[med-svn] [Git][med-team/python-misopy][upstream] New upstream version 0.5.4+dfsg
Andreas Tille
gitlab at salsa.debian.org
Tue Oct 30 06:46:09 GMT 2018
Andreas Tille pushed to branch upstream at Debian Med / python-misopy
Commits:
a7cdbd7f by Andreas Tille at 2018-10-30T06:29:06Z
New upstream version 0.5.4+dfsg
- - - - -
16 changed files:
- + MANIFEST.in
- PKG-INFO
- + 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/__init__.py
- misopy/credible_intervals.py
- misopy/run_events_analysis.py
- misopy/samples_utils.py
- pysplicing/src/miso.c
- + setup.cfg
- setup.py
Changes:
=====================================
MANIFEST.in
=====================================
@@ -0,0 +1,16 @@
+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
=====================================
@@ -1,6 +1,6 @@
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
=====================================
misopy.egg-info/PKG-INFO
=====================================
@@ -0,0 +1,21 @@
+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 at 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
=====================================
@@ -0,0 +1,387 @@
+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:- at chr17:45815912:45815950:- at chr17:45814875:45814965:-.miso
+misopy/sashimi_plot/test-data/miso-data/heartKOb/chr17/chr17:45816186:45816265:- at chr17:45815912:45815950:- at chr17:45814875:45814965:-.miso
+misopy/sashimi_plot/test-data/miso-data/heartWT1/chr17/chr17:45816186:45816265:- at chr17:45815912:45815950:- at chr17:45814875:45814965:-.miso
+misopy/sashimi_plot/test-data/miso-data/heartWT2/chr17/chr17:45816186:45816265:- at chr17:45815912:45815950:- at 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
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+pysplicing/pysplicing/__init__.py
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+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
=====================================
@@ -0,0 +1 @@
+
=====================================
misopy.egg-info/entry_points.txt
=====================================
@@ -0,0 +1,18 @@
+[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
=====================================
@@ -0,0 +1 @@
+{"is_release": false, "git_version": "b644df6"}
\ No newline at end of file
=====================================
misopy.egg-info/requires.txt
=====================================
@@ -0,0 +1,4 @@
+matplotlib
+numpy >= 1.5.0
+scipy >= 0.9.0
+pysam >= 0.6.0
=====================================
misopy.egg-info/top_level.txt
=====================================
@@ -0,0 +1,2 @@
+misopy
+pysplicing
=====================================
misopy/__init__.py
=====================================
@@ -1 +1 @@
-__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
=====================================
@@ -0,0 +1,5 @@
+[egg_info]
+tag_build =
+tag_date = 0
+tag_svn_revision = 0
+
=====================================
setup.py
=====================================
@@ -1,4 +1,4 @@
-from distutils.core import setup, Extension
+from setuptools import setup, Extension
import distutils.ccompiler
import glob
import os
@@ -74,7 +74,7 @@ for scheme in INSTALL_SCHEMES.values():
## Definition of the current version. This is defined here
## and then gets written to __init__.py in misopy.
##
-MISO_VERSION = "0.5.3"
+MISO_VERSION = "0.5.4"
##
## Generate a __version__.py attribute
View it on GitLab: https://salsa.debian.org/med-team/python-misopy/commit/a7cdbd7f99b285512161da0606ad2ca6fdc23820
--
View it on GitLab: https://salsa.debian.org/med-team/python-misopy/commit/a7cdbd7f99b285512161da0606ad2ca6fdc23820
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