HOME-pairwise for different numbers of replicate about home HOT 4 OPEN

Hi,
HOME supports samples with different number of replicates, so that's not the issue.
Is your HOME_DMR_sample_file_CG.txt tab separated?

If not, please tab separate it.

Also, there seems to be missing slash in the path for replicate 2, 3 and 4 for mutant. Please check the path for the replicates and provide the full path (HOME does not support relative path at the moment).

Thanks,
Akanksha

from home.

Hi Akanksha

As your comments, I used full path and tab separated.
but It was not working and showed same error message

pandas.parser.CParserError: Error tokenizing data. C error: Expected 5 fields in line 2, saw 7

I tested HOME_DMR_sample_file_CG.txt with blank tab to make same field number.
then it works

mutant /data/path/mutant.r1.CGmap.gz data/path/mutant.r2.CGmap.gz data/path/mutant.r3.CGmap.gz data/path/mutant.r4.CGmap.gz {tab} {tab}
WT /data/path/WT.r1.CGmap.gz /data/path/WT.r2.CGmap.gz /data/path/WT.r3.CGmap.gz /data/path/WT.r4.CGmap.gz /data/path/WT.r5.CGmap.gz /data/path/WT.r6.CGmap.gz

I don't know why but it works.
I think during HOME-pairwise, pandas.parser need same field number for mutant and WT for input.

I also used testcase file with

sample1 /home/lee/NGS/sw/HOME/testcase/CG/sample1_r1.txt /home/lee/NGS/sw/HOME/testcase/CG/sample1_r2.txt
sample2 /home/lee/NGS/sw/HOME/testcase/CG/sample2_r1.txt /home/lee/NGS/sw/HOME/testcase/CG/sample2_r2.txt /home/lee/NGS/sw/HOME/testcase/CG/sample3_r1.txt

( I added sample3_r1.txt because if use 1 replicate vs 2 replicate, I got following message)
error: cannot handle 1 replicate in 1 group and more than 1 in other

Traceback (most recent call last):
File "/home/lee/NGS/sw/HOME_met/bin/HOME-pairwise", line 4, in
import('pkg_resources').run_script('HOME==1.0.0', 'HOME-pairwise')
File "/home/lee/NGS/sw/HOME_met/lib/python2.7/site-packages/pkg_resources/init.py", line 666, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/home/lee/NGS/sw/HOME_met/lib/python2.7/site-packages/pkg_resources/init.py", line 1469, in run_script
exec(script_code, namespace, namespace)
File "/home/lee/NGS/sw/HOME_met/lib/python2.7/site-packages/HOME-1.0.0-py2.7.egg/EGG-INFO/scripts/HOME-pairwise", line 314, in

File "/home/lee/NGS/sw/HOME_met/lib/python2.7/site-packages/pandas/io/parsers.py", line 498, in parser_f
return _read(filepath_or_buffer, kwds)
File "/home/lee/NGS/sw/HOME_met/lib/python2.7/site-packages/pandas/io/parsers.py", line 285, in _read
return parser.read()
File "/home/lee/NGS/sw/HOME_met/lib/python2.7/site-packages/pandas/io/parsers.py", line 747, in read
ret = self._engine.read(nrows)
File "/home/lee/NGS/sw/HOME_met/lib/python2.7/site-packages/pandas/io/parsers.py", line 1197, in read
data = self._reader.read(nrows)
File "pandas/parser.pyx", line 766, in pandas.parser.TextReader.read (pandas/parser.c:7988)
File "pandas/parser.pyx", line 788, in pandas.parser.TextReader._read_low_memory (pandas/parser.c:8244)
File "pandas/parser.pyx", line 842, in pandas.parser.TextReader._read_rows (pandas/parser.c:8970)
File "pandas/parser.pyx", line 829, in pandas.parser.TextReader._tokenize_rows (pandas/parser.c:8838)
File "pandas/parser.pyx", line 1833, in pandas.parser.raise_parser_error (pandas/parser.c:22649)
pandas.parser.CParserError: Error tokenizing data. C error: Expected 3 fields in line 2, saw 4

if I add blank tab to make same filed number,
sample1 /home/lee/NGS/sw/HOME/testcase/CG/sample1_r1.txt /home/lee/NGS/sw/HOME/testcase/CG/sample1_r2.txt {tab}
sample2 /home/lee/NGS/sw/HOME/testcase/CG/sample2_r1.txt /home/lee/NGS/sw/HOME/testcase/CG/sample2_r2.txt /home/lee/NGS/sw/HOME/testcase/CG/sample3_r1.txt

it works
Preparing the DMRs from HOME.....
GOOD LUCK !
DMRs for sample1_VS_sample2_13 done
DMRs for sample1_VS_sample2_10 done
DMRs for sample1_VS_sample2_12 done
Congratulations the DMRs are ready

I hope this report helps for improving HOME

from home.

Ok glad it worked. We tested for equal number of replicates and it works perfectly fine but will test it again thanks.

from home.

I get the exact same error, but for me the blank tab doesn't work. There is an issue when replicate numbers are not the same. I have 2 replicates for the WT and 4 for the mutant.

from home.