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cellranger: how to convert a gtf file to string

I am using a cellranger mkref and faced with a strange python problem with GTF (custome gtf):
Traceback (most recent call last):
File "/home/user/cellranger-6.0.1/lib/python/cellranger/reference.py", line 750, in validate_gtf
subprocess.check_output(cmd, stderr=subprocess.STDOUT)
File "/home/user/cellranger-6.0.1/external/anaconda/lib/python3.7/subprocess.py", line 411, in check_output
**kwargs).stdout
File "/home/user/cellranger-6.0.1/external/anaconda/lib/python3.7/subprocess.py", line 512, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['gtf_to_gene_index', '/home/user/cellranger-6.0.1/indexes', '/home/user/cellranger-6.0.1/indexes/tmp74f_vsxg.json']' returned non-zero exit status 1.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/user/cellranger-6.0.1/bin/rna/mkref", line 139, in <module>
main()
File "/home/user/cellranger-6.0.1/bin/rna/mkref", line 130, in main
reference_builder.build_gex_reference()
File "/home/user/cellranger-6.0.1/lib/python/cellranger/reference.py", line 613, in build_gex_reference
self.validate_gtf()
File "/home/user/cellranger-6.0.1/lib/python/cellranger/reference.py", line 753, in validate_gtf
raise GexReferenceError("Error detected in GTF file: " + exc.output) from exc
TypeError: can only concatenate str (not "bytes") to str
Also, I have the similar gtf file, which cellranger accepts without problems. I compared those files (moreover, the firs one i made from the second one):
file 1: text/plain; charset=us-ascii
file 2: text/plain; charset=us-ascii
Also, I checked with cat -vE and the files is the same
How can I change the file?
Thanks in advance!

I encountered the same issue. The problem was in duplicated IDs in my GTF file. Removing those duplicates solved the issue. See the discussion on Cellranger GitHub: https://github.com/10XGenomics/cellranger/issues/125

read pictures on a local http path

I want to open a picture that is an output of another program as http://192.168.1.100:8123/pic/2021-03-31/snap/238371315.jpg
the code I'm having trouble with:
def get_pic(data):
img_path='http://192.168.1.100:8123/pic/2021-03-31/snap/238371315.jpg'
pic={'image': open(img_path, mode='rb')}
return pic
error:
Traceback (most recent call last):
File "c:\Users\USER\Desktop\linebot-client\client_script.py", line 144, in <module>
main()
File "c:\Users\USER\Desktop\linebot-client\client_script.py", line 134, in main
final_pic =get_pic(data1)
File "c:\Users\USER\Desktop\linebot-client\client_script.py", line 107, in get_pic
pic={'image': open(img_path, mode='rb')}
OSError: [Errno 22] Invalid argument: 'http://192.168.1.100:8123/pic/2021-04-01/snap/939450165.jpg'
is there anything I can change?

Parsing GFF files throws TypeError

I am trying to parse a gif file with Biopython, and am using the sample code from their website. This is the code:
from BCBio import GFF
in_file = "infile.gff"
in_handle = open(in_file)
for rec in GFF.parse(in_handle):
print(rec)
in_handle.close()
When I run the code I get the following error:
Traceback (most recent call last):
File "/Users/juliofdiaz/anaconda2/envs/python37/lib/python3.7/site-packages/Bio/SeqIO/Interfaces.py", line 47, in __init__
self.stream = open(source, "r" + mode)
TypeError: expected str, bytes or os.PathLike object, not FakeHandle
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "get_genes_dpt.py", line 37, in <module>
for rec in GFF.parse(in_handle):
File "/Users/juliofdiaz/anaconda2/envs/python37/lib/python3.7/site-packages/BCBio/GFF/GFFParser.py", line 746, in parse
target_lines):
File "/Users/juliofdiaz/anaconda2/envs/python37/lib/python3.7/site-packages/BCBio/GFF/GFFParser.py", line 322, in parse_in_parts
for results in self.parse_simple(gff_files, limit_info, target_lines):
File "/Users/juliofdiaz/anaconda2/envs/python37/lib/python3.7/site-packages/BCBio/GFF/GFFParser.py", line 343, in parse_simple
for results in self._gff_process(gff_files, limit_info, target_lines):
File "/Users/juliofdiaz/anaconda2/envs/python37/lib/python3.7/site-packages/BCBio/GFF/GFFParser.py", line 637, in _gff_process
for out in self._lines_to_out_info(line_gen, limit_info, target_lines):
File "/Users/juliofdiaz/anaconda2/envs/python37/lib/python3.7/site-packages/BCBio/GFF/GFFParser.py", line 699, in _lines_to_out_info
fasta_recs = self._parse_fasta(FakeHandle(line_iter))
File "/Users/juliofdiaz/anaconda2/envs/python37/lib/python3.7/site-packages/BCBio/GFF/GFFParser.py", line 560, in _parse_fasta
return list(SeqIO.parse(in_handle, "fasta"))
File "/Users/juliofdiaz/anaconda2/envs/python37/lib/python3.7/site-packages/Bio/SeqIO/__init__.py", line 607, in parse
return iterator_generator(handle)
File "/Users/juliofdiaz/anaconda2/envs/python37/lib/python3.7/site-packages/Bio/SeqIO/FastaIO.py", line 183, in __init__
super().__init__(source, mode="t", fmt="Fasta")
File "/Users/juliofdiaz/anaconda2/envs/python37/lib/python3.7/site-packages/Bio/SeqIO/Interfaces.py", line 51, in __init__
if source.read(0) != "":
TypeError: read() takes 1 positional argument but 2 were given
I am not sure how to fix the error as it seems I am passing a str and not a FakeHandle. I am running biopython 1.78 with conda.

Python - causes of ther error "OSError: [Errno 9] Bad file descriptor"

I get the error:
OSError: [Errno 9] Bad file descriptor
when my program calls up the line
with open(cs, 'r') as f :
list = [line.strip() for line in f]
This refers to it opening the file 'cs' and reading it. The list is then created out of every line in the text file
I cant seem to work out what is going wrong, some guidance will be helpful
Thanks
EDIT:
The traceback doesnt seem to provide much:
Traceback (most recent call last):
File "C:\Users\Sammy\Desktop\project 1\project1.py", line 85, in <module>
main() #run mainline
File "C:\Users\Sammy\Desktop\project 1\project1.py", line 83, in main
printCount(countVotes(candidateNumbers,getPapers(voteTXT,candidateNumbers)))
File "C:\Users\Wen\Desktop\project 1\project1.py", line 53, in countVotes
with open(cs, 'r') as `f :

OSError: Result too large

I'am playing around with scapy but i cant get it to work. I tried different code's but all gave me the same output:
Traceback (most recent call last):
File "<module1>", line 7, in <module>
File "C:\Python26\lib\site-packages\scapy\sendrecv.py", line 357, in srp
s = conf.L2socket(iface=iface, filter=filter, nofilter=nofilter, type=type)
File "C:\Python26\lib\site-packages\scapy\arch\pcapdnet.py", line 313, in __init__
self.outs = dnet.eth(iface)
File "dnet.pyx", line 112, in dnet.eth.__init__
OSError: Result too large
Iam using python 2.6 with all dependencies installed for scapy.
How to fix this?