MANIFEST.in

+include pysplicing/include/*
+include pysplicing/src/f2c/*
+include pysplicing/src/lapack/*
+include misopy/settings/*
+include misopy/sashimi_plot/settings/*
+include misopy/sashimi_plot/test-data/*
+include misopy/sashimi_plot/test-data/bam-data/*
+include misopy/sashimi_plot/test-data/miso-data/*
+include misopy/sashimi_plot/test-data/miso-data/heartKOa/chr17/*
+include misopy/sashimi_plot/test-data/miso-data/heartKOb/chr17/*
+include misopy/sashimi_plot/test-data/miso-data/heartWT1/chr17/*
+include misopy/sashimi_plot/test-data/miso-data/heartWT2/chr17/*
+include misopy/gff-events/mm9/*
+include misopy/gff-events/mm9/genes/*
+include misopy/test-data/sam-data/*
+include misopy/test-data/se-counts/*
\ No newline at end of file

PKG-INFO

 Metadata-Version: 1.1
 Name: misopy
-Version: 0.5.3
+Version: 0.5.4
 Summary: Mixture of Isoforms model (MISO) for isoform quantitation using RNA-Seq
 Home-page: http://genes.mit.edu/burgelab/miso/
 Author: Yarden Katz

debian/changelog

-python-misopy (0.5.3+dfsg-1) UNRELEASED; urgency=low
+python-misopy (0.5.4+dfsg-1) UNRELEASED; urgency=low
 
   * Initial release (Closes: #nnnn)
   * Not using internal f2c redistribution.
 
- -- Andreas Tille <tille@debian.org>  Sat, 13 Aug 2016 08:37:34 +0200
+ -- Andreas Tille <tille@debian.org>  Tue, 30 Oct 2018 07:34:46 +0100

debian/compat

-9
+11

debian/control

@@ -4,7 +4,7 @@ Uploaders: Steffen Moeller <moeller@debian.org>,
            Andreas Tille <tille@debian.org>
 Section: python
 Priority: optional
-Build-Depends: debhelper (>= 9~),
+Build-Depends: debhelper (>= 11~),
                dh-python,
                python-all-dev,
                python3-all-dev,
@@ -15,13 +15,13 @@ Build-Depends: debhelper (>= 9~),
                python3-pysam,
                python3-scipy,
                python3-matplotlib,
+               python3-setuptools,
                samtools,
                libf2c2-dev
-Standards-Version: 3.9.8
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/python-misopy.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/python-misopy.git
+Standards-Version: 4.2.1
+Vcs-Browser: https://salsa.debian.org/med-team/python-misopy
+Vcs-Git: https://salsa.debian.org/med-team/python-misopy.git
 Homepage: http://genes.mit.edu/burgelab/miso/
-X-Python-Version: >= 2.6
 
 Package: python-misopy
 Architecture: any

debian/copyright

-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: miso
 Source: https://pypi.python.org/pypi/misopy
 Files-Excluded: pysplicing/src/f2c

debian/rules

@@ -7,6 +7,7 @@ export PYBUILD_NAME=misopy
 	dh $@ --with python2,python3 --buildsystem=pybuild
 
 override_dh_auto_test:
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
 	PATH=$(CURDIR)/debian/bin:$${PATH} \
 	PYBUILD_SYSTEM=custom \
 	PYBUILD_TEST_ARGS="\
@@ -18,6 +19,7 @@ override_dh_auto_test:
 		cd {build_dir} && \
 		PYTHONPATH={build_dir} python -m unittest discover -v" \
 	dh_auto_test --buildsystem=pybuild || true
+endif
 
 override_dh_auto_install:
 	dh_auto_install
@@ -27,5 +29,3 @@ override_dh_clean:
 	rm -rf tmp a.out
 	dh_clean
 
-get-orig-source:
-	uscan --verbose --force-download --repack --compression xz

misopy.egg-info/PKG-INFO

+Metadata-Version: 1.1
+Name: misopy
+Version: 0.5.4
+Summary: Mixture of Isoforms model (MISO) for isoform quantitation using RNA-Seq
+Home-page: http://genes.mit.edu/burgelab/miso/
+Author: Yarden Katz
+Author-email: yarden@mit.edu
+License: UNKNOWN
+Description: MISO (Mixture of Isoforms) is a probabilistic framework that quantitates the expression level of alternatively spliced genes from RNA-Seq data, and identifies differentially regulated isoforms or exons across samples. By modeling the generative process by which reads are produced from isoforms in RNA-Seq, the MISO model uses Bayesian inference to compute the probability that a read originated from a particular isoform.
+        
+        MISO uses the inferred assignment of reads to isoforms to quantitate the abundances of the underlying set of alternative mRNA isoforms. Confidence intervals over estimates can be obtained, which quantify the reliability of the estimates. 
+        
+        Please see http://genes.mit.edu/burgelab/miso/docs/ for MISO manual and documentation.
+        
+Keywords: bioinformatics,sequence analysis,alternative splicing,RNA-Seq,probabilistic models,bayesian
+Platform: ALL
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: C
+Classifier: Programming Language :: Python
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics

misopy.egg-info/SOURCES.txt

+MANIFEST.in
+README
+setup.py
+misopy/Gene.py
+misopy/__init__.py
+misopy/as_events.py
+misopy/cluster_utils.py
+misopy/compare_miso.py
+misopy/credible_intervals.py
+misopy/exon_utils.py
+misopy/filter_events.py
+misopy/gff_utils.py
+misopy/hypothesis_test.py
+misopy/index_gff.py
+misopy/json_utils.py
+misopy/kde_subclass.py
+misopy/legacy_test_pysplicing.py
+misopy/misc_utils.py
+misopy/miso.py
+misopy/miso_db.py
+misopy/miso_pack.py
+misopy/miso_sampler.py
+misopy/miso_utils.py
+misopy/miso_zip.py
+misopy/module_availability.py
+misopy/parse_csv.py
+misopy/parse_gene.py
+misopy/pe_utils.py
+misopy/pickle_utils.py
+misopy/py2c_gene.py
+misopy/read_simulator.py
+misopy/reads_utils.py
+misopy/run_events_analysis.py
+misopy/run_miso.py
+misopy/sam_rpkm.py
+misopy/sam_to_bam.py
+misopy/sam_utils.py
+misopy/samples_utils.py
+misopy/settings.py
+misopy/summarize_miso.py
+misopy/test_cluster.py
+misopy/test_miso.py
+misopy.egg-info/PKG-INFO
+misopy.egg-info/SOURCES.txt
+misopy.egg-info/dependency_links.txt
+misopy.egg-info/entry_points.txt
+misopy.egg-info/pbr.json
+misopy.egg-info/requires.txt
+misopy.egg-info/top_level.txt
+misopy/gff-events/mm9/SE.mm9.gff
+misopy/gff-events/mm9/genes/Atp2b1.mm9.gff
+misopy/sashimi_plot/Sashimi.py
+misopy/sashimi_plot/__init__.py
+misopy/sashimi_plot/plot.py
+misopy/sashimi_plot/sashimi_plot.py
+misopy/sashimi_plot/plot_utils/__init__.py
+misopy/sashimi_plot/plot_utils/plot_gene.py
+misopy/sashimi_plot/plot_utils/plot_settings.py
+misopy/sashimi_plot/plot_utils/plotting.py
+misopy/sashimi_plot/plot_utils/samples_plotter.py
+misopy/sashimi_plot/settings/sashimi_plot_settings.txt
+misopy/sashimi_plot/test-data/events.gff
+misopy/sashimi_plot/test-data/bam-data/heartKOa.bam.bai
+misopy/sashimi_plot/test-data/bam-data/heartKOa.sorted.bam
+misopy/sashimi_plot/test-data/bam-data/heartKOa.sorted.bam.bai
+misopy/sashimi_plot/test-data/bam-data/heartKOb.sorted.bam
+misopy/sashimi_plot/test-data/bam-data/heartKOb.sorted.bam.bai
+misopy/sashimi_plot/test-data/bam-data/heartWT1.sorted.bam
+misopy/sashimi_plot/test-data/bam-data/heartWT1.sorted.bam.bai
+misopy/sashimi_plot/test-data/bam-data/heartWT2.sorted.bam
+misopy/sashimi_plot/test-data/bam-data/heartWT2.sorted.bam.bai
+misopy/sashimi_plot/test-data/miso-data/heartKOa/chr17/chr17:45816186:45816265:-@chr17:45815912:45815950:-@chr17:45814875:45814965:-.miso
+misopy/sashimi_plot/test-data/miso-data/heartKOb/chr17/chr17:45816186:45816265:-@chr17:45815912:45815950:-@chr17:45814875:45814965:-.miso
+misopy/sashimi_plot/test-data/miso-data/heartWT1/chr17/chr17:45816186:45816265:-@chr17:45815912:45815950:-@chr17:45814875:45814965:-.miso
+misopy/sashimi_plot/test-data/miso-data/heartWT2/chr17/chr17:45816186:45816265:-@chr17:45815912:45815950:-@chr17:45814875:45814965:-.miso
+misopy/settings/miso_settings.txt
+misopy/test-data/sam-data/c2c12.Atp2b1.sam
+pysplicing/include/f2c.h
+pysplicing/include/matrix.pmt
+pysplicing/include/pyerror.h
+pysplicing/include/pysplicing.h
