[med-svn] [poretools] branch upstream updated (b6b68bf -> 6e8fab5)
Afif Elghraoui
afif at moszumanska.debian.org
Mon Sep 5 00:32:20 UTC 2016
This is an automated email from the git hooks/post-receive script.
afif pushed a change to branch upstream
in repository poretools.
from b6b68bf Imported Upstream version 0.5.1
new 6e8fab5 Imported Upstream version 0.6.0+dfsg
The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
.gitignore | 4 +
Dockerfile | 40 --
MANIFEST.in | 2 +-
README.md | 23 +-
appveyor.yml | 145 ++++++
appveyor/install.ps1 | 229 ++++++++++
appveyor/run_with_env.cmd | 88 ++++
dist/poretools-0.3.0.win-amd64.exe | Bin 284988 -> 0 bytes
dist/poretools-0.3.1.win-amd64.exe | Bin 285930 -> 0 bytes
dist/poretools-0.5.0.win-amd64.exe | Bin 288186 -> 0 bytes
dist/poretools.reg | 8 -
docs/conf.py | 2 +-
docs/content/_images/qualpos.png | Bin 0 -> 24494 bytes
docs/content/examples.rst | 193 +++++---
docs/content/history.rst | 11 +
docs/content/installation.rst | 83 +---
docs/index.rst | 8 +-
docs/requirements.txt | 1 +
poretools/Event.py | 70 ++-
poretools/Fast5File.py | 287 +++++++++++-
poretools/Fast5File_pytables.py | 504 ---------------------
poretools/events.py | 16 +-
poretools/fasta.py | 8 +-
poretools/fastq.py | 23 +-
poretools/formats.py | 14 +
poretools/hist.py | 93 ++--
poretools/index.py | 66 +++
poretools/metadata.py | 22 +
poretools/occupancy.py | 229 +++-------
poretools/organise.py | 39 ++
poretools/poretools_main.py | 174 ++++++-
poretools/qual_v_pos.py | 66 +++
poretools/squiggle.py | 154 +++----
poretools/times.py | 2 +-
poretools/version.py | 2 +-
poretools/windows.py | 19 -
poretools/yield_plot.py | 200 ++++----
requirements.txt | 6 +-
setup.py | 61 +--
.../2016_3_4_3507_1_ch120_read240_strand.fast5 | Bin 0 -> 1570393 bytes
.../2016_3_4_3507_1_ch120_read353_strand.fast5 | Bin 0 -> 1238287 bytes
.../2016_3_4_3507_1_ch120_read415_strand.fast5 | Bin 0 -> 1128165 bytes
.../2016_3_4_3507_1_ch120_read418_strand.fast5 | Bin 0 -> 1289709 bytes
.../2016_3_4_3507_1_ch120_read433_strand.fast5 | Bin 0 -> 2005087 bytes
.../2016_3_4_3507_1_ch120_read443_strand.fast5 | Bin 0 -> 887162 bytes
.../2016_3_4_3507_1_ch120_read505_strand.fast5 | Bin 0 -> 1034554 bytes
.../2016_3_4_3507_1_ch120_read521_strand.fast5 | Bin 0 -> 1262508 bytes
.../2016_3_4_3507_1_ch120_read542_strand.fast5 | Bin 0 -> 2053955 bytes
.../2016_3_4_3507_1_ch120_read586_strand.fast5 | Bin 0 -> 1370058 bytes
.../2016_3_4_3507_1_ch120_read635_strand.fast5 | Bin 0 -> 1415531 bytes
.../2016_3_4_3507_1_ch120_read706_strand.fast5 | Bin 0 -> 1342813 bytes
.../2016_3_4_3507_1_ch120_read83_strand.fast5 | Bin 0 -> 1583898 bytes
.../2016_3_4_3507_1_ch120_read89_strand.fast5 | Bin 0 -> 978140 bytes
.../2016_3_4_3507_1_ch126_read1066_strand.fast5 | Bin 0 -> 1349302 bytes
.../2016_3_4_3507_1_ch126_read1079_strand.fast5 | Bin 0 -> 1879525 bytes
.../2016_3_4_3507_1_ch126_read1169_strand.fast5 | Bin 0 -> 1119763 bytes
