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Minor tweaks and fixes #3

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Minor tweaks and fixes #3

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54fe225
Remove Python byte code files
Sep 22, 2015
3877734
Add .gitignore file
Sep 22, 2015
5a3637b
Fix BAM file to SAM file in parseCovFromSAMFile
Sep 22, 2015
fc3fdb2
Join Taxdump path components with os.path.join
Sep 22, 2015
705e08d
Fix Bowtie2 options for unpaired reads
Dec 2, 2015
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1 change: 1 addition & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
*.pyc
4 changes: 2 additions & 2 deletions BlobCollection.py
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Expand Up @@ -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)
Expand Down Expand Up @@ -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()
blobs_fh.close()
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2 changes: 1 addition & 1 deletion README.md
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@@ -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 No longer maintained ...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 <a href="https://github.com/DRL/blobtools">blobtools</a>.

blobtools-light allows the visualisation of (draft) genome assemblies using TAGC (Taxon-annotated Gc-Coverage) plots (Kumar et al. 2012).

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8 changes: 4 additions & 4 deletions makeblobs.py
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Expand Up @@ -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):
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