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Directly generate compressed fastq files from HiSeq split fastqs.
[htsworkflow.git]
/
htsworkflow
/
submission
/
fastqname.py
diff --git
a/htsworkflow/submission/fastqname.py
b/htsworkflow/submission/fastqname.py
index 9dd52a0319fb9e9efa230e68344ef53156645be7..ac3d5fc4ed59a4ff944588c015ae402fba1b0e53 100644
(file)
--- a/
htsworkflow/submission/fastqname.py
+++ b/
htsworkflow/submission/fastqname.py
@@
-2,8
+2,8
@@
"""
import collections
import re
"""
import collections
import re
-PAIRED_TEMPLATE = '{lib_id}_{flowcell}_c{cycle}_l{lane}_r{read}.fastq'
-SINGLE_TEMPLATE = '{lib_id}_{flowcell}_c{cycle}_l{lane}.fastq'
+PAIRED_TEMPLATE = '{lib_id}_{flowcell}_c{cycle}_l{lane}_r{read}.fastq
{compression_extension}
'
+SINGLE_TEMPLATE = '{lib_id}_{flowcell}_c{cycle}_l{lane}.fastq
{compression_extension}
'
FASTQ_RE = re.compile(
'(?P<lib_id>[^_]+)_(?P<flowcell>[^_]+)_'\
FASTQ_RE = re.compile(
'(?P<lib_id>[^_]+)_(?P<flowcell>[^_]+)_'\
@@
-17,7
+17,7
@@
class FastqName(collections.Mapping):
Takes filename or common attributes like flowcell, lib_id, lane, read, cycle
"""
Takes filename or common attributes like flowcell, lib_id, lane, read, cycle
"""
- self._attributes = ('flowcell', 'lib_id', 'lane', 'read', 'cycle')
+ self._attributes = ('flowcell', 'lib_id', 'lane', 'read', 'cycle'
, 'compression_extension'
)
self._is_paired = is_paired
if len(kwargs) == 0:
self._is_paired = is_paired
if len(kwargs) == 0: