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 <[email protected]> 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 <[email protected]>. # @@ -269,8 +269,8 @@ SHELL=${CONFIG_SHELL-/bin/sh} # Identity of this package. PACKAGE_NAME='tophat' PACKAGE_TARNAME='tophat' -PACKAGE_VERSION='2.0.10' -PACKAGE_STRING='tophat 2.0.10' +PACKAGE_VERSION='2.0.11' +PACKAGE_STRING='tophat 2.0.11' PACKAGE_BUGREPORT='[email protected]' ac_unique_file="config.h.in" @@ -792,7 +792,7 @@ if test "$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],[[email protected]]) +AC_INIT([tophat],[2.0.11],[[email protected]]) 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) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/tophat.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
