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Dominik R Laetsch
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Diff for: ‎bloblib/BtCore.py

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@@ -7,9 +7,9 @@
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"""
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from __future__ import division
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import bloblib.BtLog as BtLog
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import bloblib.BtIO as BtIO
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import bloblib.BtTax as BtTax
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import lib.BtLog as BtLog
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import lib.BtIO as BtIO
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import lib.BtTax as BtTax
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from os.path import abspath, isfile, basename, isdir, join
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from os import getcwd, mkdir
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import json

Diff for: ‎bloblib/BtIO.py

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from collections import defaultdict
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from os.path import basename, isfile, splitext, join, isdir
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import shutil
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import bloblib.BtLog as BtLog
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import lib.BtLog as BtLog
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# CONSTs
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COMPLEMENT = {'A':'T','C':'G','G':'C','T':'A','N':'N'}

Diff for: ‎bloblib/BtLog.py

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from __future__ import division
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import sys
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from os.path import basename
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def error(message, *argv):
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if argv is None:

Diff for: ‎bloblib/BtPlot.py

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@@ -9,9 +9,9 @@
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from __future__ import division
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from numpy import array, arange, logspace, mean, std
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import math
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import bloblib.BtLog as BtLog
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import bloblib.BtIO as BtIO
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import bloblib.BtTax as BtTax
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import lib.BtLog as BtLog
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import lib.BtIO as BtIO
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import lib.BtTax as BtTax
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import matplotlib as mat
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from matplotlib import cm
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from matplotlib.ticker import NullFormatter, MultipleLocator, AutoMinorLocator

Diff for: ‎bloblib/bamfilter.py

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@@ -32,10 +32,10 @@
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path.append(dirname(dirname(abspath(__file__))))
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import blobtools
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import bloblib.BtLog as BtLog
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import bloblib.BtIO as BtIO
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import bloblib.BtCore as Bt
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import bloblib.BtPlot as BtPlot
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import lib.BtLog as BtLog
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import lib.BtIO as BtIO
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import lib.BtCore as Bt
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import lib.BtPlot as BtPlot
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def main():
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args = docopt(__doc__)

Diff for: ‎bloblib/blobplot.py

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@@ -68,10 +68,10 @@
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path.append(dirname(dirname(abspath(__file__))))
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import blobtools
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import bloblib.BtLog as BtLog
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import bloblib.BtIO as BtIO
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import bloblib.BtCore as BtCore
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import bloblib.BtPlot as BtPlot
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import lib.BtLog as BtLog
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import lib.BtIO as BtIO
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import lib.BtCore as BtCore
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import lib.BtPlot as BtPlot
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def main():
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args = docopt(__doc__)

Diff for: ‎bloblib/covplot.py

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@@ -72,10 +72,10 @@
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path.append(dirname(dirname(abspath(__file__))))
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import blobtools
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import bloblib.BtLog as BtLog
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import bloblib.BtIO as BtIO
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import bloblib.BtCore as Bt
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import bloblib.BtPlot as BtPlot
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import lib.BtLog as BtLog
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import lib.BtIO as BtIO
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import lib.BtCore as Bt
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import lib.BtPlot as BtPlot
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def main():
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args = docopt(__doc__)

Diff for: ‎bloblib/create.py

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@@ -49,9 +49,9 @@
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path.append(dirname(dirname(abspath(__file__))))
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import blobtools
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import bloblib.BtCore as BtCore
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import bloblib.BtLog as BtLog
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import bloblib.BtIO as BtIO
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import lib.BtCore as BtCore
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import lib.BtLog as BtLog
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import lib.BtIO as BtIO
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def main():
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Diff for: ‎bloblib/map2cov.py

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@@ -24,9 +24,9 @@
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path.append(dirname(dirname(abspath(__file__))))
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import blobtools
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import bloblib.BtLog as BtLog
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import bloblib.BtIO as BtIO
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import bloblib.BtCore as BtCore
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import lib.BtLog as BtLog
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import lib.BtIO as BtIO
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import lib.BtCore as BtCore
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def main():
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args = docopt(__doc__)

Diff for: ‎bloblib/seqfilter.py

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@@ -20,8 +20,8 @@
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from sys import path
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path.append(dirname(dirname(abspath(__file__))))
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import bloblib.BtLog as BtLog
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import bloblib.BtIO as BtIO
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import lib.BtLog as BtLog
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import lib.BtIO as BtIO
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def main():
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args = docopt(__doc__)

Diff for: ‎bloblib/taxify.py

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@@ -40,8 +40,8 @@
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from sys import path
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path.append(dirname(dirname(abspath(__file__))))
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import bloblib.BtLog as BtLog
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import bloblib.BtIO as BtIO
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import lib.BtLog as BtLog
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import lib.BtIO as BtIO
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def main():
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args = docopt(__doc__)

Diff for: ‎bloblib/view.py

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@@ -32,9 +32,9 @@
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path.append(dirname(dirname(abspath(__file__))))
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import blobtools
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import bloblib.BtCore as BtCore
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import bloblib.BtLog as BtLog
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import bloblib.BtIO as BtIO
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import lib.BtCore as BtCore
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import lib.BtLog as BtLog
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import lib.BtIO as BtIO
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TAXRULES = ['bestsum', 'bestsumorder']
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RANKS = ['species', 'genus', 'family', 'order', 'phylum', 'superkingdom', 'all']

Diff for: ‎blobtools.py

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@@ -7,14 +7,14 @@
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commands:
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create create a BlobDB
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view print BlobDB as a table
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blobplot plot BlobDB as a blobplot
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covplot compare BlobDB cov(s) to additional cov file
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view generate tabular view/CONCOCT/COV files from BlobDB
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plot generate a BlobPlot from a BlobDB
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covplot generate a CovPlot from a BlobDB and a COV file
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map2cov generate cov file from bam file
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seqfilter filter FASTA sequences based on header in list
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taxify assign taxids to blast-results based on list
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bamfilter filter reads in a BAM file
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map2cov generate a COV file from BAM file
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seqfilter subset sequences in FASTA file based sequence IDs in list
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taxify generate a BlobTools compatible HITS file
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bamfilter subset paired-end reads in a BAM file
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-h, --help show this
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-v, --version show version number
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sys.exit("[ERROR]\t: The module docopt is not installed. \n \tPlease run : pip install docopt")
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__version__ = "blobtools v0.9.19"
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__version__ = "blobtools v1.0"
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MAINDIR = join(dirname(__file__), '')
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DATADIR = join(MAINDIR, 'data/')
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LIBDIR = join(MAINDIR, 'bloblib/')
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LIBDIR = join(MAINDIR, 'lib/')
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if __name__ == '__main__':
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args = docopt(__doc__,

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