というわけで改めてやり直し
まずはpython2.7.13をインストーラをダウンロードしてインストール（3.6もHomebrew使ってないので）
次に
$ pip2 install misopy
Collecting misopy
Using cached misopy-0.5.3.tar.gz
Collecting matplotlib (from misopy)
Downloading matplotlib-2.0.2-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (12.8MB)
100% |=============================================| 12.8MB 97kB/s
Collecting numpy>=1.5.0 (from misopy)
Downloading numpy-1.13.0-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (4.6MB)
100% |=============================================| 4.6MB 308kB/s
Collecting scipy>=0.9.0 (from misopy)
Downloading scipy-0.19.1-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (16.2MB)
100% |=============================================| 16.2MB 78kB/s
Collecting pysam>=0.6.0 (from misopy)
Using cached pysam-0.11.2.2.tar.gz
Collecting python-dateutil (from matplotlib->misopy)
Using cached python_dateutil-2.6.0-py2.py3-none-any.whl
Collecting subprocess32 (from matplotlib->misopy)
Downloading subprocess32-3.2.7.tar.gz (54kB)
100% |=============================================| 61kB 8.4MB/s
Collecting cycler>=0.10 (from matplotlib->misopy)
Using cached cycler-0.10.0-py2.py3-none-any.whl
Collecting six>=1.10 (from matplotlib->misopy)
Using cached six-1.10.0-py2.py3-none-any.whl
Collecting pytz (from matplotlib->misopy)
Using cached pytz-2017.2-py2.py3-none-any.whl
Collecting functools32 (from matplotlib->misopy)
Downloading functools32-3.2.3-2.zip
Collecting pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=1.5.6 (from matplotlib->misopy)
Using cached pyparsing-2.2.0-py2.py3-none-any.whl
Installing collected packages: six, python-dateutil, subprocess32, cycler, pytz, functools32, numpy, pyparsing, matplotlib, scipy, pysam, misopy
Running setup.py install for subprocess32 ... done
Running setup.py install for functools32 ... done
Running setup.py install for pysam ... done
Running setup.py install for misopy ... done
Successfully installed cycler-0.10.0 functools32-3.2.3.post2 matplotlib-2.0.2 misopy-0.5.3 numpy-1.13.0 pyparsing-2.2.0 pysam-0.11.2.2 python-dateutil-2.6.0 pytz-2017.2 scipy-0.19.1 six-1.10.0 subprocess32-3.2.7こうやれば依存関係を解決してインストールしてくれるから、この方がいい。
と思ったが、まだなんかおかしいらしい・・・手強い。
も一回やり直し。
まずはvirtualenvなる仮想化環境を導入
$ pip install virtualenv Collecting virtualenv Using cached virtualenv-15.1.0-py2.py3-none-any.whl Installing collected packages: virtualenv Successfully installed virtualenv-15.1.0
この状態でpython2.7(自前でインストールした2.7.13の方）に導入されているmoduleは
$ pip list pip (9.0.1) python-dateutil (2.6.0) virtualenv (15.1.0)
これだけ。
この状態でまずはpython2.7.13のパッケージのあるディレクトリにパスを通し、仮想環境”MISO”を作る
$ export PATH=/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages:$PATH $ virtualenv MISO New python executable in /Users/hoge/MISO/bin/python Installing setuptools, pip, wheel...done.