+pysplicing/include/random.h
+pysplicing/include/splicing.h
+pysplicing/include/splicing_error.h
+pysplicing/include/splicing_lapack.h
+pysplicing/include/splicing_matrix.h
+pysplicing/include/splicing_matrix_pmt.h
+pysplicing/include/splicing_memory.h
+pysplicing/include/splicing_pmt.h
+pysplicing/include/splicing_pmt_off.h
+pysplicing/include/splicing_random.h
+pysplicing/include/splicing_vector.h
+pysplicing/include/splicing_vector_pmt.h
+pysplicing/include/vector.pmt
+pysplicing/pysplicing/__init__.py
+pysplicing/src/assignment.c
+pysplicing/src/blas.c
+pysplicing/src/complexity.c
+pysplicing/src/convert.c
+pysplicing/src/error.c
+pysplicing/src/fortran_stuff.c
+pysplicing/src/gff.c
+pysplicing/src/ident.c
+pysplicing/src/lapack.c
+pysplicing/src/lawson_hanson_nnls.c
+pysplicing/src/matrix.c
+pysplicing/src/memory.c
+pysplicing/src/miso.c
+pysplicing/src/miso_paired.c
+pysplicing/src/nnls.c
+pysplicing/src/pyconvert.c
+pysplicing/src/pyerror.c
+pysplicing/src/pyrandom.c
+pysplicing/src/pysplicing.c
+pysplicing/src/qsort.c
+pysplicing/src/qsort_r.c
+pysplicing/src/random.c
+pysplicing/src/simulator.c
+pysplicing/src/solve.c
+pysplicing/src/strvector.c
+pysplicing/src/util.c
+pysplicing/src/vector.c
+pysplicing/src/f2c/Notice
+pysplicing/src/f2c/README
+pysplicing/src/f2c/abort_.c
+pysplicing/src/f2c/arith.h
+pysplicing/src/f2c/backspac.c
+pysplicing/src/f2c/c_abs.c
+pysplicing/src/f2c/c_cos.c
+pysplicing/src/f2c/c_div.c
+pysplicing/src/f2c/c_exp.c
+pysplicing/src/f2c/c_log.c
+pysplicing/src/f2c/c_sin.c
+pysplicing/src/f2c/c_sqrt.c
+pysplicing/src/f2c/cabs.c
+pysplicing/src/f2c/changes
+pysplicing/src/f2c/close.c
+pysplicing/src/f2c/comptry.bat
+pysplicing/src/f2c/ctype.c
+pysplicing/src/f2c/d_abs.c
+pysplicing/src/f2c/d_acos.c
+pysplicing/src/f2c/d_asin.c
+pysplicing/src/f2c/d_atan.c
+pysplicing/src/f2c/d_atn2.c
+pysplicing/src/f2c/d_cnjg.c
+pysplicing/src/f2c/d_cos.c
+pysplicing/src/f2c/d_cosh.c
+pysplicing/src/f2c/d_dim.c
+pysplicing/src/f2c/d_exp.c
+pysplicing/src/f2c/d_imag.c
+pysplicing/src/f2c/d_int.c
+pysplicing/src/f2c/d_lg10.c
+pysplicing/src/f2c/d_log.c
+pysplicing/src/f2c/d_mod.c
+pysplicing/src/f2c/d_nint.c
+pysplicing/src/f2c/d_prod.c
+pysplicing/src/f2c/d_sin.c
+pysplicing/src/f2c/d_sinh.c
+pysplicing/src/f2c/d_sqrt.c
+pysplicing/src/f2c/d_tan.c
+pysplicing/src/f2c/d_tanh.c
+pysplicing/src/f2c/derf_.c
+pysplicing/src/f2c/derfc_.c
+pysplicing/src/f2c/dfe.c
+pysplicing/src/f2c/dolio.c
+pysplicing/src/f2c/dtime_.c
+pysplicing/src/f2c/due.c
+pysplicing/src/f2c/dummy.c
+pysplicing/src/f2c/ef1asc_.c
+pysplicing/src/f2c/ef1cmc_.c
+pysplicing/src/f2c/endfile.c
+pysplicing/src/f2c/erf_.c
+pysplicing/src/f2c/erfc_.c
+pysplicing/src/f2c/err.c
+pysplicing/src/f2c/etime_.c
+pysplicing/src/f2c/exit_.c
+pysplicing/src/f2c/f2c.h
+pysplicing/src/f2c/f2c.h0
+pysplicing/src/f2c/f2ch.add
+pysplicing/src/f2c/f77_aloc.c
+pysplicing/src/f2c/f77vers.c
+pysplicing/src/f2c/fctype.h
+pysplicing/src/f2c/fio.h
+pysplicing/src/f2c/fmt.c
+pysplicing/src/f2c/fmt.h
+pysplicing/src/f2c/fmtlib.c
