Hello,
sorry I am new in this I tried to convert sff file to fasta and fastq files. Firstly I installed python 2.7.6 then biopython 1.65 and finally seq_crumbs 0.1.9 and i tried sff_extract but there is a problem :
]# sff_extract IXXLJHH01.sff
Traceback (most recent call last):
File "/usr/bin/sff_extract", line 25, in <module>
from crumbs.seqio import write_seqs
File "/usr/lib/python2.6/site-packages/crumbs/seqio.py", line 35, in <module>
from crumbs.utils.file_formats import get_format, peek_chunk_from_file
File "/usr/lib/python2.6/site-packages/crumbs/utils/file_formats.py", line 22, in <module>
from crumbs.settings import get_setting
File "/usr/lib/python2.6/site-packages/crumbs/settings.py", line 133, in <module>
_settings = _Settings()
File "/usr/lib/python2.6/site-packages/crumbs/settings.py", line 114, in __init__
self.load_settings()
File "/usr/lib/python2.6/site-packages/crumbs/settings.py", line 119, in load_settings
for key, val in globals().viewitems():
AttributeError: 'dict' object has no attribute 'viewitems'
What should I do for this?
Thanks,
sorry I am new in this I tried to convert sff file to fasta and fastq files. Firstly I installed python 2.7.6 then biopython 1.65 and finally seq_crumbs 0.1.9 and i tried sff_extract but there is a problem :
]# sff_extract IXXLJHH01.sff
Traceback (most recent call last):
File "/usr/bin/sff_extract", line 25, in <module>
from crumbs.seqio import write_seqs
File "/usr/lib/python2.6/site-packages/crumbs/seqio.py", line 35, in <module>
from crumbs.utils.file_formats import get_format, peek_chunk_from_file
File "/usr/lib/python2.6/site-packages/crumbs/utils/file_formats.py", line 22, in <module>
from crumbs.settings import get_setting
File "/usr/lib/python2.6/site-packages/crumbs/settings.py", line 133, in <module>
_settings = _Settings()
File "/usr/lib/python2.6/site-packages/crumbs/settings.py", line 114, in __init__
self.load_settings()
File "/usr/lib/python2.6/site-packages/crumbs/settings.py", line 119, in load_settings
for key, val in globals().viewitems():
AttributeError: 'dict' object has no attribute 'viewitems'
What should I do for this?
Thanks,
Comment