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update srf2fastq detection code to work with byte arrays
author
Diane Trout
<diane@ghic.org>
Thu, 29 Jan 2015 23:43:51 +0000
(15:43 -0800)
committer
Diane Trout
<diane@ghic.org>
Thu, 29 Jan 2015 23:43:51 +0000
(15:43 -0800)
htsworkflow/pipelines/srf2fastq.py
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diff --git
a/htsworkflow/pipelines/srf2fastq.py
b/htsworkflow/pipelines/srf2fastq.py
index 0805879c2dad1b6a09b8090c3cc4b7661c93c094..e0c80addaaf0746513b773c579d3ca4e8cf4c962 100644
(file)
--- a/
htsworkflow/pipelines/srf2fastq.py
+++ b/
htsworkflow/pipelines/srf2fastq.py
@@
-153,7
+153,7
@@
def convert_single_to_two_fastq(instream, target1, target2, mid=None, header='')
# sequence
elif state == FASTQ_SEQUENCE:
if mid is None:
# sequence
elif state == FASTQ_SEQUENCE:
if mid is None:
- mid = len(line)
/
2
+ mid = len(line)
//
2
write_split_sequence(target1, target2, line, mid)
state = FASTQ_SEQUENCE_HEADER
# quality header
write_split_sequence(target1, target2, line, mid)
state = FASTQ_SEQUENCE_HEADER
# quality header
@@
-193,19
+193,19
@@
def is_srf(filename):
"""
Check filename to see if it is likely to be a SRF file
"""
"""
Check filename to see if it is likely to be a SRF file
"""
- f = open(filename, 'r')
+ f = open(filename, 'r
b
')
header = f.read(4)
f.close()
header = f.read(4)
f.close()
- return header == "SSRF"
+ return header ==
b
"SSRF"
def is_cnf1(filename):
"""
Brute force detection if a SRF file is using CNF1/CNF4 records
"""
max_header = 1024 ** 2
def is_cnf1(filename):
"""
Brute force detection if a SRF file is using CNF1/CNF4 records
"""
max_header = 1024 ** 2
- PROGRAM_ID = 'PROGRAM_ID\000'
- cnf4_apps = set(("solexa2srf v1.4",
- "illumina2srf v1.11.5.Illumina.1.3"))
+ PROGRAM_ID =
b
'PROGRAM_ID\000'
+ cnf4_apps = set((
b
"solexa2srf v1.4",
+
b
"illumina2srf v1.11.5.Illumina.1.3"))
if not is_srf(filename):
raise ValueError("%s must be a srf file" % (filename,))
if not is_srf(filename):
raise ValueError("%s must be a srf file" % (filename,))
@@
-215,7
+215,7
@@
def is_cnf1(filename):
# alas the max search length requires python 2.6+
program_id_location = f.find(PROGRAM_ID, 0) #, max_header)
program_header_start = program_id_location+len(PROGRAM_ID)
# alas the max search length requires python 2.6+
program_id_location = f.find(PROGRAM_ID, 0) #, max_header)
program_header_start = program_id_location+len(PROGRAM_ID)
- next_null = f.find('\000', program_header_start) #, max_header)
+ next_null = f.find(
b
'\000', program_header_start) #, max_header)
program_id_header = f[program_header_start:next_null]
f.close()
os.close(fd)
program_id_header = f[program_header_start:next_null]
f.close()
os.close(fd)