+pysplicing/src/f2c/fp.h
+pysplicing/src/f2c/ftell_.c
+pysplicing/src/f2c/getarg_.c
+pysplicing/src/f2c/getenv_.c
+pysplicing/src/f2c/h_abs.c
+pysplicing/src/f2c/h_dim.c
+pysplicing/src/f2c/h_dnnt.c
+pysplicing/src/f2c/h_indx.c
+pysplicing/src/f2c/h_len.c
+pysplicing/src/f2c/h_mod.c
+pysplicing/src/f2c/h_nint.c
+pysplicing/src/f2c/h_sign.c
+pysplicing/src/f2c/hl_ge.c
+pysplicing/src/f2c/hl_gt.c
+pysplicing/src/f2c/hl_le.c
+pysplicing/src/f2c/hl_lt.c
+pysplicing/src/f2c/i77vers.c
+pysplicing/src/f2c/i_abs.c
+pysplicing/src/f2c/i_dim.c
+pysplicing/src/f2c/i_dnnt.c
+pysplicing/src/f2c/i_indx.c
+pysplicing/src/f2c/i_len.c
+pysplicing/src/f2c/i_mod.c
+pysplicing/src/f2c/i_nint.c
+pysplicing/src/f2c/i_sign.c
+pysplicing/src/f2c/iargc_.c
+pysplicing/src/f2c/iio.c
+pysplicing/src/f2c/ilnw.c
+pysplicing/src/f2c/inquire.c
+pysplicing/src/f2c/l_ge.c
+pysplicing/src/f2c/l_gt.c
+pysplicing/src/f2c/l_le.c
+pysplicing/src/f2c/l_lt.c
+pysplicing/src/f2c/lbitbits.c
+pysplicing/src/f2c/lbitshft.c
+pysplicing/src/f2c/libf2c.lbc
+pysplicing/src/f2c/libf2c.sy
+pysplicing/src/f2c/lio.h
+pysplicing/src/f2c/lread.c
+pysplicing/src/f2c/lwrite.c
+pysplicing/src/f2c/main.c
+pysplicing/src/f2c/makefile.sy
+pysplicing/src/f2c/makefile.u
+pysplicing/src/f2c/makefile.vc
+pysplicing/src/f2c/makefile.wat
+pysplicing/src/f2c/math.hvc
+pysplicing/src/f2c/mkfile.plan9
+pysplicing/src/f2c/open.c
+pysplicing/src/f2c/pow_ci.c
+pysplicing/src/f2c/pow_dd.c
+pysplicing/src/f2c/pow_di.c
+pysplicing/src/f2c/pow_hh.c
+pysplicing/src/f2c/pow_ii.c
+pysplicing/src/f2c/pow_ri.c
+pysplicing/src/f2c/pow_zi.c
+pysplicing/src/f2c/pow_zz.c
+pysplicing/src/f2c/r_abs.c
+pysplicing/src/f2c/r_acos.c
+pysplicing/src/f2c/r_asin.c
+pysplicing/src/f2c/r_atan.c
+pysplicing/src/f2c/r_atn2.c
+pysplicing/src/f2c/r_cnjg.c
+pysplicing/src/f2c/r_cos.c
+pysplicing/src/f2c/r_cosh.c
+pysplicing/src/f2c/r_dim.c
+pysplicing/src/f2c/r_exp.c
+pysplicing/src/f2c/r_imag.c
+pysplicing/src/f2c/r_int.c
+pysplicing/src/f2c/r_lg10.c
+pysplicing/src/f2c/r_log.c
+pysplicing/src/f2c/r_mod.c
+pysplicing/src/f2c/r_nint.c
+pysplicing/src/f2c/r_sign.c
+pysplicing/src/f2c/r_sin.c
+pysplicing/src/f2c/r_sinh.c
+pysplicing/src/f2c/r_sqrt.c
+pysplicing/src/f2c/r_tan.c
+pysplicing/src/f2c/r_tanh.c
+pysplicing/src/f2c/rawio.h
+pysplicing/src/f2c/rdfmt.c
+pysplicing/src/f2c/rewind.c
+pysplicing/src/f2c/rsfe.c
+pysplicing/src/f2c/rsli.c
+pysplicing/src/f2c/rsne.c
+pysplicing/src/f2c/s_cat.c
+pysplicing/src/f2c/s_cmp.c
+pysplicing/src/f2c/s_copy.c
+pysplicing/src/f2c/s_paus.c
+pysplicing/src/f2c/s_rnge.c
+pysplicing/src/f2c/s_stop.c
+pysplicing/src/f2c/scomptry.bat
+pysplicing/src/f2c/sfe.c
+pysplicing/src/f2c/sig_die.c
+pysplicing/src/f2c/signal1.h
+pysplicing/src/f2c/signal1.h0
+pysplicing/src/f2c/signal_.c
+pysplicing/src/f2c/signbit.c
+pysplicing/src/f2c/sue.c
+pysplicing/src/f2c/sysdep1.h
+pysplicing/src/f2c/sysdep1.h0
+pysplicing/src/f2c/system_.c
+pysplicing/src/f2c/typesize.c
+pysplicing/src/f2c/uio.c
+pysplicing/src/f2c/uninit.c
+pysplicing/src/f2c/util.c
