[Torst]

I installed nesoni-0.58 and SHRiMP_2_2_1.
And ran "nesoni samshrimp"
>nesoni samshrimp test_out J_mapper.fasta J.fq
Error: No read files given
anyone can tell me what problem is ??

if you just type "nesoni samshrimp" you will get the help:

    nesoni samshrimp: output_directory [options] \
        reference.fa/.gbk [...] \
        [reads: single.fq | single.fa [...]] \
        [interleaved: interleaved.fq | interleaved.fa [...]] \
        [pairs: left.fq right.fq | left.fa right.fa] \
        [shrimp-options: ...options to pass directly to gmapper-ls... ]

You have not supplied the read file correctly. Is it interleaved pairs, or single shotgun reads?
If single end, this is the command you want:

nesoni samshrimp: test_out J_mapper.fasta reads: J.fq

[sirius]

Get it~~
Thanks for your help

[Mona]

Hello,

I am trying to install nesoni,
I installed bowtie2 as the manual says shrimp or bowtie2 in the requirements. I then installed nesoni but when i type the command nesoni, it gives the following error message:

Traceback (most recent call last):
File "/usr/local/bin/nesoni", line 8, in <module>
load_entry_point('nesoni==0.101', 'console_scripts', 'nesoni')()
File "/System/Library/Frameworks/Python.framework/Versions/2.6/Extras/lib/python/pkg_resources.py", line 271, in load_entry_point
return get_distribution(dist).load_entry_point(group, name)
File "/System/Library/Frameworks/Python.framework/Versions/2.6/Extras/lib/python/pkg_resources.py", line 2174, in load_entry_point
return ep.load()
File "/System/Library/Frameworks/Python.framework/Versions/2.6/Extras/lib/python/pkg_resources.py", line 1907, in load
entry = __import__(self.module_name, globals(),globals(), ['__name__'])
File "/Library/Python/2.6/site-packages/nesoni-0.101-py2.6.egg/nesoni/__init__.py", line 8, in <module>
from reference_directory import Make_reference
File "/Library/Python/2.6/site-packages/nesoni-0.101-py2.6.egg/nesoni/reference_directory.py", line 5, in <module>
from nesoni import io, grace, config, annotation
File "/Library/Python/2.6/site-packages/nesoni-0.101-py2.6.egg/nesoni/io.py", line 837, in <module>
class Grouped_table(collections.OrderedDict):
AttributeError: 'module' object has no attribute 'OrderedDict'


As i m not a unix expert, so need help...

[pfh]

Hi Mona,

Looks like OrderedDict was added in Python 2.7. I need to update the requirements in the README!

Ok, two options:

1. Install Python 2.7. I don't know enough about package management on OS X to know how hard this is.

2. (preferable) Install virtualenv, eg by following the instructions on virtualenv.org. Download and untar the latest PyPy from pypy.org. Using the instructions in the nesoni README, create a virtualenv using the pypy you just untarred, and install BioPython and nesoni in it.

[Mona]

Thanks pfh,

To me installing python 2.7 seems to be an easy option, I have done that now, but I think nisoni is still using python 2.6 as I am getting the same error. May be I should try to un install python 2.6 so it will then be using 2.7.

[pfh]

You need to make sure you run the setup.py script with python 2.7. First work out how to run python 2.7, eg rather than typing "python" you might need to type "python2.7". Then to install nesoni from source:

python2.7 setup.py install

This should install a "nesoni" script on your path that uses the same version of python as the setup.py script used.


I do still recommend using "virtualenv". I have a shell script to set up a virtualenv and install nesoni and a few other python tools that I use using pip. This serves as documentation of the entire processes of installing them, and of all their dependancies.

[Shah Md Tamim Kabir]

Nesoni can do this for you. Feed it your 454 contigs as the "reference" and the Illumina reads as the "reads". Run "nesoni shrimp" then "nesoni consensus". The working folder will contain "reference_consensus.fa" or similar which is effectively the "corrected" 454 contigs.

Download site: http://www.vicbioinformatics.com/nesoni.shtml

Hi,

I want eheck homopolymer error in my 454 reference assembly using illumina data by using nesoni. With your recommendation I have downloaded nesoni-0.36 and after running "nesoni shrimp" output a reference.fa file. But tuning "nesoni consensus" made the following error--


nesoni-0.36]$ ./nesoni_scripts/nesoni consensus
Loading
Error compiling Cython file:
------------------------------------------------------------
...

"""

cdef public object seqs, seq_order, used_hit_file, unambiguous_seps, shrimp_threshold
cdef public int infidelity
cdef public bool is_paired_end, same_direction, is_monogamous, is_circular, only_pairs, whole_read_only
^
------------------------------------------------------------

nesoni/consensus.pyx:475:16: 'bool' is not a type identifier

Error compiling Cython file:
------------------------------------------------------------
...

