From b4de09ebe99cc622d1e3abc106779b8d1e300a7c Mon Sep 17 00:00:00 2001 From: Lorena Pantano Date: Wed, 14 Oct 2020 17:59:50 -0400 Subject: [PATCH 1/3] fix bug in report making profile with long tail --- HISTORY.md | 4 ++++ seqcluster/libs/read.py | 2 +- setup.py | 2 +- 3 files changed, 6 insertions(+), 2 deletions(-) diff --git a/HISTORY.md b/HISTORY.md index 5bb9ff9..a53a802 100644 --- a/HISTORY.md +++ b/HISTORY.md @@ -1,3 +1,7 @@ +- 1.2.8a + + * Fix bug when detecting the end of the cluster due to big gaps in biopython function + - 1.2.7 * Fix bug when writing files for debug of big meta-clusters: diff --git a/seqcluster/libs/read.py b/seqcluster/libs/read.py index 860fffc..0e777bf 100644 --- a/seqcluster/libs/read.py +++ b/seqcluster/libs/read.py @@ -103,7 +103,7 @@ def _align(x, y, local = False): sorted_alignments = sorted(aligned_x, key=operator.itemgetter(2)) e = enumerate(sorted_alignments[0][0]) nts = [i for i,c in e if c != "-"] - return [min(nts), max(nts)] + return [min(nts), min(nts)+len(x)] def map_to_precursor_biopython(seqs, names, loci, args): """map the sequences using biopython package""" diff --git a/setup.py b/setup.py index ea50706..f723ba9 100644 --- a/setup.py +++ b/setup.py @@ -13,7 +13,7 @@ def readme(): setup(name='seqcluster', - version='1.2.7', + version='1.2.8a', description='Small RNA-seq pipeline', long_description=readme(), long_description_content_type="text/markdown", From 26f92fd296245689d65a5cb31bcd5aae74336e90 Mon Sep 17 00:00:00 2001 From: Lorena Pantano Date: Thu, 4 Mar 2021 08:23:53 -0500 Subject: [PATCH 2/3] make release --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index f723ba9..fa368e7 100644 --- a/setup.py +++ b/setup.py @@ -13,7 +13,7 @@ def readme(): setup(name='seqcluster', - version='1.2.8a', + version='1.2.8', description='Small RNA-seq pipeline', long_description=readme(), long_description_content_type="text/markdown", From 334197d1e035e9a39af8e58fa434e7cd1f180e24 Mon Sep 17 00:00:00 2001 From: Lorena Pantano Date: Thu, 4 Mar 2021 08:24:11 -0500 Subject: [PATCH 3/3] Update HISTORY.md --- HISTORY.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/HISTORY.md b/HISTORY.md index a53a802..c3f32e7 100644 --- a/HISTORY.md +++ b/HISTORY.md @@ -1,4 +1,4 @@ -- 1.2.8a +- 1.2.8 * Fix bug when detecting the end of the cluster due to big gaps in biopython function