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22 Sep 2015 11:26:31 +0100 Subject: [PATCH 2/5] Add .gitignore file --- .gitignore | 1 + 1 file changed, 1 insertion(+) create mode 100644 .gitignore diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..0d20b64 --- /dev/null +++ b/.gitignore @@ -0,0 +1 @@ +*.pyc From 5a3637b0a075443a23e2f44c2c2b9aa8e31d05fd Mon Sep 17 00:00:00 2001 From: tw164 Date: Tue, 22 Sep 2015 12:38:15 +0100 Subject: [PATCH 3/5] Fix BAM file to SAM file in parseCovFromSAMFile --- BlobCollection.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/BlobCollection.py b/BlobCollection.py index dc74b1a..ac5bd1e 100644 --- a/BlobCollection.py +++ b/BlobCollection.py @@ -229,7 +229,7 @@ def parseCovFromSAMFile(self, lib_name, sam_file): contig_base_cov[contig_name] = contig_base_cov.get(contig_name, 0) + sum_of_matchin_bases for contig_id, base_cov in contig_base_cov.items(): if contig_id not in self.contigs: - sys.exit("[ERROR] - Sequence header %s in %s does not seem to be part of the assembly. FASTA header of sequence in assembly MUST equal reference sequence name in BAM file. Please check your input files." % (contig_id, bam_file)) + sys.exit("[ERROR] - Sequence header %s in %s does not seem to be part of the assembly. FASTA header of sequence in assembly MUST equal reference sequence name in BAM file. Please check your input files." % (contig_id, sam_file)) else: contig_cov = base_cov / self.contigs[contig_id].corrected_length self.addBlobCov(contig_id, lib_name, contig_cov) @@ -508,4 +508,4 @@ def writeOutput(self, version): blobs_string += tax_string[0:-1] blobs_string += "\n" blobs_fh.write(blobs_string) - blobs_fh.close() \ No newline at end of file + blobs_fh.close() From fc3fdb25391ca417cd6688c84fbf2623b7b2fa7e Mon Sep 17 00:00:00 2001 From: tw164 Date: Tue, 22 Sep 2015 12:40:18 +0100 Subject: [PATCH 4/5] Join Taxdump path components with os.path.join --- makeblobs.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/makeblobs.py b/makeblobs.py index 4d218c9..57fe177 100755 --- a/makeblobs.py +++ b/makeblobs.py @@ -128,14 +128,14 @@ def getDictOfTaxDB(self, taxdb_dir): if not taxdb_dir: sys.exit("[ERROR] : Please specify the path to NCBI TaxDB.") if os.path.exists(taxdb_dir): - if not os.path.exists(taxdb_dir + "nodes.dmp"): + if not os.path.exists( os.path.join(taxdb_dir, "nodes.dmp") ): sys.exit("[ERROR] : 'nodes.dmp' from NCBI TaxDB could not be found in %s." %taxdb_dir) - if not os.path.exists(taxdb_dir + "names.dmp"): + if not os.path.exists( os.path.join(taxdb_dir, "names.dmp") ): sys.exit("[ERROR] : 'names.dmp' from NCBI TaxDB could not be found in %s." %taxdb_dir) else: sys.exit("[ERROR] : NCBI TaxDB could not be found in %s." %taxdb_dir) - taxdb['nodes'] = taxdb_dir + "nodes.dmp" - taxdb['names'] = taxdb_dir + "names.dmp" + taxdb['nodes'] = os.path.join(taxdb_dir, "nodes.dmp") + taxdb['names'] = os.path.join(taxdb_dir, "names.dmp") return taxdb def getDictOfOutfiles(self, outprefix): From 705e08dbdc20270b544a5086b697bbfdabe09361 Mon Sep 17 00:00:00 2001 From: tw164 Date: Wed, 2 Dec 2015 16:48:22 +0000 Subject: [PATCH 5/5] Fix Bowtie2 options for unpaired reads --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 39fc18e..8c923c4 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,5 @@ # blobtools-light -Light version of the upcoming blobtools package +Light version of the blobtools package. No longer maintained ... please check out blobtools. blobtools-light allows the visualisation of (draft) genome assemblies using TAGC (Taxon-annotated Gc-Coverage) plots (Kumar et al. 2012).