[med-svn] [tophat] 02/05: Imported Upstream version 2.0.11
Andreas Tille
tille at debian.org
Tue Mar 18 13:17:01 UTC 2014
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository tophat.
commit 2770873f365405e551fcaddbd831c4bb53476ea6
Author: Andreas Tille <tille at debian.org>
Date: Tue Mar 18 13:58:17 2014 +0100
Imported Upstream version 2.0.11
---
configure | 24 +++++++++++-----------
configure.ac | 2 +-
src/tophat-fusion-post | 55 ++++++++++++++++++++++++++------------------------
src/tophat.py | 2 +-
4 files changed, 43 insertions(+), 40 deletions(-)
diff --git a/configure b/configure
index 932984f..115b8dc 100755
--- a/configure
+++ b/configure
@@ -1,6 +1,6 @@
#! /bin/sh
# Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.59 for tophat 2.0.10.
+# Generated by GNU Autoconf 2.59 for tophat 2.0.11.
#
# Report bugs to <tophat.cufflinks at gmail.com>.
#
@@ -269,8 +269,8 @@ SHELL=${CONFIG_SHELL-/bin/sh}
# Identity of this package.
PACKAGE_NAME='tophat'
PACKAGE_TARNAME='tophat'
-PACKAGE_VERSION='2.0.10'
-PACKAGE_STRING='tophat 2.0.10'
+PACKAGE_VERSION='2.0.11'
+PACKAGE_STRING='tophat 2.0.11'
PACKAGE_BUGREPORT='tophat.cufflinks at gmail.com'
ac_unique_file="config.h.in"
@@ -792,7 +792,7 @@ if test "$ac_init_help" = "long"; then
# Omit some internal or obsolete options to make the list less imposing.
# This message is too long to be a string in the A/UX 3.1 sh.
cat <<_ACEOF
-\`configure' configures tophat 2.0.10 to adapt to many kinds of systems.
+\`configure' configures tophat 2.0.11 to adapt to many kinds of systems.
Usage: $0 [OPTION]... [VAR=VALUE]...
@@ -858,7 +858,7 @@ fi
if test -n "$ac_init_help"; then
case $ac_init_help in
- short | recursive ) echo "Configuration of tophat 2.0.10:";;
+ short | recursive ) echo "Configuration of tophat 2.0.11:";;
esac
cat <<\_ACEOF
@@ -1009,7 +1009,7 @@ fi
test -n "$ac_init_help" && exit 0
if $ac_init_version; then
cat <<\_ACEOF
-tophat configure 2.0.10
+tophat configure 2.0.11
generated by GNU Autoconf 2.59
Copyright (C) 2003 Free Software Foundation, Inc.
@@ -1023,7 +1023,7 @@ cat >&5 <<_ACEOF
This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.
-It was created by tophat $as_me 2.0.10, which was
+It was created by tophat $as_me 2.0.11, which was
generated by GNU Autoconf 2.59. Invocation command line was
$ $0 $@
@@ -1361,7 +1361,7 @@ ac_compiler_gnu=$ac_cv_c_compiler_gnu
cat >>confdefs.h <<\_ACEOF
-#define SVN_REVISION "4167"
+#define SVN_REVISION "4203"
_ACEOF
@@ -1675,7 +1675,7 @@ fi
# Define the identity of the package.
PACKAGE='tophat'
- VERSION='2.0.10'
+ VERSION='2.0.11'
cat >>confdefs.h <<_ACEOF
@@ -7134,7 +7134,7 @@ fi
# Define the identity of the package.
PACKAGE='tophat'
- VERSION='2.0.10'
+ VERSION='2.0.11'
cat >>confdefs.h <<_ACEOF
@@ -7966,7 +7966,7 @@ _ASBOX
} >&5
cat >&5 <<_CSEOF
-This file was extended by tophat $as_me 2.0.10, which was
+This file was extended by tophat $as_me 2.0.11, which was
generated by GNU Autoconf 2.59. Invocation command line was
CONFIG_FILES = $CONFIG_FILES
@@ -8029,7 +8029,7 @@ _ACEOF
cat >>$CONFIG_STATUS <<_ACEOF
ac_cs_version="\\
-tophat config.status 2.0.10
+tophat config.status 2.0.11
configured by $0, generated by GNU Autoconf 2.59,
with options \\"`echo "$ac_configure_args" | sed 's/[\\""\`\$]/\\\\&/g'`\\"
diff --git a/configure.ac b/configure.ac
index 7fc65ab..936d4ec 100644
--- a/configure.ac
+++ b/configure.ac
@@ -4,7 +4,7 @@ m4_include([ax_bam.m4])
#m4_include([ax_check_zlib.m4])
define([svnversion], esyscmd([sh -c "svnversion|tr -d '\n'"]))dnl
-AC_INIT([tophat],[2.0.10],[tophat.cufflinks at gmail.com])
+AC_INIT([tophat],[2.0.11],[tophat.cufflinks at gmail.com])
AC_DEFINE(SVN_REVISION, "svnversion", [SVN Revision])
AC_CONFIG_SRCDIR([config.h.in])
diff --git a/src/tophat-fusion-post b/src/tophat-fusion-post
index 20a8f44..c4be6bc 100755
--- a/src/tophat-fusion-post
+++ b/src/tophat-fusion-post
@@ -35,6 +35,8 @@ Options:
-p/--num-threads <int> [ default: 1 ]
+ --no-filter-by-annotation
+
--skip-fusion-kmer
--skip-filter-fusion
--skip-blast
@@ -69,6 +71,8 @@ class TopHatFusionParams:
self.is_human = True
self.num_threads = 1
+
+ self.filter_by_annotation = True
self.skip_fusion_kmer = False
self.skip_filter_fusion = False
@@ -95,6 +99,7 @@ class TopHatFusionParams:
"fusion-multireads=",
"non-human",
"num-threads=",
+ "no-filter-by-annotation",
"skip-fusion-kmer",
"skip-filter-fusion",
"skip-blast",
@@ -129,6 +134,8 @@ class TopHatFusionParams:
output_dir = value + "/"
logging_dir = output_dir + "logs/"
tmp_dir = output_dir + "tmp/"
+ if option == "--no-filter-by-annotation":
+ self.filter_by_annotation = False
if option == "--skip-fusion-kmer":
self.skip_fusion_kmer = True
if option == "--skip-filter-fusion":
@@ -435,8 +442,9 @@ def filter_fusion(bwt_idx_prefix, params):
fusion_file.readline()
for line in fusion_file:
info, sim, left_seq_org, right_seq_org, left_dist, right_dist, pair_list = line[:-1].split('\t@\t')[:7]
-
info = info.split('\t')
+ if sim.strip() == "":
+ continue
sim = sim.split(' ')
left_seq = left_seq_org.replace(' ', '')
right_seq = right_seq_org.replace(' ', '')
@@ -460,17 +468,8 @@ def filter_fusion(bwt_idx_prefix, params):
else:
single = False
- if string.find(data, "maher") != -1:
- extent = min(10, num_reads)
- if single:
- if left_ext < 25 + extent * 2 or right_ext < 25 + extent * 2:
- continue
- else:
- if left_ext < 14 + extent or right_ext < 14 + extent:
- continue
- else:
- if left_ext < 16 or right_ext < 16:
- continue
+ if left_ext < 16 or right_ext < 16:
+ continue
both = num_reads + num_pair_ends_both
all = both
@@ -483,9 +482,11 @@ def filter_fusion(bwt_idx_prefix, params):
both < params.num_fusion_both:
continue
+ """
if (chr1 != chr2 and num_unsupport_reads > num_reads) or \
(chr1 == chr2 and num_unsupport_reads > all + num_pair_ends + 5):
continue
+ """
pairs = []
if num_pair_ends >= 1:
@@ -500,7 +501,6 @@ def filter_fusion(bwt_idx_prefix, params):
