From 0931224148ee8f3ec36a4238f637723aceb67b5d Mon Sep 17 00:00:00 2001 From: Ilya Shlyakhter Date: Tue, 14 Aug 2018 12:09:44 -0400 Subject: [PATCH] update spades to 3.12.0 (#878) --- requirements-conda.txt | 2 +- test/unit/test_assembly.py | 10 ++++++---- tools/spades.py | 2 +- 3 files changed, 8 insertions(+), 6 deletions(-) diff --git a/requirements-conda.txt b/requirements-conda.txt index cb028bdce..fc271db80 100644 --- a/requirements-conda.txt +++ b/requirements-conda.txt @@ -23,7 +23,7 @@ pigz=2.4 prinseq=0.20.4 samtools=1.9 snpeff=4.3.1t -spades=3.11.1 +spades=3.12.0 tbl2asn=25.6 trimmomatic=0.38 trinity=date.2011_11_26 diff --git a/test/unit/test_assembly.py b/test/unit/test_assembly.py index 67c7fe502..857cc4d4b 100644 --- a/test/unit/test_assembly.py +++ b/test/unit/test_assembly.py @@ -157,8 +157,9 @@ def test_assembly(self): assembly.assemble_spades(in_bam=inBam, clip_db=clipDb, out_fasta=outFasta) self.assertGreater(os.path.getsize(outFasta), 0) contig_lens = list(sorted(len(seq.seq) for seq in Bio.SeqIO.parse(outFasta, 'fasta'))) - print('test_assembly_contigs_lens:', contig_lens) - self.assertEqual(contig_lens, [168, 170, 177, 180, 184, 187, 190, 191, 195, 197, 211, 243, 244, 247, 328, 348, 430]) + #import sys + #print('test_assembly_contigs_lens:', contig_lens, file=sys.stderr) + self.assertEqual(contig_lens, [168, 170, 177, 180, 184, 187, 190, 191, 194, 197, 211, 243, 244, 247, 288, 328, 348, 430]) def test_assembly_with_previously_assembled_contigs(self): inDir = util.file.get_test_input_path(self) @@ -170,8 +171,9 @@ def test_assembly_with_previously_assembled_contigs(self): out_fasta=outFasta, mem_limit_gb=1) self.assertGreater(os.path.getsize(outFasta), 0) contig_lens = list(sorted(len(seq.seq) for seq in Bio.SeqIO.parse(outFasta, 'fasta'))) - print('test_assembly_with_previously_assembled_contigs_contigs_lens:', contig_lens) - self.assertEqual(contig_lens, [168, 170, 177, 180, 184, 187, 190, 191, 195, 197, 211, 243, 244, 321, 328, 348, 430]) + #import sys + #print('test_assembly_with_previously_assembled_contigs_contigs_lens:', contig_lens, file=sys.stderr) + self.assertEqual(contig_lens, [168, 170, 177, 180, 184, 187, 190, 191, 194, 197, 211, 243, 244, 247, 288, 328, 348, 430]) def test_empty_input_succeed(self): inDir = util.file.get_test_input_path() diff --git a/tools/spades.py b/tools/spades.py index eec60a803..93726414c 100644 --- a/tools/spades.py +++ b/tools/spades.py @@ -18,7 +18,7 @@ import util.misc TOOL_NAME = 'spades' -TOOL_VERSION = '3.11.1' +TOOL_VERSION = '3.12.0' log = logging.getLogger(__name__)