.../2016_3_4_3507_1_ch126_read1250_strand.fast5 | Bin 0 -> 1167710 bytes
.../2016_3_4_3507_1_ch126_read1377_strand.fast5 | Bin 0 -> 828114 bytes
.../2016_3_4_3507_1_ch126_read1387_strand.fast5 | Bin 0 -> 1031775 bytes
.../2016_3_4_3507_1_ch126_read160_strand.fast5 | Bin 0 -> 952615 bytes
.../2016_3_4_3507_1_ch126_read217_strand.fast5 | Bin 0 -> 1920500 bytes
.../2016_3_4_3507_1_ch126_read223_strand.fast5 | Bin 0 -> 1116589 bytes
.../2016_3_4_3507_1_ch126_read249_strand.fast5 | Bin 0 -> 1402714 bytes
.../2016_3_4_3507_1_ch126_read324_strand.fast5 | Bin 0 -> 1498465 bytes
.../2016_3_4_3507_1_ch126_read326_strand.fast5 | Bin 0 -> 852262 bytes
.../2016_3_4_3507_1_ch126_read382_strand.fast5 | Bin 0 -> 1031446 bytes
.../2016_3_4_3507_1_ch126_read42_strand.fast5 | Bin 0 -> 1858993 bytes
.../2016_3_4_3507_1_ch126_read501_strand.fast5 | Bin 0 -> 1870086 bytes
.../2016_3_4_3507_1_ch126_read562_strand.fast5 | Bin 0 -> 2290355 bytes
.../2016_3_4_3507_1_ch126_read601_strand.fast5 | Bin 0 -> 1096349 bytes
.../2016_3_4_3507_1_ch126_read618_strand.fast5 | Bin 0 -> 1225540 bytes
.../2016_3_4_3507_1_ch126_read700_strand.fast5 | Bin 0 -> 1332148 bytes
.../2016_3_4_3507_1_ch126_read743_strand.fast5 | Bin 0 -> 1688147 bytes
.../2016_3_4_3507_1_ch126_read831_strand.fast5 | Bin 0 -> 1437489 bytes
.../2016_3_4_3507_1_ch126_read833_strand.fast5 | Bin 0 -> 1577416 bytes
.../2016_3_4_3507_1_ch126_read843_strand.fast5 | Bin 0 -> 1575973 bytes
.../2016_3_4_3507_1_ch126_read857_strand.fast5 | Bin 0 -> 1320571 bytes
.../2016_3_4_3507_1_ch126_read899_strand.fast5 | Bin 0 -> 1070267 bytes
.../2016_3_4_3507_1_ch126_read914_strand.fast5 | Bin 0 -> 956454 bytes
.../2016_3_4_3507_1_ch126_read940_strand.fast5 | Bin 0 -> 1030131 bytes
.../2016_3_4_3507_1_ch126_read969_strand.fast5 | Bin 0 -> 1039441 bytes
.../2016_3_4_3507_1_ch128_read204_strand.fast5 | Bin 0 -> 1061048 bytes
.../2016_3_4_3507_1_ch128_read270_strand.fast5 | Bin 0 -> 1469918 bytes
.../2016_3_4_3507_1_ch128_read361_strand.fast5 | Bin 0 -> 1684091 bytes
.../2016_3_4_3507_1_ch128_read365_strand.fast5 | Bin 0 -> 1530857 bytes
.../2016_3_4_3507_1_ch128_read376_strand.fast5 | Bin 0 -> 1902400 bytes
.../2016_3_4_3507_1_ch128_read384_strand.fast5 | Bin 0 -> 1183780 bytes
.../2016_3_4_3507_1_ch128_read404_strand.fast5 | Bin 0 -> 1709831 bytes
.../2016_3_4_3507_1_ch128_read422_strand.fast5 | Bin 0 -> 1177979 bytes
.../2016_3_4_3507_1_ch128_read430_strand.fast5 | Bin 0 -> 811659 bytes
.../2016_3_4_3507_1_ch128_read503_strand.fast5 | Bin 0 -> 1605461 bytes
.../2016_3_4_3507_1_ch128_read521_strand.fast5 | Bin 0 -> 1509399 bytes
.../2016_3_4_3507_1_ch128_read635_strand.fast5 | Bin 0 -> 1608095 bytes
.../2016_3_4_3507_1_ch128_read647_strand.fast5 | Bin 0 -> 1040252 bytes
.../2016_3_4_3507_1_ch128_read723_strand.fast5 | Bin 0 -> 1540447 bytes
.../2016_3_4_3507_1_ch128_read753_strand.fast5 | Bin 0 -> 1366371 bytes
.../2016_3_4_3507_1_ch128_read763_strand.fast5 | Bin 0 -> 1192962 bytes
.../2016_3_4_3507_1_ch128_read783_strand.fast5 | Bin 0 -> 1556061 bytes
