_path){
+        $BLASTN = "$blast_path/$BLASTN";
+      }
       if($word_size){
         $BLASTN .= " -word_size $word_size";
       }
diff --git a/makefile b/makefile
index a1cb2ab..233c53a 100644
--- a/makefile
+++ b/makefile
@@ -1,5 +1,5 @@
 APPNAME = 'sprai'
-VERSION = '0.9.9.18'
+VERSION = '0.9.9.19'
 
 PREFIX=$(PWD)
 COMPILED= \
diff --git a/wscript b/wscript
index a197d2e..53f8cec 100644
--- a/wscript
+++ b/wscript
@@ -1,5 +1,5 @@
 APPNAME = 'sprai'
-VERSION = '0.9.9.18'
+VERSION = '0.9.9.19'
 
 srcdir = '.'
 blddir = 'build'

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/sprai.git