+pysplicing/src/f2c/wref.c
+pysplicing/src/f2c/wrtfmt.c
+pysplicing/src/f2c/wsfe.c
+pysplicing/src/f2c/wsle.c
+pysplicing/src/f2c/wsne.c
+pysplicing/src/f2c/xsum0.out
+pysplicing/src/f2c/xwsne.c
+pysplicing/src/f2c/z_abs.c
+pysplicing/src/f2c/z_cos.c
+pysplicing/src/f2c/z_div.c
+pysplicing/src/f2c/z_exp.c
+pysplicing/src/f2c/z_log.c
+pysplicing/src/f2c/z_sin.c
+pysplicing/src/f2c/z_sqrt.c
+pysplicing/src/lapack/blas.inc
+pysplicing/src/lapack/dbdsdc.c
+pysplicing/src/lapack/dbdsqr.c
+pysplicing/src/lapack/dcopy.c
+pysplicing/src/lapack/ddot.c
+pysplicing/src/lapack/debug.h
+pysplicing/src/lapack/dgebd2.c
+pysplicing/src/lapack/dgebrd.c
+pysplicing/src/lapack/dgelq2.c
+pysplicing/src/lapack/dgelqf.c
+pysplicing/src/lapack/dgemm.c
+pysplicing/src/lapack/dgemv.c
+pysplicing/src/lapack/dgeqr2.c
+pysplicing/src/lapack/dgeqrf.c
+pysplicing/src/lapack/dger.c
+pysplicing/src/lapack/dgesdd.c
+pysplicing/src/lapack/disnan.c
+pysplicing/src/lapack/dlabrd.c
+pysplicing/src/lapack/dlacpy.c
+pysplicing/src/lapack/dlaed6.c
+pysplicing/src/lapack/dlaisnan.c
+pysplicing/src/lapack/dlamch.c
+pysplicing/src/lapack/dlamrg.c
+pysplicing/src/lapack/dlange.c
+pysplicing/src/lapack/dlanst.c
+pysplicing/src/lapack/dlapy2.c
+pysplicing/src/lapack/dlarf.c
+pysplicing/src/lapack/dlarfb.c
+pysplicing/src/lapack/dlarfg.c
+pysplicing/src/lapack/dlarft.c
+pysplicing/src/lapack/dlartg.c
+pysplicing/src/lapack/dlas2.c
+pysplicing/src/lapack/dlascl.c
+pysplicing/src/lapack/dlasd0.c
+pysplicing/src/lapack/dlasd1.c
+pysplicing/src/lapack/dlasd2.c
+pysplicing/src/lapack/dlasd3.c
+pysplicing/src/lapack/dlasd4.c
+pysplicing/src/lapack/dlasd5.c
+pysplicing/src/lapack/dlasd6.c
+pysplicing/src/lapack/dlasd7.c
+pysplicing/src/lapack/dlasd8.c
+pysplicing/src/lapack/dlasda.c
+pysplicing/src/lapack/dlasdq.c
+pysplicing/src/lapack/dlasdt.c
+pysplicing/src/lapack/dlaset.c
+pysplicing/src/lapack/dlasq1.c
+pysplicing/src/lapack/dlasq2.c
+pysplicing/src/lapack/dlasq3.c
+pysplicing/src/lapack/dlasq4.c
+pysplicing/src/lapack/dlasq5.c
+pysplicing/src/lapack/dlasq6.c
+pysplicing/src/lapack/dlasr.c
+pysplicing/src/lapack/dlasrt.c
+pysplicing/src/lapack/dlassq.c
+pysplicing/src/lapack/dlasv2.c
+pysplicing/src/lapack/dnrm2.c
+pysplicing/src/lapack/dorg2r.c
+pysplicing/src/lapack/dorgbr.c
+pysplicing/src/lapack/dorgl2.c
+pysplicing/src/lapack/dorglq.c
+pysplicing/src/lapack/dorgqr.c
+pysplicing/src/lapack/dorm2r.c
+pysplicing/src/lapack/dormbr.c
+pysplicing/src/lapack/dorml2.c
+pysplicing/src/lapack/dormlq.c
+pysplicing/src/lapack/dormqr.c
+pysplicing/src/lapack/drot.c
+pysplicing/src/lapack/dscal.c
+pysplicing/src/lapack/dswap.c
+pysplicing/src/lapack/dtrmm.c
+pysplicing/src/lapack/dtrmv.c
+pysplicing/src/lapack/ieeeck.c
+pysplicing/src/lapack/iladlc.c
+pysplicing/src/lapack/iladlr.c
+pysplicing/src/lapack/ilaenv.c
+pysplicing/src/lapack/iparmq.c
+pysplicing/src/lapack/lapack.inc
+pysplicing/src/lapack/len_trim.c
+pysplicing/src/lapack/lsame.c
+pysplicing/src/lapack/stat.h
+pysplicing/src/lapack/xerbla.c
\ No newline at end of file

