dangertrip/libis

libis's Issues

关于病毒整合的检测

Hi YueYin,
最近在用LiBis对一批WGBS的数据进行分析，看到文档说LiBis支持检测病毒整合，但是文档中没有说明如何使用。
请问LIBis对BS数据检测病毒嵌合的具体用法是什么呢？
i wonder how to use LiBis to identify virus integration.

Thank you.

Is LiBis suitable for single-cell bisulfite sequencing data analysis？

Hello,
Thanks to developing such a nice tool! As described in the issue title, is LiBis performing well in scWGBS or scRRBS sequencing?

RELEASE file missing from 0.0.13 tarball on pypi

FYI, the RELEASE file is missing from the 0.0.13 tarball on pypi and this makes installation impossible:

06:12:17 BIOCONDA INFO (OUT) Processing $SRC_DIR
06:12:17 BIOCONDA INFO (OUT)   Created temporary directory: /tmp/pip-req-build-x6dksqn2
06:12:17 BIOCONDA INFO (OUT)   Added file://$SRC_DIR to build tracker '/tmp/pip-req-tracker-vnydtp64'
06:12:17 BIOCONDA INFO (OUT)     Running command python setup.py egg_info
06:12:17 BIOCONDA INFO (OUT)     Running setup.py (path:/tmp/pip-req-build-x6dksqn2/setup.py) egg_info for package from file://$SRC_DIR
06:12:17 BIOCONDA INFO (OUT)     Traceback (most recent call last):
06:12:17 BIOCONDA INFO (OUT)       File "<string>", line 1, in <module>
06:12:17 BIOCONDA INFO (OUT)       File "/tmp/pip-req-build-x6dksqn2/setup.py", line 23, in <module>
06:12:17 BIOCONDA INFO (OUT)         with open('RELEASE') as f:
06:12:17 BIOCONDA INFO (OUT)     FileNotFoundError: [Errno 2] No such file or directory: 'RELEASE'

Final report not working

Hi,

First of all I would like to congratulate for creating this tool. I'm working with low input bisulfite sequencing and I wanted to give it a try and compare to the current methodology I'm using. I took an small piece of my data just to see if it was working and everything seems fine except that despite using the -plot command, still doesn't procude the final report.

Here is my code:

LiBis -f 0 -n case_50_R1_val_1.fq.gz case_50_R2_val_2.fq.gz -c 1 -r GRCh38.fa -w 30 -s 5 -ft 45 --plot

I would most definetly appreciate your help. I would love to know if the mapping efficiency increases so I can start using this tool.

Pair end read name bug

Due to multiple format for pair end reads' name, program is unable to locate the correct position of reads' order (mate1/mate2).

path

Hey. Can you help me with this? Sorry to bother you with this. I'm with problems after the trimming step. The program is running and creating the files in trim dir but when the bsmap is called in the next step it is not finding the trim file that the own program created.
I'm sure it's a simple mistake on my part.

After trim he it is going to bsmap step:

2023-03-16 13:28:30.413695 command: bsmap -a Trim/B14_R1_val_1.fq.gz -b Trim/B14_R2_val_2.fq.gz -z 33 -d /run/media/ambrizi/sata/Master/references/Bos_taurus.ARS-UCD1.2.dna_sm.toplevel.fa -o B14_R1_val_1.bam -U -S 123 -n 1 -r 0 -u -p 2 1>>LiBis_log 2>>BAM_FILE/B14_R1_val_1_originallog.record
Output:

Thanks!

UnboundLocalError: local variable 'c' referenced before assignment

I have this error when running LiBis with:

LiBis -n CFD1601224-NBL_R1.fastq.gz -r GRCh37.fa  -g GRCh37 --plot --fullmode -qc

