test has crashed, Pandas-related issue

[jperales]

Hi,
I was using an old version of CNVkit (March 2015) very well. I just updated to the last version (August 2015), so I installed Pandas (new dependency). However when I tried out the test, I got the following errors:

python ../cnvkit.py scatter -s build/p2-9_2.cns build/p2-9_2.cnr -c 'chr9:150000-45000000' -o p2-9_2-chr9p-scatter.pdf
Traceback (most recent call last):
  File "../cnvkit.py", line 9, in <module>
    args.func(args)
  File "/local/jperales/TMP/cnvkit/cnvlib/commands.py", line 800, in _cmd_scatter
    args.y_max)
  File "/local/jperales/TMP/cnvkit/cnvlib/commands.py", line 867, in do_scatter
    start, end)[chrom]
  File "/local/jperales/TMP/cnvkit/cnvlib/plots.py", line 437, in gene_coords_by_range
    for row in probes.in_range(chrom, start, end):
  File "/local/jperales/TMP/cnvkit/cnvlib/gary.py", line 248, in in_range
    table = table[table.start.searchsorted(start):]
  File "/usr/lib/python2.7/dist-packages/pandas/core/generic.py", line 1815, in __getattr__
    (type(self).__name__, name))
AttributeError: 'Series' object has no attribute 'searchsorted'

[...]

python ../cnvkit.py scatter -s build/p2-9_2.cns build/p2-9_2.cnr -g SMARCA2,PTPRD -w 4e6 -o p2-9_2-SMARCA2-PTPRD-scatter.pdf
Traceback (most recent call last):
  File "../cnvkit.py", line 9, in <module>
    args.func(args)
  File "/local/jperales/TMP/cnvkit/cnvlib/commands.py", line 800, in _cmd_scatter
    args.y_max)
  File "/local/jperales/TMP/cnvkit/cnvlib/commands.py", line 891, in do_scatter
    sel_probes = pset_cvg.in_range(chrom, *window_coords)
  File "/local/jperales/TMP/cnvkit/cnvlib/gary.py", line 255, in in_range
    table = table[:table.end.searchsorted(end, 'right')]
  File "/usr/lib/python2.7/dist-packages/pandas/core/generic.py", line 1815, in __getattr__
    (type(self).__name__, name))
AttributeError: 'Series' object has no attribute 'searchsorted'
make: *** [p2-9_2-SMARCA2-PTPRD-scatter.pdf] Error 1

Here are my module versions (taken from $lib.__version__):

Module	Version
Python	2.7.6
Biopython	1.65
Reportlab	(unknown)
matplotlib	1.3.1
Numpy	1.8.2
SciPy	0.13.3
Pandas	0.13.1
pysam	0.8.2.1
PyVCF	(unknown)

uname -srvmo
Linux 3.13.0-49-generic #83-Ubuntu SMP Fri Apr 10 20:11:33 UTC 2015 x86_64 GNU/Linux

Thanks in advance,
Javier Perales

[etal]

Sorry for the trouble, but thanks for letting me know. It looks like CNVkit's installation specified a pandas version that was too old and didn't have the "Series.searchsorted" method yet. I've updated setup.py to ask for a newer version (e570295).