この状態でホームディレクトリにMISOというディレクトリができる
$ ls MISO bin lib pip-selfcheck.json include misopy
さてようやく仮想環境ができたのでその中にインストールしていく
$ MISO/bin/pip install misopy Collecting misopy Using cached misopy-0.5.3.tar.gz Collecting matplotlib (from misopy) Using cached matplotlib-2.0.2-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl Collecting numpy>=1.5.0 (from misopy) Using cached numpy-1.13.0-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl Collecting scipy>=0.9.0 (from misopy) Using cached scipy-0.19.1-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl Collecting pysam>=0.6.0 (from misopy) Using cached pysam-0.11.2.2.tar.gz Collecting python-dateutil (from matplotlib->misopy) Using cached python_dateutil-2.6.0-py2.py3-none-any.whl Collecting subprocess32 (from matplotlib->misopy) Using cached subprocess32-3.2.7.tar.gz Collecting cycler>=0.10 (from matplotlib->misopy) Using cached cycler-0.10.0-py2.py3-none-any.whl Collecting six>=1.10 (from matplotlib->misopy) Using cached six-1.10.0-py2.py3-none-any.whl Collecting pytz (from matplotlib->misopy) Using cached pytz-2017.2-py2.py3-none-any.whl Collecting functools32 (from matplotlib->misopy) Using cached functools32-3.2.3-2.zip Collecting pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=1.5.6 (from matplotlib->misopy) Using cached pyparsing-2.2.0-py2.py3-none-any.whl Building wheels for collected packages: misopy, pysam, subprocess32, functools32 Running setup.py bdist_wheel for misopy ... done Stored in directory: /Users/hoge/Library/Caches/pip/wheels/8d/7a/aa/eb0b855275e5ae17fef663067b0a06a6d3895a2ba8b7ea4077 Running setup.py bdist_wheel for pysam ... done Stored in directory: /Users/hoge/Library/Caches/pip/wheels/46/11/cc/f4a7a7048ae3f5d9e81d3bf3724aaa692fdef080ae46940092 Running setup.py bdist_wheel for subprocess32 ... done Stored in directory: /Users/hoge/Library/Caches/pip/wheels/7d/4c/a4/ce9ceb463dae01f4b95e670abd9afc8d65a45f38012f8030cc Running setup.py bdist_wheel for functools32 ... done Stored in directory: /Users/hoge/Library/Caches/pip/wheels/3c/d0/09/cd78d0ff4d6cfecfbd730782a7815a4571cd2cd4d2ed6e69d9 Successfully built misopy pysam subprocess32 functools32 Installing collected packages: six, python-dateutil, subprocess32, cycler, pytz, functools32, numpy, pyparsing, matplotlib, scipy, pysam, misopy Successfully installed cycler-0.10.0 functools32-3.2.3.post2 matplotlib-2.0.2 misopy-0.5.3 numpy-1.13.0 pyparsing-2.2.0 pysam-0.11.2.2 python-dateutil-2.6.0 pytz-2017.2 scipy-0.19.1 six-1.10.0 subprocess32-3.2.7
この操作でモジュールをインストールしても元のpythonのディレクトリにはインストールされず~/MISO以下に導入される
$ pip list --format=legacy pip (9.0.1) python-dateutil (2.6.0) virtualenv (15.1.0) $ MISO/bin/pip list --format=legacy cycler (0.10.0) functools32 (3.2.3.post2) matplotlib (2.0.2) misopy (0.5.3) numpy (1.13.0) pip (9.0.1) pyparsing (2.2.0) pysam (0.11.2.2) python-dateutil (2.6.0) pytz (2017.2) scipy (0.19.1) setuptools (36.0.1) six (1.10.0) subprocess32 (3.2.7) wheel (0.29.0)
ファイルの在処はここらしい。