Traceback (most recent call last):
  File "/apps/gent/CO7/haswell-ib/software/LiBis/20200428-foss-2019b-Python-3.7.4/bin/LiBis", line 215, in <module>
    main()
  File "/apps/gent/CO7/haswell-ib/software/LiBis/20200428-foss-2019b-Python-3.7.4/bin/LiBis", line 212, in main
    computeProcess(input_args())
  File "/apps/gent/CO7/haswell-ib/software/LiBis/20200428-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/LiBis/computeProcess.py", line 136, in computeProcess
    name,bsmapresult = computeBsmap(name,bsmap,param) 
  File "/apps/gent/CO7/haswell-ib/software/LiBis/20200428-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/LiBis/computeProcess.py", line 76, in computeBsmap
    newname,logname = bsmap.clipping(n,param,given_bam,given_label)
  File "/apps/gent/CO7/haswell-ib/software/LiBis/20200428-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/LiBis/moabs.py", line 134, in clipping
    newname,log = clipmode(filenames,param, given_bam_file,given_label)
  File "/apps/gent/CO7/haswell-ib/software/LiBis/20200428-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/LiBis/clipmode.py", line 400, in clipmode
    newn,originallog,splitlog,cleanname=clip_process(name,param, given_bam_file,given_label)
  File "/apps/gent/CO7/haswell-ib/software/LiBis/20200428-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/LiBis/clipmode.py", line 311, in clip_process
    reads_num_dist,reads_len_dist = unsortedCombine(unmapped_file[:unmapped_file.find('fastq')-1],args)
  File "/apps/gent/CO7/haswell-ib/software/LiBis/20200428-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/LiBis/mapreduce.py", line 515, in unsortedCombine
    pure_name = c[0]
UnboundLocalError: local variable 'c' referenced before assignment

Log files:

[ 2020-08-03 16:21:05.905030 ]	Running quality control for samples...
[ 2020-08-03 16:22:38.799056 ]	Finish quality control for samples
[ 2020-08-03 16:22:38.875621 ]	Running Alignment for samples...
[ 2020-08-03 16:22:38.897955 ]	Temprary files cleaning...
[ 2020-08-03 16:22:38.897989 ]	Begin the alignment process with clipping.
[ 2020-08-03 16:22:38.898028 ]	Begin the 1st round full reads mapping.
[ 2020-08-03 17:05:27.474592 ]	Filtering and clipping unmapped reads.
Temporary file doesn't exist: CFD1601224-NBL_R1.unmapped.fastq !
[ 2020-08-03 17:08:21.553470 ]	Begin the 2st round mapping for clipped fragments.
[ 2020-08-03 17:57:55.572260 ]	Recombining uniquely mapped fragments...

2020-08-03 16:22:38.798689	command: fastqc -o ./Fastqc CFD1601224-NBL_R1.fastq.gz 
Output:
Started analysis of CFD1601224-NBL_R1.fastq.gz
Approx 5% complete for CFD1601224-NBL_R1.fastq.gz
Approx 10% complete for CFD1601224-NBL_R1.fastq.gz
Approx 15% complete for CFD1601224-NBL_R1.fastq.gz
Approx 20% complete for CFD1601224-NBL_R1.fastq.gz
Approx 25% complete for CFD1601224-NBL_R1.fastq.gz
Approx 30% complete for CFD1601224-NBL_R1.fastq.gz
Approx 35% complete for CFD1601224-NBL_R1.fastq.gz
Approx 40% complete for CFD1601224-NBL_R1.fastq.gz
Approx 45% complete for CFD1601224-NBL_R1.fastq.gz
Approx 50% complete for CFD1601224-NBL_R1.fastq.gz
Approx 55% complete for CFD1601224-NBL_R1.fastq.gz
Approx 60% complete for CFD1601224-NBL_R1.fastq.gz
Approx 65% complete for CFD1601224-NBL_R1.fastq.gz
Approx 70% complete for CFD1601224-NBL_R1.fastq.gz
Approx 75% complete for CFD1601224-NBL_R1.fastq.gz
Approx 80% complete for CFD1601224-NBL_R1.fastq.gz
Approx 85% complete for CFD1601224-NBL_R1.fastq.gz
Approx 90% complete for CFD1601224-NBL_R1.fastq.gz
Approx 95% complete for CFD1601224-NBL_R1.fastq.gz


2020-08-03 17:05:27.472918	command: bsmap -a CFD1601224-NBL_R1.fastq.gz -z 33 -d /data/gent/vo/000/gvo00027/RNA_seq_pipeline/resources_Ruben/GRCh37-lite.fa  -o CFD1601224-NBL_R1.bam -S 123 -n 1 -r 0 -U -u -p 8 1>>LiBis_log 2>>BAM_FILE/CFD1601224-NBL_R1_originallog.record
Output:


2020-08-03 17:57:55.570410	command: bsmap -a CFD1601224-NBL_R1.unmapped.fastq -d /data/gent/vo/000/gvo00027/RNA_seq_pipeline/resources_Ruben/GRCh37-lite.fa  -o CFD1601224-NBL_R1.unmapped.bam -n 1 -r 0 -U -R -p 8 1>>LiBis_log 2>>BAM_FILE/CFD1601224-NBL_R1.unmapped_log.txt
Output: