cooler balance HB_Cool.cool
variance is 115532.067933
variance is 1880.1202993
variance is 142.980174133
variance is 16.5192880813
variance is 1.92663361978
variance is 0.25196914841
variance is 0.0346924669294
variance is 0.00558787607212
variance is 0.00103577668573
variance is 0.000235077586937
variance is 6.00085555451e-05
variance is 1.68418189549e-05
variance is 4.89101936518e-06
cooler dump --annotate weight
Nezar, I tried do cooler balance and then cooler dump, then I thought weights should be there in my cool file, but I still get this error through python API
matb = c.matrix(balance=True).fetch('chr5:10,000,000-15,000,000')
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "cooler/core.py", line 360, in fetch
File "cooler/api.py", line 311, in _slice
File "cooler/api.py", line 560, in matrix
ValueError: No column 'bins/weight' found. Use cooler.ice to calculate balancing weights.
Is there any step I am missing?
Also another thing, I tried is cooler show, which again gave me error :(
cooler show --out test.png --dpi 200 HB_Cool.cool chr3:0-80,000,000
Traceback (most recent call last):
File "/usr/bin/cooler", line 9, in <module>
load_entry_point('cooler==0.5.2', 'console_scripts', 'cooler')()
File "/usr/lib/python2.7/site-packages/click/core.py", line 716, in call
return self.main(args, kwargs)
File "/usr/lib/python2.7/site-packages/click/core.py", line 696, in main
rv = self.invoke(ctx)
File "/usr/lib/python2.7/site-packages/click/core.py", line 1060, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/usr/lib/python2.7/site-packages/click/core.py", line 889, in invoke
return ctx.invoke(self.callback, ctx.params)
File "/usr/lib/python2.7/site-packages/click/core.py", line 534, in invoke
return callback(args, kwargs)
File "/home/ankita/4DN/cooler/cooler/cooler/cli/show.py", line 135, in show
'log10' : 'log 10 ( relative contact frequency '}[scale]))
File "/usr/lib64/python2.7/site-packages/matplotlib/pyplot.py", line 1976, in colorbar
ret = gcf().colorbar(mappable, cax = cax, ax=ax, kw)
File "/usr/lib64/python2.7/site-packages/matplotlib/figure.py", line 1387, in colorbar
cb = cbar.colorbar_factory(cax, mappable, kw)
File "/usr/lib64/python2.7/site-packages/matplotlib/colorbar.py", line 1173, in colorbar_factory
cb = Colorbar(cax, mappable, kwargs)
File "/usr/lib64/python2.7/site-packages/matplotlib/colorbar.py", line 854, in init
ColorbarBase.init(self, ax, **kw)
TypeError: init() got an unexpected keyword argument 'label'
h5py. f = h5py.File('myfile.cool', 'r')
'weight' in f['bins']cooler show. I suspect it's related to the matplotlib version. Could you print the results of pip list?
-ipap11helper (0.1)
backports.ssl-match-hostname (3.4.0.2)
Beaker (1.5.4)
biopython (1.68)
blivet (0.61.15.37)
Brlapi (0.6.0)
cffi (0.8.6)
chardet (2.2.1)
click (6.6)
configobj (4.7.2)
configshell-fb (1.1.18)
cooler (0.5.2, /home/ankita/4DN/cooler/cooler)
coverage (3.6b3)
cryptography (0.8.2)
cupshelpers (1.0)
decorator (3.4.0)
di (0.3)
dnspython (1.12.0)
enum34 (1.0.4)
ethtool (0.8)
firstboot (19.5)
freeipa (2.0.0a0)
fros (1.0)
fuse-python (0.2.1)
h5py (2.6.0)
iniparse (0.4)
initial-setup (0.3.9.30)
ipaplatform (4.2.0)
ipapython (4.2.0)
IPy (0.75)
javapackages (1.0.0)
kerberos (1.1)
kitchen (1.1.1)
kmod (0.1)
langtable (0.0.31)
lxml (3.2.1)
Mako (0.8.1)
MarkupSafe (0.11)
matplotlib (1.2.0)
netaddr (0.7.5)
nose (1.3.0)
ntplib (0.3.2)
numpy (1.11.1)
pandas (0.18.1)
Paste (1.7.5.1)
perf (0.1)
pip (7.1.0)
ply (3.4)
policycoreutils-default-encoding (0.1)
pyasn1 (0.1.6)
pycparser (2.14)
pycups (1.9.63)
pycurl (7.19.0)
pyfaidx (0.4.6)
pygobject (3.14.0)
pygpgme (0.3)
pyinotify (0.9.4)
pykickstart (1.99.66.6)
pyliblzma (0.5.3)
pyOpenSSL (0.13.1)
pyparsing (1.5.6)
pyparted (3.9)
pysam (0.9.1.4)
pysmbc (1.0.13)
python-augeas (0.5.0)
python-dateutil (1.5)
python-default-encoding (0.1)
python-dmidecode (3.10.13)
python-ldap (2.4.15)
python-meh (0.25.2)
python-nss (0.16.0)
python-yubico (1.2.3)
pytz (2012d)
pyudev (0.15)
pyusb (1.0.0b1)
pyxattr (0.5.1)
qrcode (5.0.1)
rtslib-fb (2.1.57)
scipy (0.18.0)
seobject (0.1)
sepolicy (1.1)
setroubleshoot (1.1)
setuptools (0.9.8)
six (1.9.0)
slip (0.4.0)
slip.dbus (0.4.0)
SSSDConfig (1.13.0)
targetcli-fb (2.1.fb41)
Tempita (0.5.1)
urlgrabber (3.10)
urwid (1.1.1)
yum-langpacks (0.4.2)
yum-metadata-parser (1.1.4)
[ankita@localhost cooler]$
So, I am not sure if it is correct to ask but we do these steps
$ cooler makebins $CHROMSIZES_FILE 10000 > bins.10kb.bed
$ cooler cload bins.10kb.bed $CONTACTS_FILE out.cool
As I understood I am getting a cool file which is 10 kb binned. What if I don't want it to be binned and create a cool file ? Does that make sense?
[ankita@localhost cooler]$ cooler dump -t pixels -r 10:10,000,000-20,000,000 -r2 10:30,000,000-80,000,000 --header --join HB_Cool.cool | head
Traceback (most recent call last):
File "/usr/bin/cooler", line 9, in <module>
load_entry_point('cooler==0.5.2', 'console_scripts', 'cooler')()
File "/usr/lib/python2.7/site-packages/click/core.py", line 716, in call
return self.main(args, kwargs)
File "/usr/lib/python2.7/site-packages/click/core.py", line 696, in main
rv = self.invoke(ctx)
File "/usr/lib/python2.7/site-packages/click/core.py", line 1060, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/usr/lib/python2.7/site-packages/click/core.py", line 889, in invoke
return ctx.invoke(self.callback, ctx.params)
File "/usr/lib/python2.7/site-packages/click/core.py", line 534, in invoke
return callback(args, kwargs)
File "/home/ankita/4DN/cooler/cooler/cooler/cli/dump.py", line 105, in dump
selector = c.matrix(as_pixels=True).fetch(range, range2)
File "/home/ankita/4DN/cooler/cooler/cooler/core.py", line 359, in fetch
i0, i1, j0, j1 = self._fetch(*args, kwargs)
File "/home/ankita/4DN/cooler/cooler/cooler/api.py", line 317, in _fetch
region1 = parse_region(region, self._chromsizes)
File "/home/ankita/4DN/cooler/cooler/cooler/util.py", line 105, in parse_region
raise ValueError("Unknown sequence label: {}".format(chrom))
ValueError: Unknown sequence label: 10
AttributeError Traceback (most recent call last)
<ipython-input-1-8423f6653a05> in <module>()
10
11 where = np.flatnonzero
---> 12 chromsizes = cooler.read_chromsizes('http://s3.amazonaws.com/pkerp/data/mm9/chromInfo.txt') # defaults to reading chr#,X,Y,M
13 chromosomes = list(chromsizes.keys())
14 cumullengths = np.r[0, np.cumsum(chromsizes)]
AttributeError: module 'cooler' has no attribute 'read_chromsizes'
higlass_getter.py
chr10
As I understood I am getting a cool file which is 10 kb binned. What if I don't want it to be binned and create a cool file ? Does that make sense?
So what you are asking for is a binary version of the contact list? Cool files represent contact matrices so by definition they must be binned (i.e. aggregated) some way
cooler digest can make a fragment-delimited bin file
Hi, I would like to import a bed file in Hi-Glass where it is overlapping intervals of chromosome as following:
id start end mid-point Value
chr1 1 100000 50000 53.696604901
chr1 5001 105000 55000 53.3929395224
chr1 10001 110000 60000 53.393254991
chr1 15001 115000 65000 53.3523366425 ..
as a hitile file. Any suggestion on how should I do this?