isa-tools / biopy-isatab Goto Github PK

There are no restrictions in the category names in ISA-TAB and the parser fails when they are not valid field names for the namedtuple.

rec = isatab.parse("/Users/agbeltran/workspace/datasets/harvard-CD133")
Traceback (most recent call last):
File "", line 1, in
File "bcbio/isatab/parser.py", line 57, in parse
rec = s_parser.parse(rec)
File "bcbio/isatab/parser.py", line 192, in parse
["Raw Data File", "Derived Data File", "Image File"])
File "bcbio/isatab/parser.py", line 228, in _parse_study
node.metadata)
File "bcbio/isatab/parser.py", line 246, in _line_keyvals
self._collapse_attributes)
File "bcbio/isatab/parser.py", line 260, in _line_by_type
val = collapse_quals_fn(line, header, hgroups[index])
File "bcbio/isatab/parser.py", line 275, in _collapse_attributes
Attrs = collections.namedtuple('Attrs', names)
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/collections.py", line 253, in namedtuple
ValueError: Type names and field names cannot start with a number: '57B_antigen_expression_by_IHC'

Please specify the license of this code. Check license compatibility in case parts of the codebase
were taken from other code (ignore the last bit if it was written from scratch). Thanks, Steffen

When trying to install biopy-isatab via pip I run into an AttributeError when it tries to create the install egg. We would like to try using this package in a deployed virtual environment via pip. Can someone please take a look at this?

Thx!

C:\Dropbox\Code\isa-tab>pip install biopy-isatab
Downloading/unpacking biopy-isatab
  Downloading biopy-isatab-0.1.tar.gz
  Running setup.py egg_info for package biopy-isatab

    Traceback (most recent call last):
      File "<string>", line 14, in <module>
      File "C:\Dropbox\Code\isa-tab\build\biopy-isatab\setup.py", line 16, in <module>
        install_requires = [
      File "C:\Python27\lib\distutils\core.py", line 152, in setup
        dist.run_commands()
      File "C:\Python27\lib\distutils\dist.py", line 953, in run_commands
        self.run_command(cmd)
      File "C:\Python27\lib\distutils\dist.py", line 972, in run_command
        cmd_obj.run()
      File "<string>", line 12, in replacement_run
      File "C:\Python27\lib\site-packages\setuptools\command\egg_info.py", line 254, in find_sources
        mm.run()
      File "C:\Python27\lib\site-packages\setuptools\command\egg_info.py", line 310, in run
        self.read_template()
      File "C:\Python27\lib\site-packages\setuptools\command\sdist.py", line 209, in read_template
        sys.exc_info()[2].tb_next.tb_frame.f_locals['template'].close()
      File "C:\Python27\lib\distutils\text_file.py", line 128, in close
        self.file.close ()
    AttributeError: 'NoneType' object has no attribute 'close'
    Complete output from command python setup.py egg_info:
    running egg_info

creating pip-egg-info\biopy_isatab.egg-info

writing pip-egg-info\biopy_isatab.egg-info\PKG-INFO

writing namespace_packages to pip-egg-info\biopy_isatab.egg-info\namespace_packages.txt

writing top-level names to pip-egg-info\biopy_isatab.egg-info\top_level.txt

writing dependency_links to pip-egg-info\biopy_isatab.egg-info\dependency_links.txt

writing manifest file 'pip-egg-info\biopy_isatab.egg-info\SOURCES.txt'

warning: manifest_maker: standard file '-c' not found



reading manifest file 'pip-egg-info\biopy_isatab.egg-info\SOURCES.txt'

reading manifest template 'MANIFEST.in'

Traceback (most recent call last):

  File "<string>", line 14, in <module>

  File "C:\Dropbox\Code\isa-tab\build\biopy-isatab\setup.py", line 16, in <module>

    install_requires = [

  File "C:\Python27\lib\distutils\core.py", line 152, in setup

    dist.run_commands()

  File "C:\Python27\lib\distutils\dist.py", line 953, in run_commands

    self.run_command(cmd)

  File "C:\Python27\lib\distutils\dist.py", line 972, in run_command

    cmd_obj.run()

  File "<string>", line 12, in replacement_run

  File "C:\Python27\lib\site-packages\setuptools\command\egg_info.py", line 254, in find_sources

    mm.run()

  File "C:\Python27\lib\site-packages\setuptools\command\egg_info.py", line 310, in run

    self.read_template()

  File "C:\Python27\lib\site-packages\setuptools\command\sdist.py", line 209, in read_template

    sys.exc_info()[2].tb_next.tb_frame.f_locals['template'].close()

  File "C:\Python27\lib\distutils\text_file.py", line 128, in close

    self.file.close ()

AttributeError: 'NoneType' object has no attribute 'close'

----------------------------------------
Command python setup.py egg_info failed with error code 1
Storing complete log in C:\Users\felciano\AppData\Roaming\pip\pip.log

C:\Dropbox\Code\isa-tab>pip install biopy-isatab

Error when parsing Study or Assay files with repeated header names (as Term Source REF)
The code builds a named tuple to store the attributes in multiple columns and named tuples don't allow duplicates.
Some output for a few datasets below.

Error with Yox1 data

Python 2.7.1 (r271:86832, Jul 31 2011, 19:30:53)
[GCC 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2335.15.00)] on darwin
Type "help", "copyright", "credits" or "license" for more information.

from bcbio import isatab
rec = isatab.parse("/Users/agbeltran/workspace/datasets/Yox1")
Traceback (most recent call last):
File "", line 1, in
File "bcbio/isatab/parser.py", line 57, in parse
rec = s_parser.parse(rec)
File "bcbio/isatab/parser.py", line 192, in parse
["Raw Data File"])
File "bcbio/isatab/parser.py", line 228, in _parse_study
node.metadata)
File "bcbio/isatab/parser.py", line 248, in _line_keyvals
self._collapse_attributes)
File "bcbio/isatab/parser.py", line 260, in _line_by_type
val = collapse_quals_fn(line, header, hgroups[index])
File "bcbio/isatab/parser.py", line 275, in _collapse_attributes
Attrs = collections.namedtuple('Attrs', names)
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/collections.py", line 259, in namedtuple
ValueError: Encountered duplicate field name: 'Term_Source_REF'

Error with BII-S-6

rec = isatab.parse("/Users/agbeltran/workspace/datasets/BII-S-6")
Traceback (most recent call last):
File "", line 1, in
File "bcbio/isatab/parser.py", line 57, in parse
rec = s_parser.parse(rec)
File "bcbio/isatab/parser.py", line 185, in parse
["Sample Name", "Comment[ENA_SAMPLE]"])
File "bcbio/isatab/parser.py", line 228, in _parse_study
node.metadata)
File "bcbio/isatab/parser.py", line 248, in _line_keyvals
self._collapse_attributes)
File "bcbio/isatab/parser.py", line 260, in _line_by_type
val = collapse_quals_fn(line, header, hgroups[index])
File "bcbio/isatab/parser.py", line 275, in _collapse_attributes
Attrs = collections.namedtuple('Attrs', names)
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/collections.py", line 259, in namedtuple
ValueError: Encountered duplicate field name: 'Term_Source_REF'

Error with mtbls2

rec = isatab.parse("/Users/agbeltran/workspace/datasets/mtbls2")
Traceback (most recent call last):
File "", line 1, in
File "bcbio/isatab/parser.py", line 57, in parse
rec = s_parser.parse(rec)
File "bcbio/isatab/parser.py", line 192, in parse
["Raw Data File"])
File "bcbio/isatab/parser.py", line 228, in _parse_study
node.metadata)
File "bcbio/isatab/parser.py", line 248, in _line_keyvals
self._collapse_attributes)
File "bcbio/isatab/parser.py", line 260, in _line_by_type
val = collapse_quals_fn(line, header, hgroups[index])
File "bcbio/isatab/parser.py", line 275, in _collapse_attributes
Attrs = collections.namedtuple('Attrs', names)
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/collections.py", line 259, in namedtuple
ValueError: Encountered duplicate field name: 'Term_Source_REF'

The parser doesn't adequately handle reading UTF8 characters in input strings.

There looks like a fix in forked repo in this commit: timeu@a2cd7b9 but need to test if the fix works as expected.

Currently, as stated in the comments, the code is biased towards microarray and next-gen sequencing data. The nodes considered are those containing a "Raw Data File". This needs to be extended to support other assay types.