misopy.egg-info/dependency_links.txt

+

misopy.egg-info/entry_points.txt

+[console_scripts]
+compare_miso = misopy.compare_miso:main
+exon_utils = misopy.exon_utils:main
+filter_events = misopy.filter_events:main
+index_gff = misopy.index_gff:main
+miso = misopy.miso:main
+miso_pack = misopy.miso_pack:main
+miso_zip = misopy.miso_zip:main
+module_availability = misopy.module_availability:main
+pe_utils = misopy.pe_utils:main
+plot.py = misopy.sashimi_plot.plot:main
+run_events_analysis.py = misopy.run_events_analysis:main
+run_miso.py = misopy.run_miso:main
+sam_to_bam = misopy.sam_to_bam:main
+sashimi_plot = misopy.sashimi_plot.sashimi_plot:main
+summarize_miso = misopy.summarize_miso:main
+test_miso = misopy.test_miso:main
+

misopy.egg-info/pbr.json

+{"is_release": false, "git_version": "b644df6"}
\ No newline at end of file

misopy.egg-info/requires.txt

+matplotlib
+numpy >= 1.5.0
+scipy >= 0.9.0
+pysam >= 0.6.0

misopy.egg-info/top_level.txt

+misopy
+pysplicing

misopy/__init__.py

-__version__ = "0.5.3"
+__version__ = "0.5.4"

misopy/credible_intervals.py

@@ -43,10 +43,10 @@ def compute_credible_intervals(samples, confidence_level=.95):
     # compute the lower bound of the interval
     # the lower bound is the (alpha/2)*n-th smallest sample, where n is the
     # number of samples
-    lower_bound_indx = round((alpha/2)*num_samples) - 1
+    lower_bound_indx = int(round((alpha/2)*num_samples)) - 1
     # the upper bound is the (1-alpha/2)*n nth smallest sample, where n is
     # the number of samples
-    upper_bound_indx = round((1-alpha/2)*num_samples) - 1
+    upper_bound_indx = int(round((1-alpha/2)*num_samples)) - 1
     assert(lower_bound_indx > 0)
     assert(upper_bound_indx > 0)
     # sort samples along first axis

misopy/run_events_analysis.py

@@ -168,11 +168,11 @@ def check_gff_and_bam(gff_dir, bam_filename, main_logger,
     if bam_starts_with_chr != gff_starts_with_chr:
         mismatch_found = True
     if mismatch_found:
-        miso_logger.warning("It looks like your GFF annotation file and your BAM " \
+        main_logger.warning("It looks like your GFF annotation file and your BAM " \
                             "file might not have matching headers (chromosome names.) " \
                             "If this is the case, your run will fail as no reads from " \
                             "the BAM could be matched up with your annotation.")
-        miso_logger.warning("Please see:\n\t%s\n for more information." %(manual_url))
+        main_logger.warning("Please see:\n\t%s\n for more information." %(manual_url))
         # Default: assume BAM starts with chr headers
         chr_containing = "BAM file (%s)" %(bam_filename)
         not_chr_containing = "GFF annotation (%s)" %(gff_dir)
@@ -180,16 +180,16 @@ def check_gff_and_bam(gff_dir, bam_filename, main_logger,
             # BAM does not start with chr, GFF does
             chr_containing, not_chr_containing = \
                 not_chr_containing, chr_containing
-        miso_logger.warning("It looks like your %s contains \'chr\' chromosomes (UCSC-style) " \
+        main_logger.warning("It looks like your %s contains \'chr\' chromosomes (UCSC-style) " \
                             "while your %s does not." %(chr_containing,
                                                         not_chr_containing))
-        miso_logger.warning("The first few BAM chromosomes were: %s" \
+        main_logger.warning("The first few BAM chromosomes were: %s" \
                             %(",".join(bam_chroms.keys())))
         print "BAM references: "
         print bam_file.references
-        miso_logger.warning("The first few GFF chromosomes were: %s" \
+        main_logger.warning("The first few GFF chromosomes were: %s" \
                             %(",".join(gff_chroms.keys())))
-        miso_logger.warning("Run is likely to fail or produce empty output. Proceeding " \
+        main_logger.warning("Run is likely to fail or produce empty output. Proceeding " \
                             "anyway...")
         time.sleep(15)
 

misopy/samples_utils.py

@@ -303,7 +303,7 @@ def summarize_sampler_results(samples_dir, summary_filename,
         counts_info = samples_results[5]
         shape_len = len(shape(samples))
         if shape_len < 2:
-            print "WARNING: Skipping %s -- mishaped file" %(samples_filename)
+            print "WARNING: Skipping %s -- mishaped file" %(event_name)
             continue
         num_samples, num_isoforms = shape(samples)
         output_fields = format_credible_intervals(event_name, samples)

pysplicing/src/miso.c

@@ -365,7 +365,6 @@ int splicing_drift_proposal_init(int noiso, int noChains,
 	MATRIX(*respsi, 0, j) = RNG_UNIF01();
 	MATRIX(*respsi, 1, j) = 1 - MATRIX(*respsi, j, 0);
 	MATRIX(*resalpha, 0, j) = 0.0;
-	MATRIX(*resalpha, 1, j) = 0.0;
       }
       *ressigma = SIGMA;
     }

setup.cfg

+[egg_info]
+tag_build = 
+tag_date = 0
+tag_svn_revision = 0
+