"""

cdef public object seqs, seq_order, used_hit_file, unambiguous_seps, shrimp_threshold
cdef public int infidelity
cdef public bool is_paired_end, same_direction, is_monogamous, is_circular, only_pairs, whole_read_only
^
------------------------------------------------------------

nesoni/consensus.pyx:475:21: C attribute of type '<error>' cannot be accessed from Python

Error compiling Cython file:
------------------------------------------------------------
...

"""

cdef public object seqs, seq_order, used_hit_file, unambiguous_seps, shrimp_threshold
cdef public int infidelity
cdef public bool is_paired_end, same_direction, is_monogamous, is_circular, only_pairs, whole_read_only
^
------------------------------------------------------------

nesoni/consensus.pyx:475:36: C attribute of type '<error>' cannot be accessed from Python

Error compiling Cython file:
------------------------------------------------------------
...

"""

cdef public object seqs, seq_order, used_hit_file, unambiguous_seps, shrimp_threshold
cdef public int infidelity
cdef public bool is_paired_end, same_direction, is_monogamous, is_circular, only_pairs, whole_read_only
^
------------------------------------------------------------

nesoni/consensus.pyx:475:52: C attribute of type '<error>' cannot be accessed from Python

Error compiling Cython file:
------------------------------------------------------------
...

"""

cdef public object seqs, seq_order, used_hit_file, unambiguous_seps, shrimp_threshold
cdef public int infidelity
cdef public bool is_paired_end, same_direction, is_monogamous, is_circular, only_pairs, whole_read_only
^
------------------------------------------------------------

nesoni/consensus.pyx:475:67: C attribute of type '<error>' cannot be accessed from Python

Error compiling Cython file:
------------------------------------------------------------
...

"""

cdef public object seqs, seq_order, used_hit_file, unambiguous_seps, shrimp_threshold
cdef public int infidelity
cdef public bool is_paired_end, same_direction, is_monogamous, is_circular, only_pairs, whole_read_only
^
------------------------------------------------------------

nesoni/consensus.pyx:475:80: C attribute of type '<error>' cannot be accessed from Python

Error compiling Cython file:
------------------------------------------------------------
...

"""

cdef public object seqs, seq_order, used_hit_file, unambiguous_seps, shrimp_threshold
cdef public int infidelity
cdef public bool is_paired_end, same_direction, is_monogamous, is_circular, only_pairs, whole_read_only
^
------------------------------------------------------------

nesoni/consensus.pyx:475:92: C attribute of type '<error>' cannot be accessed from Python

Error compiling Cython file:
------------------------------------------------------------
...

cdef public int n_single, n_single_with_hits, n_single_unambiguous, n_pair, n_pair_with_hits, n_pair_valid, n_pair_valid_unambiguous

ATTRIBUTES = [ 'seqs', 'seq_order' ] # Only those relevant to reconsensusing

def __init__(self, bool is_paired_end, bool same_direction, int max_pair_sep, int trim, shrimp_threshold, int infidelity, bool is_monogamous, bool is_circular, bool only_pairs, bool whole_read_only, used_hit_file):
^
------------------------------------------------------------

nesoni/consensus.pyx:482:23: 'bool' is not a type identifier

Error compiling Cython file:
------------------------------------------------------------
...

cdef public int n_single, n_single_with_hits, n_single_unambiguous, n_pair, n_pair_with_hits, n_pair_valid, n_pair_valid_unambiguous

ATTRIBUTES = [ 'seqs', 'seq_order' ] # Only those relevant to reconsensusing

def __init__(self, bool is_paired_end, bool same_direction, int max_pair_sep, int trim, shrimp_threshold, int infidelity, bool is_monogamous, bool is_circular, bool only_pairs, bool whole_read_only, used_hit_file):
^
------------------------------------------------------------

nesoni/consensus.pyx:482:43: 'bool' is not a type identifier

Error compiling Cython file:
------------------------------------------------------------
...

cdef public int n_single, n_single_with_hits, n_single_unambiguous, n_pair, n_pair_with_hits, n_pair_valid, n_pair_valid_unambiguous

ATTRIBUTES = [ 'seqs', 'seq_order' ] # Only those relevant to reconsensusing

def __init__(self, bool is_paired_end, bool same_direction, int max_pair_sep, int trim, shrimp_threshold, int infidelity, bool is_monogamous, bool is_circular, bool only_pairs, bool whole_read_only, used_hit_file):
^
------------------------------------------------------------

nesoni/consensus.pyx:482:126: 'bool' is not a type identifier

Error compiling Cython file:
------------------------------------------------------------
...

cdef public int n_single, n_single_with_hits, n_single_unambiguous, n_pair, n_pair_with_hits, n_pair_valid, n_pair_valid_unambiguous

ATTRIBUTES = [ 'seqs', 'seq_order' ] # Only those relevant to reconsensusing

def __init__(self, bool is_paired_end, bool same_direction, int max_pair_sep, int trim, shrimp_threshold, int infidelity, bool is_monogamous, bool is_circular, bool only_pairs, bool whole_read_only, used_hit_file):
^
------------------------------------------------------------

nesoni/consensus.pyx:482:146: 'bool' is not a type identifier

Error compiling Cython file:
------------------------------------------------------------
...

cdef public int n_single, n_single_with_hits, n_single_unambiguous, n_pair, n_pair_with_hits, n_pair_valid, n_pair_valid_unambiguous

ATTRIBUTES = [ 'seqs', 'seq_order' ] # Only those relevant to reconsensusing

def __init__(self, bool is_paired_end, bool same_direction, int max_pair_sep, int trim, shrimp_threshold, int infidelity, bool is_monogamous, bool is_circular, bool only_pairs, bool whole_read_only, used_hit_file):
^
------------------------------------------------------------

nesoni/consensus.pyx:482:164: 'bool' is not a type identifier

Error compiling Cython file:
------------------------------------------------------------
...

cdef public int n_single, n_single_with_hits, n_single_unambiguous, n_pair, n_pair_with_hits, n_pair_valid, n_pair_valid_unambiguous

ATTRIBUTES = [ 'seqs', 'seq_order' ] # Only those relevant to reconsensusing

def __init__(self, bool is_paired_end, bool same_direction, int max_pair_sep, int trim, shrimp_threshold, int infidelity, bool is_monogamous, bool is_circular, bool only_pairs, bool whole_read_only, used_hit_file):
^
------------------------------------------------------------

nesoni/consensus.pyx:482:181: 'bool' is not a type identifier
/home/tamim/.pyxbld/temp.linux-x86_64-2.6/pyrex/nesoni/consensus.c:1:2: error: #error Do not use this file, it is the result of a failed Cython compilation.
Traceback (most recent call last):
File "./nesoni_scripts/nesoni", line 15, in <module>
sys.exit(nesoni.main(sys.argv[1:]))
File "/home/smp2_arr_j/tamim_analysis/tools/nesoni-0.36/nesoni/__init__.py", line 177, in main
recombination
File "/home/smp2_arr_j/tamim_analysis/tools/nesoni-0.36/nesoni/grace.py", line 160, in execute
commands[args[start]](args[start+1:end])
File "/home/smp2_arr_j/tamim_analysis/tools/nesoni-0.36/nesoni/__init__.py", line 89, in consensus
grace.load('consensus').main(args)
File "/home/smp2_arr_j/tamim_analysis/tools/nesoni-0.36/nesoni/grace.py", line 44, in load
m = __import__(module_name, globals())
File "/usr/lib64/python2.6/site-packages/Cython-0.23.4-py2.6-linux-x86_64.egg/pyximport/pyximport.py", line 435, in load_module
language_level=self.language_level)
File "/usr/lib64/python2.6/site-packages/Cython-0.23.4-py2.6-linux-x86_64.egg/pyximport/pyximport.py", line 227, in load_module
exec("raise exc, None, tb", {'exc': exc, 'tb': tb})
File "/usr/lib64/python2.6/site-packages/Cython-0.23.4-py2.6-linux-x86_64.egg/pyximport/pyximport.py", line 209, in load_module
inplace=build_inplace, language_level=language_level)
File "/usr/lib64/python2.6/site-packages/Cython-0.23.4-py2.6-linux-x86_64.egg/pyximport/pyximport.py", line 186, in build_module
reload_support=pyxargs.reload_support)
File "/usr/lib64/python2.6/site-packages/Cython-0.23.4-py2.6-linux-x86_64.egg/pyximport/pyxbuild.py", line 100, in pyx_to_dll
dist.run_commands()
File "/usr/lib64/python2.6/distutils/dist.py", line 975, in run_commands
self.run_command(cmd)
File "/usr/lib64/python2.6/distutils/dist.py", line 995, in run_command
cmd_obj.run()
File "/usr/lib64/python2.6/site-packages/Cython-0.23.4-py2.6-linux-x86_64.egg/Cython/Distutils/build_ext.py", line 164, in run
_build_ext.build_ext.run(self)
File "/usr/lib64/python2.6/distutils/command/build_ext.py", line 340, in run
self.build_extensions()
File "/usr/lib64/python2.6/site-packages/Cython-0.23.4-py2.6-linux-x86_64.egg/Cython/Distutils/build_ext.py", line 172, in build_extensions
self.build_extension(ext)
File "/usr/lib64/python2.6/distutils/command/build_ext.py", line 499, in build_extension
depends=ext.depends)
File "/usr/lib64/python2.6/distutils/ccompiler.py", line 621, in compile
self._compile(obj, src, ext, cc_args, extra_postargs, pp_opts)
File "/usr/lib64/python2.6/distutils/unixccompiler.py", line 180, in _compile
raise CompileError, msg
ImportError: Building module nesoni.consensus failed: ["CompileError: command 'gcc' failed with exit status 1\n"]


Can you please help me its urgent.