projects
/
htsworkflow.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
Initial port to python3
[htsworkflow.git]
/
htsworkflow
/
pipelines
/
genomemap.py
diff --git
a/htsworkflow/pipelines/genomemap.py
b/htsworkflow/pipelines/genomemap.py
index 1dd95df86578bd83b75468779f1d08e1c4f3988e..87d65eba01ff3ba51e906398b26cc385a5985c81 100644
(file)
--- a/
htsworkflow/pipelines/genomemap.py
+++ b/
htsworkflow/pipelines/genomemap.py
@@
-17,7
+17,7
@@
class GenomeMap(collections.MutableMapping):
return len(self._contigs)
def __iter__(self):
return len(self._contigs)
def __iter__(self):
- return
self._contigs.iterkeys(
)
+ return
iter(self._contigs.keys()
)
def __getitem__(self, name):
return self._contigs[name]
def __getitem__(self, name):
return self._contigs[name]
@@
-68,7
+68,7
@@
class GenomeMap(collections.MutableMapping):
genome = guess_genome(sizes)
genome = guess_genome(sizes)
- for contig, basese in
sizes.items(
):
+ for contig, basese in
list(sizes.items()
):
name = filenames[contig]
self._contigs[name] = genome + '/' + name
name = filenames[contig]
self._contigs[name] = genome + '/' + name
@@
-93,6
+93,6
@@
def guess_genome(contig_sizes):
return genomes[key][size]
if len(contig_sizes) == 1:
return genomes[key][size]
if len(contig_sizes) == 1:
- return os.path.splitext(
contig_sizes.keys(
)[0])[0]
+ return os.path.splitext(
list(contig_sizes.keys()
)[0])[0]
raise RuntimeError("Unrecognized genome type, update detection code.")
raise RuntimeError("Unrecognized genome type, update detection code.")