-ipap11helper (0.1)
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cffi (0.8.6)
chardet (2.2.1)
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[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?