pssun / circcode

A Python3-base pipeline for translated circular RNA(circRNA) identification

Hi, welcome to my GitHub HomePage 🍉

👤 About me:

• 🔭 I’m currently working on ST-seq
• 🌱 I’m currently studying at XJTU
• 📫 How to reach me: [email protected] / [email protected]
• 🖥 Major: Control Science and Engineering / Bioinformatics

📑 Paper:

• [1] Sun P, Li G . CircCode: A Powerful Tool for Identifying circRNA Coding Ability[J]. Frontiers in Genetics, 2019, 10:981.
• [2] Sun P, Wang H, Li G . Rcirc: An R Package for circRNA Analyses and Visualization[J]. Frontiers in Genetics, 2020, 11.

📑 ORCID:

  https://orcid.org/0000-0003-0796-2133

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Visitor count

circcode's Issues

Problem of pipeline

Hello,

I'm using CircCode, such a powerful tool, but I have problem, every files I used here are from your example.
When I run: python3 make_virtual_genomes.py -y config.yaml, the err is:
No. 1 length: 281
Traceback (most recent call last):
File "make_virtual_genomes.py", line 218, in
main()
File "make_virtual_genomes.py", line 210, in main
info.make_genome()
File "make_virtual_genomes.py", line 95, in make_genome
self.genome += (circrna.seq * 2 + polyN)
TypeError: unsupported operand type(s) for *: 'Seq' and 'int'

Could you give me some advice? Thank you very much!

Best,

Lu Han

find_RCRJ_and_classify.py

Hey

I'm using CircCode, but every time I am facing the same problem. I would appreciate any help to resolve this issue:

When I run - find_RCRJ_and_classify.py it gives following error:
Error in (function (edges, n = max(edges), directed = TRUE) :
At type_indexededgelist.c:117 : cannot create empty graph with negative number of vertices, Invalid value
Calls: classification -> createNet -> graph -> do.call ->
In addition: Warning message:
In max(edges) : no non-missing arguments to max; returning -Inf
Execution halted
Classify successfully!
sed: can't read /userdata/lab/RPFAligned.sortedByCoord.out.bam.merge_result.RCRJ_result.csv_translated_circ.fa: No such file or directory
Traceback (most recent call last):
File "find_RCRJ_and_classify.py", line 369, in
main()
File "find_RCRJ_and_classify.py", line 355, in main
classify(coding_seq,
File "find_RCRJ_and_classify.py", line 102, in classify
seqs = SeqIO.parse(final_trans_file, 'fasta')
File "/home/lab/.conda/envs/circcode_env/lib/python3.8/site-packages/Bio/SeqIO/init.py", line 607, in parse
return iterator_generator(handle)
File "/home/lab/.conda/envs/circcode_env/lib/python3.8/site-packages/Bio/SeqIO/FastaIO.py", line 183, in init
super().init(source, mode="t", fmt="Fasta")
File "/home/lab/.conda/envs/circcode_env/lib/python3.8/site-packages/Bio/SeqIO/Interfaces.py", line 47, in init
self.stream = open(source, "r" + mode)
FileNotFoundError: [Errno 2] No such file or directory: '/userdata/lab/RPFAligned.sortedByCoord.out.bam.merge_result.RCRJ_result.csv_translated_circ.fa'

Please note that -

"RPFAligned.sortedByCoord.out.bam.merge_result.RCRJ_result.csv_translated_circ.fa" no such file is getting generated after mapping in previous step.

Could you help me figure out this? Thanks in advance.

Best,

Tanvi

Bug of output function

There is a bug in the last function.

This will cause circcode to fail to output the final .csv file. This error will not affect the entire process but will cause the .csv file to fail to generate.

We have temporarily removed this feature and will fix it soon.

example.tar.xz is just a 'tar' but not 'tar.xz'

Hi, your example.tar.xz is example.tar.xz is just a 'tar' but not 'tar.xz'. Please fix it, thanks.

find_RCRJ_and_classify.py error

We met an error while perform 'find_RCRJ_and_classify.py', which is as follow:

~/miniconda3/lib/python3.6/site-packages/Bio/Seq.py:2715: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future.
  BiopythonWarning)
Traceback (most recent call last):
  File "find_RCRJ_and_classify.py", line 292, in <module>
    main()
  File "find_RCRJ_and_classify.py", line 288, in main
    find_longest(tmp_file_location, ribo_name, result_file_location, number)
  File "find_RCRJ_and_classify.py", line 115, in find_longest
    end = seq.id.split(':')[-1].split('-')[1]
IndexError: list index out of range

My python is poor, could you please fix it ?