ls MISO/lib/python2.7/site-packages/ _posixsubprocess.so cycler-0.10.0.dist-info cycler.py cycler.pyc dateutil easy_install.py easy_install.pyc functools32 functools32-3.2.3.post2.dist-info matplotlib matplotlib-2.0.2-py2.7-nspkg.pth matplotlib-2.0.2.dist-info misopy misopy-0.5.3.dist-info mpl_toolkits numpy numpy-1.13.0.dist-info pip pip-9.0.1.dist-info pkg_resources pylab.py pylab.pyc pyparsing-2.2.0.dist-info pyparsing.py pyparsing.pyc pysam pysam-0.11.2.2.dist-info pysplicing python_dateutil-2.6.0.dist-info pytz pytz-2017.2.dist-info scipy scipy-0.19.1.dist-info setuptools setuptools-36.0.1.dist-info six-1.10.0.dist-info six.py six.pyc subprocess32-3.2.7.dist-info subprocess32.py subprocess32.pyc wheel wheel-0.29.0.dist-info
元の場所はここだった
$ ls /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/ README python_dateutil-2.6.0.dist-info dateutil setuptools easy_install.pyo virtualenv-15.1.0.dist-info pip virtualenv.py pip-9.0.1.dist-info virtualenv.pyc pkg_resources virtualenv_support
おもむろにMISO環境に突入
$ source MISO/bin/activate (MISO) hogemac:~ hoge$
プロンプトの頭に（MISO)ってついた。
ちなみにMISO/bin/activateの中身は
# This file must be used with "source bin/activate" *from bash*
# you cannot run it directly
deactivate () {
unset -f pydoc >/dev/null 2>&1
# reset old environment variables
# ! [ -z ${VAR+_} ] returns true if VAR is declared at all
if ! [ -z "${_OLD_VIRTUAL_PATH+_}" ] ; then
PATH="$_OLD_VIRTUAL_PATH"
export PATH
unset _OLD_VIRTUAL_PATH
fi
if ! [ -z "${_OLD_VIRTUAL_PYTHONHOME+_}" ] ; then
PYTHONHOME="$_OLD_VIRTUAL_PYTHONHOME"
export PYTHONHOME
unset _OLD_VIRTUAL_PYTHONHOME
fi
# This should detect bash and zsh, which have a hash command that must
# be called to get it to forget past commands. Without forgetting
# past commands the $PATH changes we made may not be respected
if [ -n "${BASH-}" ] || [ -n "${ZSH_VERSION-}" ] ; then
hash -r 2>/dev/null
fi
if ! [ -z "${_OLD_VIRTUAL_PS1+_}" ] ; then
PS1="$_OLD_VIRTUAL_PS1"
export PS1
unset _OLD_VIRTUAL_PS1
fi
unset VIRTUAL_ENV
if [ ! "${1-}" = "nondestructive" ] ; then
# Self destruct!
unset -f deactivate
fi
}
# unset irrelevant variables
deactivate nondestructive
VIRTUAL_ENV="/Users/hoge/MISO"
export VIRTUAL_ENV
_OLD_VIRTUAL_PATH="$PATH"
PATH="$VIRTUAL_ENV/bin:$PATH"
export PATH
# unset PYTHONHOME if set
if ! [ -z "${PYTHONHOME+_}" ] ; then
_OLD_VIRTUAL_PYTHONHOME="$PYTHONHOME"
unset PYTHONHOME
fi
if [ -z "${VIRTUAL_ENV_DISABLE_PROMPT-}" ] ; then
_OLD_VIRTUAL_PS1="$PS1"
if [ "x" != x ] ; then
PS1="$PS1"
else
PS1="(`basename \"$VIRTUAL_ENV\"`) $PS1"
fi
export PS1
fi
# Make sure to unalias pydoc if it's already there
alias pydoc 2>/dev/null >/dev/null && unalias pydoc
pydoc () {
python -m pydoc "$@"
}
# This should detect bash and zsh, which have a hash command that must
# be called to get it to forget past commands. Without forgetting
# past commands the $PATH changes we made may not be respected
if [ -n "${BASH-}" ] || [ -n "${ZSH_VERSION-}" ] ; then
hash -r 2>/dev/null
fiちゃんとインストールされているだろうか？
(MISO) hogeMac:~ hoge$ miso MISO (Mixture of Isoforms model) Probabilistic analysis of RNA-Seq data for detecting differential isoforms Use --help argument to view options. Using MISO settings file: /Users/hoge/MISO/lib/python2.7/site-packages/misopy/settings/miso_settings.txt Error: Settings file /Users/hoge/MISO/lib/python2.7/site-packages/misopy/settings/miso_settings.txt does not exist.
MISO setting fileがないぞというエラーは出たが、とりあえずインストールされているらしい。
SAMtoolsのバージョンが0.xでないと動かないという噂もあるので
$ ls local/bin/samtools-0.1.19/ AUTHORS bam_reheader.c khash.h COPYING bam_rmdup.c klist.h ChangeLog.old bam_rmdupse.c knetfile.c INSTALL bam_sort.c knetfile.h Makefile bam_stat.c kprobaln.c Makefile.mingw bam_tview.c kprobaln.h NEWS bam_tview.h kseq.h bam.c bam_tview_curses.c ksort.h bam.h bam_tview_html.c kstring.c bam.h~ bamshuf.c kstring.h bam2bcf.c bamtk.c misc bam2bcf.h bcftools padding.c bam2bcf_indel.c bedcov.c phase.c bam2depth.c bedidx.c razf.c bam_aux.c bgzf.c razf.h bam_cat.c bgzf.h razip.c bam_color.c bgzip.c sam.c bam_endian.h cut_target.c sam.h bam_import.c errmod.c sam_header.c bam_index.c errmod.h sam_header.h bam_lpileup.c examples sam_view.c bam_mate.c faidx.c sample.c bam_md.c faidx.h sample.h bam_pileup.c kaln.c samtools.1 bam_plcmd.c kaln.h win32
ここに用意してみた。PATHを通すかスクリプトの該当箇所で明示的に指定してやる必要あると思う。
→別に1.4で問題ないみたい？
更にインストールがチャンとされているかのテスト
$ module_availability
Checking availability of Python modules for MISO
Looking for required Python modules..
Checking for availability of: numpy
Checking for availability of: scipy
Checking for availability of: json
Checking for availability of: matplotlib
Traceback (most recent call last):
File "/Users/hoge/MISO/bin/module_availability", line 11, in <module>
sys.exit(main())
File "/Users/hoge/MISO/lib/python2.7/site-packages/misopy/module_availability.py", line 60, in main
check_module_availability(required_modules)
File "/Users/hoge/MISO/lib/python2.7/site-packages/misopy/module_availability.py", line 22, in check_module_availability
import matplotlib.pyplot as plt
File "/Users/hoge/MISO/lib/python2.7/site-packages/matplotlib/pyplot.py", line 115, in <module>
_backend_mod, new_figure_manager, draw_if_interactive, _show = pylab_setup()
File "/Users/hoge/MISO/lib/python2.7/site-packages/matplotlib/backends/__init__.py", line 32, in pylab_setup
globals(),locals(),[backend_name],0)
File "/Users/hoge/MISO/lib/python2.7/site-packages/matplotlib/backends/backend_macosx.py", line 19, in <module>
from matplotlib.backends import _macosx
RuntimeError: Python is not installed as a framework. The Mac OS X backend will not be able to function correctly if Python is not installed as a framework. See the Python documentation for more information on installing Python as a framework on Mac OS X. Please either reinstall Python as a framework, or try one of the other backends. If you are using (Ana)Conda please install python.app and replace the use of 'python' with 'pythonw'. See 'Working with Matplotlib on OSX' in the Matplotlib FAQ for more information.https://github.com/JuliaPy/PyCall.jl/issues/218
ここの書き込みに従って
$ nano .matplotlib/matplotlibrc backend: TkAgg $ module_availability Checking availability of Python modules for MISO Looking for required Python modules.. Checking for availability of: numpy Checking for availability of: scipy Checking for availability of: json Checking for availability of: matplotlib Checking for availability of: pysam All modules are available! Looking for required executables.. Checking if samtools is available - samtools is available Checking if bedtools is available - bedtools is available
通った！なんなんだ？
最後にMISOのテスト
$ python -m unittest discover misopy
Testing gene-level Psi...
Executing: python /Users/hoge/MISO/lib/python2.7/site-packages/misopy/index_gff.py --index /Users/hoge/MISO/lib/python2.7/site-packages/misopy/gff-events/mm9/genes/Atp2b1.mm9.gff /Users/hoge/MISO/lib/python2.7/site-packages/misopy/gff-events/mm9/indexed
Indexing GFF...
- GFF: /Users/hoge/MISO/lib/python2.7/site-packages/misopy/gff-events/mm9/genes/Atp2b1.mm9.gff
- Outputting to: /Users/hoge/MISO/lib/python2.7/site-packages/misopy/gff-events/mm9/indexed
Traceback (most recent call last):
File "/Users/hoge/MISO/lib/python2.7/site-packages/misopy/index_gff.py", line 199, in <module>
main()
File "/Users/hoge/MISO/lib/python2.7/site-packages/misopy/index_gff.py", line 191, in main
compress_id=options.compress_id)
File "/Users/hoge/MISO/lib/python2.7/site-packages/misopy/index_gff.py", line 153, in index_gff
gff_genes = gene_utils.load_genes_from_gff(gff_filename)
File "/Users/hoge/MISO/lib/python2.7/site-packages/misopy/Gene.py", line 878, in load_genes_from_gff
reverse_recs=reverse_recs)
File "/Users/hoge/MISO/lib/python2.7/site-packages/misopy/gff_utils.py", line 191, in __init__
include_introns=include_introns)
File "/Users/hoge/MISO/lib/python2.7/site-packages/misopy/gff_utils.py", line 201, in from_file
FILE = open(filename, "r")
IOError: [Errno 2] No such file or directory: '/Users/hoge/MISO/lib/python2.7/site-packages/misopy/gff-events/mm9/genes/Atp2b1.mm9.gff'
Executing: python /Users/hoge/MISO/lib/python2.7/site-packages/misopy/run_events_analysis.py --compute-genes-psi /Users/hoge/MISO/lib/python2.7/site-packages/misopy/gff-events/mm9/indexed /Users/hoge/MISO/lib/python2.7/site-packages/misopy/test-output/sam-output/c2c12.Atp2b1.sorted.bam --output-dir /Users/hoge/MISO/lib/python2.7/site-packages/misopy/test-output/gene-psi-output --read-len 36 --paired-end 250 30 --use-cluster
MISO (Mixture of Isoforms model)
To run MISO, please use "miso" instead.
.Testing single-end SE event interface...
Executing: python /Users/hoge/MISO/lib/python2.7/site-packages/misopy/run_events_analysis.py --compute-events-psi se-sample /Users/hoge/MISO/lib/python2.7/site-packages/misopy/test-data/se-counts/se_test.counts --output-dir /Users/hoge/MISO/lib/python2.7/site-packages/misopy/test-output/SE-output --read-len 35 --overhang-len 4 --event-type SE --use-cluster
MISO (Mixture of Isoforms model)
To run MISO, please use "miso" instead.
.Testing fr-unstranded...
Checking read f_read against +
Checking read f_read against -
Checking read r_read against +
Checking read r_read against -
Testing fr-firststrand...
.Testing conversion of SAM to BAM...
Executing: sam_to_bam --convert /Users/hoge/MISO/lib/python2.7/site-packages/misopy/test-data/sam-data/c2c12.Atp2b1.sam /Users/hoge/MISO/lib/python2.7/site-packages/misopy/test-output/sam-output
Converting SAM to BAM...
- Executing: samtools view -Sbh /Users/hoge/MISO/lib/python2.7/site-packages/misopy/test-data/sam-data/c2c12.Atp2b1.sam > /Users/hoge/MISO/lib/python2.7/site-packages/misopy/test-output/sam-output/c2c12.Atp2b1.bam
[E::hts_open_format] fail to open file '/Users/hoge/MISO/lib/python2.7/site-packages/misopy/test-data/sam-data/c2c12.Atp2b1.sam'
samtools view: failed to open "/Users/hoge/MISO/lib/python2.7/site-packages/misopy/test-data/sam-data/c2c12.Atp2b1.sam" for reading: No such file or directory
Sorting BAM file...
- Executing: samtools sort /Users/hoge/MISO/lib/python2.7/site-packages/misopy/test-output/sam-output/c2c12.Atp2b1.bam /Users/hoge/MISO/lib/python2.7/site-packages/misopy/test-output/sam-output/c2c12.Atp2b1.sorted
[bam_sort] Use -T PREFIX / -o FILE to specify temporary and final output files
Usage: samtools sort [options...] [in.bam]
Options:
-l INT Set compression level, from 0 (uncompressed) to 9 (best)
-m INT Set maximum memory per thread; suffix K/M/G recognized [768M]
-n Sort by read name
-o FILE Write final output to FILE rather than standard output
-T PREFIX Write temporary files to PREFIX.nnnn.bam
--input-fmt-option OPT[=VAL]
Specify a single input file format option in the form
of OPTION or OPTION=VALUE
-O, --output-fmt FORMAT[,OPT[=VAL]]...