.../2016_3_4_3507_1_ch128_read790_strand.fast5 | Bin 0 -> 1625467 bytes
.../2016_3_4_3507_1_ch128_read95_strand.fast5 | Bin 0 -> 781306 bytes
.../2016_3_4_3507_1_ch13_read1130_strand.fast5 | Bin 0 -> 1472869 bytes
.../2016_3_4_3507_1_ch13_read1132_strand.fast5 | Bin 0 -> 1730815 bytes
.../2016_3_4_3507_1_ch13_read1150_strand.fast5 | Bin 0 -> 1361446 bytes
.../2016_3_4_3507_1_ch13_read1404_strand.fast5 | Bin 0 -> 1426971 bytes
.../2016_3_4_3507_1_ch13_read1414_strand.fast5 | Bin 0 -> 1135261 bytes
.../2016_3_4_3507_1_ch13_read1456_strand.fast5 | Bin 0 -> 1440622 bytes
.../2016_3_4_3507_1_ch13_read1474_strand.fast5 | Bin 0 -> 1305443 bytes
...K12_1D_R9_SpotON_41280_ch52_read58_strand.fast5 | Bin 0 -> 1914989 bytes
108 files changed, 1664 insertions(+), 1228 deletions(-)
create mode 100644 .gitignore
delete mode 100644 Dockerfile
create mode 100644 appveyor.yml
create mode 100644 appveyor/install.ps1
create mode 100644 appveyor/run_with_env.cmd
delete mode 100644 dist/poretools-0.3.0.win-amd64.exe
delete mode 100644 dist/poretools-0.3.1.win-amd64.exe
delete mode 100644 dist/poretools-0.5.0.win-amd64.exe
delete mode 100644 dist/poretools.reg
create mode 100644 docs/content/_images/qualpos.png
create mode 100644 docs/content/history.rst
create mode 100644 docs/requirements.txt
delete mode 100644 poretools/Fast5File_pytables.py
create mode 100644 poretools/index.py
create mode 100644 poretools/metadata.py
create mode 100644 poretools/organise.py
create mode 100644 poretools/qual_v_pos.py
delete mode 100644 poretools/windows.py
create mode 100644 test_data/2016_3_4_3507_1_ch120_read240_strand.fast5
create mode 100644 test_data/2016_3_4_3507_1_ch120_read353_strand.fast5
create mode 100644 test_data/2016_3_4_3507_1_ch120_read415_strand.fast5
create mode 100644 test_data/2016_3_4_3507_1_ch120_read418_strand.fast5
create mode 100644 test_data/2016_3_4_3507_1_ch120_read433_strand.fast5
create mode 100644 test_data/2016_3_4_3507_1_ch120_read443_strand.fast5
create mode 100644 test_data/2016_3_4_3507_1_ch120_read505_strand.fast5
create mode 100644 test_data/2016_3_4_3507_1_ch120_read521_strand.fast5
create mode 100644 test_data/2016_3_4_3507_1_ch120_read542_strand.fast5
create mode 100644 test_data/2016_3_4_3507_1_ch120_read586_strand.fast5
create mode 100644 test_data/2016_3_4_3507_1_ch120_read635_strand.fast5
create mode 100644 test_data/2016_3_4_3507_1_ch120_read706_strand.fast5
create mode 100644 test_data/2016_3_4_3507_1_ch120_read83_strand.fast5
create mode 100644 test_data/2016_3_4_3507_1_ch120_read89_strand.fast5
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create mode 100644 test_data/2016_3_4_3507_1_ch128_read723_strand.fast5
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create mode 100644 test_data/COLLES_L160693_20160728_FNFAB23794_MN17350_sequencing_run_E_coli_K12_1D_R9_SpotON_41280_ch52_read58_strand.fast5
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