find_RCRJ_and_classify.py

Hello,

When I run "python3.7 find_RCRJ_and_classify.py -y config.yaml". I got the err :
Traceback (most recent call last):
File "find_RCRJ_and_classify.py", line 8, in
import rpy2.robjects as robjects
File "/software/biosoft/software/python/python2019/lib/python3.7/site-packages/rpy2/robjects/init.py", line 27, in
from . import language
File "/software/biosoft/software/python/python2019/lib/python3.7/site-packages/rpy2/robjects/language.py", line 16, in
_str2lang = ri.baseenv['str2lang']
File "/software/biosoft/software/python/python2019/lib/python3.7/site-packages/rpy2/rinterface_lib/conversion.py", line 44, in _
cdata = function(*args, **kwargs)
File "/software/biosoft/software/python/python2019/lib/python3.7/site-packages/rpy2/rinterface_lib/_rinterface_capi.py", line 282, in _
robj = function(*args, **kwargs)
File "/software/biosoft/software/python/python2019/lib/python3.7/site-packages/rpy2/rinterface_lib/sexp.py", line 355, in getitem
raise KeyError("'%s' not found" % key)
KeyError: "'str2lang' not found"

I guess the err is related to previous steps, because there are no "junction_result" and "junction_filter_result files" in tmp_file folder. And all files I used are from your example, could you give me some advice?

Thank you very much!

Lu

Welcome to submit any questions here

Dear users,
If you encounter any problems/bugs/doubts during use, or if you have any suggestions, you are welcome to submit them here to help us to improve CircCode.
Thank you for your using.
：）

Bug in find_RCRJ_and_classify.py

Fixed an issue where the 'coverage_counts' parameter specified by the user in the configuration file could not be properly applied to the process.

Error in running python3 find_RCRJ_and_classify.py -y config.yaml

15447
15448
15449
15450
15451
Error in (function (edges, n = max(edges), directed = TRUE) :
At type_indexededgelist.c:117 : cannot create empty graph with negative number of vertices, Invalid value
Calls: classification -> createNet -> graph -> do.call ->
In addition: Warning message:
In max(edges) : no non-missing arguments to max; returning -Inf
Execution halted
Classify successfully!
sed: can't read /path/to/my_directory/CircCode_tem/ERR45678Aligned.sortedByCoord.out.bam.merge_result.RCRJ_result.csv_translated_circ.fa: No such file or directory
Traceback (most recent call last):
File "find_RCRJ_and_classify.py", line 369, in
main()
File "find_RCRJ_and_classify.py", line 355, in main
classify(coding_seq,
File "find_RCRJ_and_classify.py", line 102, in classify
seqs = SeqIO.parse(final_trans_file, 'fasta')
File "/home/.conda/envs/circcode_env/lib/python3.8/site-packages/Bio/SeqIO/init.py", line 607, in parse
return iterator_generator(handle)
File "/home/.conda/envs/circcode_env/lib/python3.8/site-packages/Bio/SeqIO/FastaIO.py", line 183, in init
super().init(source, mode="t", fmt="Fasta")
File "/home/.conda/envs/circcode_env/lib/python3.8/site-packages/Bio/SeqIO/Interfaces.py", line 47, in init
self.stream = open(source, "r" + mode)
FileNotFoundError: [Errno 2] No such file or directory: '/path/to/my_directory/CircCode_tem/ERR45678Aligned.sortedByCoord.out.bam.merge_result.RCRJ_result.csv_translated_circ.fa'

Help needed!

使用示例数据，报错TypeError: load() missing 1 required positional argument: 'Loader'

您好，我使用示例数据，填写了config.yaml文件，但是报错TypeError: load() missing 1 required positional argument: 'Loader'，请问问题出在哪里，该怎么解决，谢谢！

find_RCRJ_and_classify.py error

当我是用命令find_RCRJ_and_classify.py，最后报错
Error in seq_len(limitThreshold) : 参数必需能被强制改变成非负整数
Calls: classification -> sapply -> lapply
此外: Warning message:
In max(numeric(0), ..., na.rm = na.rm) : max里所有的参数都不存在；回覆-Inf
停止执行

请问怎么能解决这个问题，谢谢

Issue of find_RCRJ_and_classify.py with parameter merge==T

Hi, when using find_RCRJ_and_classify.py, I found rcrj was missing in the main function with parameter merge==T. Maybe it should be "merge_result.RCRJ_result.csv" ?

Access to necessary data for running Circcode

hi guys,
it is not clear to me where you have acquired the sequence of ribosomal RNA for human from ensembl.
Similarly, it is not clear to me what you mean by coding and non-coding sequences
Also I was wondering if the tool can be used on RNA seq data from ribosomal RNA depleted RNA seq

regards

could not find 'one_step_script.sh'

Hi, i can find 'one_step_script.sh' nowhere.