Specify output format (SAM, BAM, CRAM)
--output-fmt-option OPT[=VAL]
Specify a single output file format option in the form
of OPTION or OPTION=VALUE
--reference FILE
Reference sequence FASTA FILE [null]
-@, --threads INT
Number of additional threads to use [0]
Indexing BAM...
- Executing: samtools index /Users/hoge/MISO/lib/python2.7/site-packages/misopy/test-output/sam-output/c2c12.Atp2b1.sorted.bam
[E::hts_open_format] fail to open file '/Users/hoge/MISO/lib/python2.7/site-packages/misopy/test-output/sam-output/c2c12.Atp2b1.sorted.bam'
samtools index: failed to open "/Users/hoge/MISO/lib/python2.7/site-packages/misopy/test-output/sam-output/c2c12.Atp2b1.sorted.bam": No such file or directory
Conversion took 0.00 minutes.
FTesting gene-level Psi...
Testing GFF indexing of: /Users/hoge/MISO/lib/python2.7/site-packages/misopy/gff-events/mm9/genes/Atp2b1.mm9.gff
Executing: index_gff --index /Users/hoge/MISO/lib/python2.7/site-packages/misopy/gff-events/mm9/genes/Atp2b1.mm9.gff /Users/hoge/MISO/lib/python2.7/site-packages/misopy/gff-events/mm9/genes/Atp2b1/indexed
Indexing GFF...
- GFF: /Users/hoge/MISO/lib/python2.7/site-packages/misopy/gff-events/mm9/genes/Atp2b1.mm9.gff
- Outputting to: /Users/hoge/MISO/lib/python2.7/site-packages/misopy/gff-events/mm9/genes/Atp2b1/indexed
Traceback (most recent call last):
File "/Users/hoge/MISO/bin/index_gff", line 11, in <module>
sys.exit(main())
File "/Users/hoge/MISO/lib/python2.7/site-packages/misopy/index_gff.py", line 191, in main
compress_id=options.compress_id)
File "/Users/hoge/MISO/lib/python2.7/site-packages/misopy/index_gff.py", line 153, in index_gff
gff_genes = gene_utils.load_genes_from_gff(gff_filename)
File "/Users/hoge/MISO/lib/python2.7/site-packages/misopy/Gene.py", line 878, in load_genes_from_gff
reverse_recs=reverse_recs)
File "/Users/hoge/MISO/lib/python2.7/site-packages/misopy/gff_utils.py", line 191, in __init__
include_introns=include_introns)
File "/Users/hoge/MISO/lib/python2.7/site-packages/misopy/gff_utils.py", line 201, in from_file
FILE = open(filename, "r")
IOError: [Errno 2] No such file or directory: '/Users/hoge/MISO/lib/python2.7/site-packages/misopy/gff-events/mm9/genes/Atp2b1.mm9.gff'
Executing: miso --run /Users/hoge/MISO/lib/python2.7/site-packages/misopy/gff-events/mm9/genes/Atp2b1/indexed /Users/hoge/MISO/lib/python2.7/site-packages/misopy/test-output/sam-output/c2c12.Atp2b1.sorted.bam --output-dir /Users/hoge/MISO/lib/python2.7/site-packages/misopy/test-output/gene-psi-output --read-len 36
MISO (Mixture of Isoforms model)
Probabilistic analysis of RNA-Seq data for detecting differential isoforms
Use --help argument to view options.
Using MISO settings file: /Users/hoge/MISO/lib/python2.7/site-packages/misopy/settings/miso_settings.txt
Error: Settings file /Users/hoge/MISO/lib/python2.7/site-packages/misopy/settings/miso_settings.txt does not exist.
.
======================================================================
FAIL: test_a_sam_to_bam (misopy.test_miso.TestMISO)
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Traceback (most recent call last):
File "/Users/hoge/MISO/lib/python2.7/site-packages/misopy/test_miso.py", line 51, in test_a_sam_to_bam
"c2c12.Atp2b1.sorted.bam")))
AssertionError
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Ran 5 tests in 1.618s
FAILED (failures=1)案の定、エラーでまくる。
対処すべきポイントは以下だと思われる。
IOError: [Errno 2] No such file or directory: '/Users/hoge/MISO/lib/python2.7/site-packages/misopy/gff-events/mm9/genes/Atp2b1.mm9.gff' [E::hts_open_format] fail to open file '/Users/hoge/MISO/lib/python2.7/site-packages/misopy/test-data/sam-data/c2c12.Atp2b1.sam' [E::hts_open_format] fail to open file '/Users/hoge/MISO/lib/python2.7/site-packages/misopy/test-output/sam-output/c2c12.Atp2b1.sorted.bam' s
この辺のファイルが実際ない。pipからじゃなくてバイナリ版から該当ファイルをフォルダごとコピー。
すると
$ python -m unittest discover misopy
Testing gene-level Psi...
Executing: python /Users/hoge/MISO/lib/python2.7/site-packages/misopy/index_gff.py --index /Users/hoge/MISO/lib/python2.7/site-packages/misopy/gff-events/mm9/genes/Atp2b1.mm9.gff /Users/hoge/MISO/lib/python2.7/site-packages/misopy/gff-events/mm9/indexed
Indexing GFF...
/Users/hoge/MISO/lib/python2.7/site-packages/misopy/gff-events/mm9/genes/Atp2b1.mm9.gff appears to already be indexed. Aborting.
Executing: python /Users/hoge/MISO/lib/python2.7/site-packages/misopy/run_events_analysis.py --compute-genes-psi /Users/hoge/MISO/lib/python2.7/site-packages/misopy/gff-events/mm9/indexed /Users/hoge/MISO/lib/python2.7/site-packages/misopy/test-output/sam-output/c2c12.Atp2b1.sorted.bam --output-dir /Users/hoge/MISO/lib/python2.7/site-packages/misopy/test-output/gene-psi-output --read-len 36 --paired-end 250 30 --use-cluster
MISO (Mixture of Isoforms model)
To run MISO, please use "miso" instead.
.Testing single-end SE event interface...
Executing: python /Users/hoge/MISO/lib/python2.7/site-packages/misopy/run_events_analysis.py --compute-events-psi se-sample /Users/hoge/MISO/lib/python2.7/site-packages/misopy/test-data/se-counts/se_test.counts --output-dir /Users/hoge/MISO/lib/python2.7/site-packages/misopy/test-output/SE-output --read-len 35 --overhang-len 4 --event-type SE --use-cluster
MISO (Mixture of Isoforms model)
To run MISO, please use "miso" instead.
.Testing fr-unstranded...
Checking read f_read against +
Checking read f_read against -
Checking read r_read against +
Checking read r_read against -
Testing fr-firststrand...
.Testing conversion of SAM to BAM...
Executing: sam_to_bam --convert /Users/hoge/MISO/lib/python2.7/site-packages/misopy/test-data/sam-data/c2c12.Atp2b1.sam /Users/hoge/MISO/lib/python2.7/site-packages/misopy/test-output/sam-output
Converting SAM to BAM...
- Executing: samtools view -Sbh /Users/hoge/MISO/lib/python2.7/site-packages/misopy/test-data/sam-data/c2c12.Atp2b1.sam > /Users/hoge/MISO/lib/python2.7/site-packages/misopy/test-output/sam-output/c2c12.Atp2b1.bam
Sorting BAM file...
- Executing: samtools sort /Users/hoge/MISO/lib/python2.7/site-packages/misopy/test-output/sam-output/c2c12.Atp2b1.bam /Users/hoge/MISO/lib/python2.7/site-packages/misopy/test-output/sam-output/c2c12.Atp2b1.sorted
[bam_sort] Use -T PREFIX / -o FILE to specify temporary and final output files
Usage: samtools sort [options...] [in.bam]
Options:
-l INT Set compression level, from 0 (uncompressed) to 9 (best)
-m INT Set maximum memory per thread; suffix K/M/G recognized [768M]
-n Sort by read name
-o FILE Write final output to FILE rather than standard output
-T PREFIX Write temporary files to PREFIX.nnnn.bam
--input-fmt-option OPT[=VAL]
Specify a single input file format option in the form
of OPTION or OPTION=VALUE
-O, --output-fmt FORMAT[,OPT[=VAL]]...
Specify output format (SAM, BAM, CRAM)
--output-fmt-option OPT[=VAL]
Specify a single output file format option in the form
of OPTION or OPTION=VALUE
--reference FILE
Reference sequence FASTA FILE [null]
-@, --threads INT
Number of additional threads to use [0]
Indexing BAM...
- Executing: samtools index /Users/hoge/MISO/lib/python2.7/site-packages/misopy/test-output/sam-output/c2c12.Atp2b1.sorted.bam
Conversion took 0.00 minutes.
.Testing gene-level Psi...
Testing GFF indexing of: /Users/hoge/MISO/lib/python2.7/site-packages/misopy/gff-events/mm9/genes/Atp2b1.mm9.gff
Executing: index_gff --index /Users/hoge/MISO/lib/python2.7/site-packages/misopy/gff-events/mm9/genes/Atp2b1.mm9.gff /Users/hoge/MISO/lib/python2.7/site-packages/misopy/gff-events/mm9/genes/Atp2b1/indexed
Indexing GFF...
/Users/hoge/MISO/lib/python2.7/site-packages/misopy/gff-events/mm9/genes/Atp2b1.mm9.gff appears to already be indexed. Aborting.
Executing: miso --run /Users/hoge/MISO/lib/python2.7/site-packages/misopy/gff-events/mm9/genes/Atp2b1/indexed /Users/hoge/MISO/lib/python2.7/site-packages/misopy/test-output/sam-output/c2c12.Atp2b1.sorted.bam --output-dir /Users/hoge/MISO/lib/python2.7/site-packages/misopy/test-output/gene-psi-output --read-len 36
MISO (Mixture of Isoforms model)
Probabilistic analysis of RNA-Seq data for detecting differential isoforms
Use --help argument to view options.
Using MISO settings file: /Users/hoge/MISO/lib/python2.7/site-packages/misopy/settings/miso_settings.txt
Computing Psi values...
- GFF index: /Users/hoge/MISO/lib/python2.7/site-packages/misopy/gff-events/mm9/genes/Atp2b1/indexed
- BAM: /Users/hoge/MISO/lib/python2.7/site-packages/misopy/test-output/sam-output/c2c12.Atp2b1.sorted.bam
- Read length: 36
- Output directory: /Users/hoge/MISO/lib/python2.7/site-packages/misopy/test-output/gene-psi-output
Checking your GFF annotation and BAM for mismatches...
Checking if BAM has mixed read lengths...
Found reads of length 36 in BAM.
Mapping genes to their indexed GFF representation, using /Users/hoge/MISO/lib/python2.7/site-packages/misopy/gff-events/mm9/genes/Atp2b1/indexed
Searching for /Users/hoge/MISO/lib/python2.7/site-packages/misopy/gff-events/mm9/genes/Atp2b1/indexed/genes_to_filenames.shelve..
- Found shelved file.
Preparing to run 1 batches of jobs...
Running batch of 1 genes..
- Executing: python /Users/hoge/MISO/lib/python2.7/site-packages/misopy/run_miso.py --compute-genes-from-file "/Users/hoge/MISO/lib/python2.7/site-packages/misopy/test-output/gene-psi-output/batch-genes/batch-0_genes.txt" /Users/hoge/MISO/lib/python2.7/site-packages/misopy/test-output/sam-output/c2c12.Atp2b1.sorted.bam /Users/hoge/MISO/lib/python2.7/site-packages/misopy/test-output/gene-psi-output --read-len 36 --overhang-len 1 --settings-filename /Users/hoge/MISO/lib/python2.7/site-packages/misopy/settings/miso_settings.txt
- Submitted thread batch-0
Waiting on 1 threads...
.
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Ran 5 tests in 10.041s
OKと、テスト解析は無事走りきるようになった。
次、実際の公開データで試してみるが、その前にヒトゲノムのGFFファイルを準備しないといけないはず。
