Hi,

I have some questions when I use the eclipdemux, Please take a look at the questions I mentioned below.

I can call the main function (demux -h), but when I run the command, I get an error.

The command I used:

demux --metrics IP3_PE_clip.---.--.metrics --expectedbarcodeida bc1 --expectedbarcodeidb bc2 --fastq_1 ../../0-data/R21046039-SGC-IP-SGC-IP_combined_R1.fastq.gz --fastq_2 ../../0-data/R21046039-SGC-IP-SGC-IP_combined_R2.fastq.gz --newname IP3_clip --dataset IP3_PE --barcodesfile ./barcode.fasta --length 10 > IP3.log

error:

Traceback (most recent call last):
File "/home/disk/software/anaconda3/bin/demux", line 33, in
sys.exit(load_entry_point('eclipdemux-distribution==0.0.1', 'console_scripts', 'demux')())
File "/home/disk/software/anaconda3/lib/python3.8/site-packages/eclipdemux_distribution-0.0.1-py3.8.egg/eclipdemux_package/demux.py", line 907, in main
demux(datastr,
File "/home/disk/software/anaconda3/lib/python3.8/site-packages/eclipdemux_distribution-0.0.1-py3.8.egg/eclipdemux_package/demux.py", line 822, in demux
bcassigned = assignbarcode(fastqread1["sequence"],
File "/home/disk/software/anaconda3/lib/python3.8/site-packages/eclipdemux_distribution-0.0.1-py3.8.egg/eclipdemux_package/demux.py", line 430, in assignbarcode
distances_to_bcseqs = [(hamming_loose(bcfound, bcseq), bcseq)
File "/home/disk/software/anaconda3/lib/python3.8/site-packages/eclipdemux_distribution-0.0.1-py3.8.egg/eclipdemux_package/demux.py", line 430, in
distances_to_bcseqs = [(hamming_loose(bcfound, bcseq), bcseq)
File "/home/disk/software/anaconda3/lib/python3.8/site-packages/eclipdemux_distribution-0.0.1-py3.8.egg/eclipdemux_package/demux.py", line 360, in hamming_loose
return _hamming(_matching_loose, word1, word2)
File "/home/disk/software/anaconda3/lib/python3.8/site-packages/eclipdemux_distribution-0.0.1-py3.8.egg/eclipdemux_package/demux.py", line 332, in _hamming
return sum(not matching_function(letter1, letter2)
File "/home/disk/software/anaconda3/lib/python3.8/site-packages/eclipdemux_distribution-0.0.1-py3.8.egg/eclipdemux_package/demux.py", line 332, in
return sum(not matching_function(letter1, letter2)
File "/home/disk/software/anaconda3/lib/python3.8/site-packages/eclipdemux_distribution-0.0.1-py3.8.egg/eclipdemux_package/demux.py", line 312, in _matching_loose
_assert_in_alphabet(nucl1)
File "/home/disk/software/anaconda3/lib/python3.8/site-packages/eclipdemux_distribution-0.0.1-py3.8.egg/eclipdemux_package/demux.py", line 288, in _assert_in_alphabet
raise_with_traceback(IllegalBarcodeSeqValueError(nucl))
File "/home/disk/software/anaconda3/lib/python3.8/site-packages/future/utils/init.py", line 446, in raise_with_traceback
raise exc.with_traceback(traceback)
eclipdemux_package.demux.IllegalBarcodeSeqValueError: 65

I also called the python script(demux.py) directly and it ran successfully

The command I used:

demux.py --metrics IP2_PE_clip.---.--.metrics --expectedbarcodeida bc1 --expectedbarcodeidb bc2 --fastq_1 ../../0-data/R21046039-SGC-IP-SGC-IP_combined_R1.fastq.gz --fastq_2 ../../0-data/R21046039-SGC-IP-SGC-IP_combined_R2.fastq.gz --newname IP2_clip --dataset IP2_PE --barcodesfile ./barcode.fasta --length 10 > IP2.log

However, the file of NIL is very large, while the file of barcode(bc1 and bc2) is very small. Which file should I use for subsequent analysis?

Here are my questions:
1、Is there any difference between calling demux and calling the demux.py directly?
2、How do I handle the above error when I run demux?
3、When I provide specific barcode for IP, but the result shows that the NIL file is larger than the corresponding barcode file , which file should I use for subsequent analysis?

Two issues are encountered while running Python3 -
I) zip is built-in and need not be imported
II) Files opened in binary format cannot be written on to using 'str'. These need to be wrapped around the .encode() function/

Hi there,
After downloading files 'eclipdemux', I installed it using the following command

>sudo python setup.py build
>sudo python setup.py. install

When I try to use "eclipdemux" order, there shows no eclipdemux tool on my system. Could you tell me how to install eclipdexmux and how to use it ?
>eclipdemux --help

Best,
Jessica