[med-svn] [sprai] 01/04: Imported Upstream version 0.9.9.17+dfsg
Afif Elghraoui
afif at moszumanska.debian.org
Thu Jun 9 13:09:54 UTC 2016
This is an automated email from the git hooks/post-receive script.
afif pushed a commit to branch master
in repository sprai.
commit c078e5ff21dcd06193c8fc9d4267f53a86aea6cd
Author: Afif Elghraoui <afif at debian.org>
Date: Tue Jun 7 19:09:05 2016 -0700
Imported Upstream version 0.9.9.17+dfsg
---
doc/_build/html/_sources/Download.txt | 4 +++-
doc/_build/html/_sources/index.txt | 4 +++-
ec.spec | 3 +++
ezez4makefile_v4.pl | 8 ++++++++
ezez4qsub_vx1.pl | 9 +++++++++
ezez_vx1.pl | 8 ++++++++
makefile | 2 +-
wscript | 2 +-
8 files changed, 36 insertions(+), 4 deletions(-)
diff --git a/doc/_build/html/_sources/Download.txt b/doc/_build/html/_sources/Download.txt
index b658f02..4c0f946 100644
--- a/doc/_build/html/_sources/Download.txt
+++ b/doc/_build/html/_sources/Download.txt
@@ -1,11 +1,13 @@
===========================
Download The Latest Version
===========================
-http://zombie.cb.k.u-tokyo.ac.jp/sprai/dist/sprai-0.9.9.15.tar.gz
+http://zombie.cb.k.u-tokyo.ac.jp/sprai/dist/sprai-0.9.9.16.tar.gz
==============
Older releases
==============
+http://zombie.cb.k.u-tokyo.ac.jp/sprai/dist/sprai-0.9.9.15.tar.gz
+
http://zombie.cb.k.u-tokyo.ac.jp/sprai/dist/sprai-0.9.9.14.tar.gz
http://zombie.cb.k.u-tokyo.ac.jp/sprai/dist/sprai-0.9.9.13.tar.gz
diff --git a/doc/_build/html/_sources/index.txt b/doc/_build/html/_sources/index.txt
index 317a77a..ece3817 100644
--- a/doc/_build/html/_sources/index.txt
+++ b/doc/_build/html/_sources/index.txt
@@ -20,7 +20,9 @@ Contents
Changelogs
=============
-2016.5.31 v0.9.9.15: ezez4makefile_v4.pl was added. You can use Makefile when execute Sprai. (Thanks to Tomoaki Nishiyama for code modifications)
+2016.6.1 v0.9.9.16: ezez_vx1.pl & ezez4qsub_vx1.pl: set -o pipefail was added.
+
+2016.5.31 v0.9.9.15: ezez4makefile_v4.pl was added. You can use Makefile when execute Sprai. See README. (Thanks to Tomoaki Nishiyama for code modifications)
2016.4.15: v0.9.9.14: -ec_only mode can be run without a spec file of Celera Assembler. (Thanks to Afif Elghraoui for a report)
diff --git a/ec.spec b/ec.spec
index df49b5d..1c16fd3 100644
--- a/ec.spec
+++ b/ec.spec
@@ -52,6 +52,9 @@ max_target_seqs 100
#trim: both ends of each alignment by blastn will be trimmed 'trim' bases to detect chimeric reads
trim 42
+# if not 0, use only one subread per one molecule
+use_one_subread 0
+
# direct_vote & copy_blastdb are used by ezez4makefile_v4.pl
direct_vote 0
# skip writing the blast results once to disk before selecting
diff --git a/ezez4makefile_v4.pl b/ezez4makefile_v4.pl
index bc83b9c..8fb62cf 100755
--- a/ezez4makefile_v4.pl
+++ b/ezez4makefile_v4.pl
@@ -95,6 +95,7 @@ my $param_assembly_rreq = "";
my $filter_same_lib = "| cat";
my $min_len_for_query=1;
my $max_len_for_query=1000000000000000;
+my $use_one_subread=0;
my $command="";
@@ -182,6 +183,9 @@ if(defined($params{max_read_length})){
if(defined($params{trim})){
$trim = $params{trim};
}
+if(defined($params{use_one_subread})){
+ $use_one_subread = $params{use_one_subread};
+}
if(defined($params{ca_path})){
$ca_path = $params{ca_path};
}
@@ -264,6 +268,7 @@ if($max_target_seqs){
}
printf STDERR ("valid_voters %s\n",join(" ", @voters));
printf STDERR ("trim %d\n",$trim);
+printf STDERR ("use_one_subread %d\n",$use_one_subread);
printf STDERR ("ca_path %s\n",$ca_path);
printf STDERR ("blast_path %s\n",$blast_path);