# are the sequences around the breakpoint different enough?
if int(sim[0]) < 8:
continue
-
# is the reads distributed symmetrically?
if sym >= 22 + max(0, 6 - num_reads):
@@ -511,7 +511,7 @@ def filter_fusion(bwt_idx_prefix, params):
coord_dif = coord2 - coord1
if coord_dif > 0 and coord_dif < max_intron_len:
continue
-
+
if not left_seq[half_len-kmer_len:half_len] in seq_chr_dic or not right_seq[half_len:half_len+kmer_len] in seq_chr_dic:
continue
@@ -531,7 +531,7 @@ def filter_fusion(bwt_idx_prefix, params):
if same:
continue
-
+
for chr_coord in right_chrs:
chr, coord = chr_coord.split(':')
coord = int(coord)
@@ -555,12 +555,12 @@ def filter_fusion(bwt_idx_prefix, params):
dir = info[3]
gene1, gene1_name, gene1_where, gene1_belong, gene1_sense, ens_gene1, ens_gene1_name = find_gene(chr1, coord1, dir[0], True)
gene2, gene2_name, gene2_where, gene2_belong, gene2_sense, ens_gene2, ens_gene2_name = find_gene(chr2, coord2, dir[1], False)
+ if params.filter_by_annotation:
+ if gene1_name == gene2_name or ens_gene1_name == ens_gene2_name or ens_gene1 == ens_gene2:
+ continue
- if gene1_name == gene2_name or ens_gene1_name == ens_gene2_name or ens_gene1 == ens_gene2:
- continue
-
- if gene1 == "N/A" or gene2 == "N/A" or (string.find(gene1, "ENS") == 0 and string.find(gene2, "ENS") == 0):
- continue
+ if gene1 == "N/A" or gene2 == "N/A" or (string.find(gene1, "ENS") == 0 and string.find(gene2, "ENS") == 0):
+ continue
left_diff = how_diff(left_seq[half_len - 20:half_len], right_seq[half_len - 20:half_len])
if left_diff <= 8:
@@ -582,9 +582,9 @@ def filter_fusion(bwt_idx_prefix, params):
swap = False
if (dir == 'ff' and gene1_sense == '-' and gene2_sense == '-') or \
- (dir == 'rr' and gene1_sense == '+' and gene2_sense == '+') or \
- (dir == 'fr' and gene1_sense == '-' and gene2_sense == '+') or \
- (dir == 'rf' and gene1_sense == '+' and gene2_sense == '-'):
+ (dir == 'rr' and gene1_sense == '+' and gene2_sense == '+') or \
+ (dir == 'fr' and gene1_sense == '-' and gene2_sense == '+') or \
+ (dir == 'rf' and gene1_sense == '+' and gene2_sense == '-'):
swap = True
if swap:
@@ -692,8 +692,11 @@ def filter_fusion(bwt_idx_prefix, params):
return gene_list
- refGene_list = read_genes("refGene.txt")
- ensGene_list = read_genes("ensGene.txt")
+ refGene_list, ensGene_list = [], []
+ if os.path.exists("refGene.txt"):
+ refGene_list = read_genes("refGene.txt")
+ if os.path.exists("ensGene.txt"):
+ ensGene_list = read_genes("ensGene.txt")
fusion_gene_list = []
for file in sorted(os.listdir(".")):
@@ -2585,7 +2588,7 @@ def prog_path(program):
def get_version():
- return "2.1.0"
+ return "2.0.11"
def main(argv=None):
diff --git a/src/tophat.py b/src/tophat.py
index 94f5848..b4677b3 100755
--- a/src/tophat.py
+++ b/src/tophat.py
@@ -1496,7 +1496,7 @@ def get_index_sam_header(params, idx_prefix, name = ""):
def check_bowtie(params):
bowtie_req=""
if params.bowtie2:
- bowtie_req="2-align"
+ bowtie_req="2"
log_msg = "Checking for Bowtie"
th_log(log_msg)
--
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