diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..0d20b64 --- /dev/null +++ b/.gitignore @@ -0,0 +1 @@ +*.pyc 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() diff --git a/BlobCollection.pyc b/BlobCollection.pyc deleted file mode 100644 index 76d1bb0..0000000 Binary files a/BlobCollection.pyc and /dev/null differ diff --git a/MiscFunctions.pyc b/MiscFunctions.pyc deleted file mode 100644 index 1e41b14..0000000 Binary files a/MiscFunctions.pyc and /dev/null differ 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 No longer maintained ...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). 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):