printf STDERR ("sprai_path %s\n",$sprai_path);
@@ -362,6 +367,9 @@ for($libi = 0; $libi < $nlibs; $libi++){
my $PG0="$bindir/fa2fq.pl";
my $PG2="$bindir/fqfilt.pl";
my $PG3="$bindir/dumbbell_filter.pl";
+ if(!$use_one_subread){
+ $PG3="cat";
+ }
my $command = "STMP=`mktemp -d --tmpdir sprai-XXXXXX` ; set -o pipefail; $PG0 \$\< | $PG3 - | $PG - --prefix $iprefix | gzip -c -1 > \$\$STMP/c_l${libi}.idfq.gz && cp -p \$\$STMP/c_l${libi}.idfq.gz \$@ && openssl dgst \$\$STMP/c_l${libi}.idfq.gz \$@; status=\$\$?; rm -fr \$\$STMP;exit \$\$status";
$rreq = "";
diff --git a/ezez4qsub_vx1.pl b/ezez4qsub_vx1.pl
index 6ed1751..67db42d 100755
--- a/ezez4qsub_vx1.pl
+++ b/ezez4qsub_vx1.pl
@@ -130,6 +130,7 @@ my $min_len_for_query=1;
my $max_len_for_query=1000000000000000;
my $sge="";
my $estimated_depth=0;
+my $use_one_subread=0;
if(defined($params{input_for_database})){
$input_for_database = $params{input_for_database};
@@ -235,6 +236,10 @@ if(defined($params{max_target_seqs})){
$max_target_seqs = $params{max_target_seqs};
}
+if(defined($params{use_one_subread})){
+ $use_one_subread = $params{use_one_subread};
+}
+
printf STDERR ("#>- params -<#\n");
printf STDERR ("input_for_database %s\n",$input_for_database);
printf STDERR ("estimated_genome_size %g\n",$estimated_genome_size);
@@ -250,6 +255,7 @@ printf STDERR ("evalue %g\n",$evalue);
printf STDERR ("num_threads %d\n",$num_threads);
printf STDERR ("valid_voters %s\n",$valid_voters);
printf STDERR ("trim %d\n",$trim);
+printf STDERR ("use_one_subread %d\n",$use_one_subread);
if($ca_path){
printf STDERR ("ca_path %s\n",$ca_path);
}
@@ -371,6 +377,9 @@ if($from == 0)
my $PG = "$bindir/fq2idfq.pl";
my $PG2 = "$bindir/fqfilt.pl";
my $dumbbell_filter = "$bindir/dumbbell_filter.pl";
+ if(!$use_one_subread){
+ $dumbbell_filter = "cat";
+ }
if($input_for_database !~ /^\//){
$input_for_database = sprintf("$pwd/$input_for_database");
diff --git a/ezez_vx1.pl b/ezez_vx1.pl
index f470750..a4abbd3 100755
--- a/ezez_vx1.pl
+++ b/ezez_vx1.pl
@@ -94,6 +94,7 @@ my $word_size=0;
my $min_len_for_query=1;
my $max_len_for_query=1000000000000000;
my $estimated_depth=0;
+my $use_one_subread=0;
my $blasr_path="";
my $blasr_opt="";
@@ -184,6 +185,9 @@ if(defined($params{max_len_for_query})){
if(defined($params{max_target_seqs})){
$max_target_seqs = $params{max_target_seqs};
}
+if(defined($params{use_one_subread})){
+ $use_one_subread = $params{use_one_subread};
+}
printf STDERR ("#>- params -<#\n");
printf STDERR ("input_for_database %s\n",$input_for_database);
@@ -196,6 +200,7 @@ printf STDERR ("evalue %g\n",$evalue);
printf STDERR ("num_threads %d\n",$num_threads);
printf STDERR ("valid_voters %s\n",$valid_voters);
printf STDERR ("trim %d\n",$trim);
+printf STDERR ("use_one_subread %d\n",$use_one_subread);
if($ca_path){
printf STDERR ("ca_path %s\n",$ca_path);
}
@@ -287,6 +292,9 @@ if($from == 0)
if($sprai_path){
$dumbbell_filter = "$sprai_path/$dumbbell_filter";
}
+ if(!$use_one_subread){
+ $dumbbell_filter = "cat";
+ }
my $com1;
my $com2;
diff --git a/makefile b/makefile
index 8f78f13..efeae27 100644
--- a/makefile
+++ b/makefile
@@ -1,5 +1,5 @@
APPNAME = 'sprai'
-VERSION = '0.9.9.16'
+VERSION = '0.9.9.17'
PREFIX=$(PWD)
COMPILED= \
diff --git a/wscript b/wscript
index 645b700..7ca444a 100644
--- a/wscript
+++ b/wscript
@@ -1,5 +1,5 @@
APPNAME = 'sprai'
-VERSION = '0.9.9.16'
+VERSION = '0.9.9.17'
srcdir = '.'
blddir = 'build'
--
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