Download

[nbisweden]

Download

[Juke34]

Which Biopython do you use? You must use version <=1.77
I have made some fix in speed branch for this, but I'm waiting feedback before to merge

[henricheng]

I have 1.78 installed through conda.
Will the update allow this version or do I have to install 1.77 instead?

[Juke34]

The new version will constraint to install v1.77 and not later version. So do the change yourself in your conda env and it should work. It would be easier.

[henricheng]

I'm still getting this error when trying to download through conda.

Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: \
Found conflicts! Looking for incompatible packages.
This can take several minutes. Press CTRL-C to abort.
failed

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versions

[Juke34]

Then it is better to install the version from the speed branch. Let me know if you do not know how to proceed

[henricheng]

No, I don't.

[Juke34]

Give me feedback if the speed branch is working fine. (If you do not encounter any problem), then I would merge to the master

[henricheng]

I finally got it installed but once I tried to run it I get this error. I provided it a gff and fa file in that order.

#############################################################################
# EMBLmyGFF3 v2                                                             #
# NBIS - National Bioinformatics Infrastructure Sweden                      #
# Authors: Martin Norling, Niclas Jareborg, Jacques Dainat                  #
# Please visit https://github.com/NBISweden/EMBLmyGFF3 for more information #
#############################################################################

Traceback (most recent call last):
File "/Users/chengh1/miniconda3/lib/python3.8/site-packages/Bio/SeqIO/Interfaces.py", line 42, 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 "/Users/chengh1/miniconda3/bin/EMBLmyGFF3", line 33, in
sys.exit(load_entry_point('EMBLmyGFF3==2', 'console_scripts', 'EMBLmyGFF3')())
File "/Users/chengh1/miniconda3/lib/python3.8/site-packages/EMBLmyGFF3-2-py3.8.egg/EMBLmyGFF3/EMBLmyGFF3.py", line 1346, in main
for record in GFF.parse(infile, base_dict=seq_dict):
File "/Users/chengh1/miniconda3/lib/python3.8/site-packages/BCBio/GFF/GFFParser.py", line 745, in parse
for rec in parser.parse_in_parts(gff_files, base_dict, limit_info,
File "/Users/chengh1/miniconda3/lib/python3.8/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/chengh1/miniconda3/lib/python3.8/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/chengh1/miniconda3/lib/python3.8/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/chengh1/miniconda3/lib/python3.8/site-packages/BCBio/GFF/GFFParser.py", line 699, in _lines_to_out_info
fasta_recs = self._parse_fasta(FakeHandle(line_iter))
File "/Users/chengh1/miniconda3/lib/python3.8/site-packages/BCBio/GFF/GFFParser.py", line 560, in _parse_fasta
return list(SeqIO.parse(in_handle, "fasta"))
File "/Users/chengh1/miniconda3/lib/python3.8/site-packages/Bio/SeqIO/init.py", line 627, in parse
i = iterator_generator(handle)
File "/Users/chengh1/miniconda3/lib/python3.8/site-packages/Bio/SeqIO/FastaIO.py", line 181, in init
super().init(source, alphabet=alphabet, mode="t", fmt="Fasta")
File "/Users/chengh1/miniconda3/lib/python3.8/site-packages/Bio/SeqIO/Interfaces.py", line 46, in init
if source.read(0) != "":
TypeError: read() takes 1 positional argument but 2 were given

[Juke34]

could you try in python 3.7?

[Juke34]

And can you share your command?

[henricheng]

This is what I typed in for the command.
I'm not sure how to switch over to python3.7.

chengh1$ EMBLmyGFF3 chr1.gff3 chr1.fasta > results.embl

#############################################################################
# EMBLmyGFF3 v2                                                             #
# NBIS - National Bioinformatics Infrastructure Sweden                      #
# Authors: Martin Norling, Niclas Jareborg, Jacques Dainat                  #
# Please visit https://github.com/NBISweden/EMBLmyGFF3 for more information #
#############################################################################

Traceback (most recent call last):
File "/Users/chengh1/miniconda3/lib/python3.8/site-packages/Bio/SeqIO/Interfaces.py", line 42, 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 "/Users/chengh1/miniconda3/bin/EMBLmyGFF3", line 33, in
sys.exit(load_entry_point('EMBLmyGFF3==2', 'console_scripts', 'EMBLmyGFF3')())
File "/Users/chengh1/miniconda3/lib/python3.8/site-packages/EMBLmyGFF3-2-py3.8.egg/EMBLmyGFF3/EMBLmyGFF3.py", line 1346, in main
for record in GFF.parse(infile, base_dict=seq_dict):
File "/Users/chengh1/miniconda3/lib/python3.8/site-packages/BCBio/GFF/GFFParser.py", line 745, in parse
for rec in parser.parse_in_parts(gff_files, base_dict, limit_info,
File "/Users/chengh1/miniconda3/lib/python3.8/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/chengh1/miniconda3/lib/python3.8/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/chengh1/miniconda3/lib/python3.8/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/chengh1/miniconda3/lib/python3.8/site-packages/BCBio/GFF/GFFParser.py", line 699, in _lines_to_out_info
fasta_recs = self._parse_fasta(FakeHandle(line_iter))
File "/Users/chengh1/miniconda3/lib/python3.8/site-packages/BCBio/GFF/GFFParser.py", line 560, in _parse_fasta
return list(SeqIO.parse(in_handle, "fasta"))
File "/Users/chengh1/miniconda3/lib/python3.8/site-packages/Bio/SeqIO/init.py", line 627, in parse
i = iterator_generator(handle)
File "/Users/chengh1/miniconda3/lib/python3.8/site-packages/Bio/SeqIO/FastaIO.py", line 181, in init
super().init(source, alphabet=alphabet, mode="t", fmt="Fasta")
File "/Users/chengh1/miniconda3/lib/python3.8/site-packages/Bio/SeqIO/Interfaces.py", line 46, in init
if source.read(0) != "":
TypeError: read() takes 1 positional argument but 2 were given

[Juke34]

Could you try -o results.embl instead of > results.embl

[henricheng]

I'm getting the same error message.

chengh1$ EMBLmyGFF3 chr1.gff3 chr1.fasta > results.embl

#############################################################################
# EMBLmyGFF3 v2                                                             #
# NBIS - National Bioinformatics Infrastructure Sweden                      #
# Authors: Martin Norling, Niclas Jareborg, Jacques Dainat                  #
# Please visit https://github.com/NBISweden/EMBLmyGFF3 for more information #
#############################################################################

Traceback (most recent call last):
File "/Users/chengh1/miniconda3/lib/python3.8/site-packages/Bio/SeqIO/Interfaces.py", line 42, 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 "/Users/chengh1/miniconda3/bin/EMBLmyGFF3", line 33, in
sys.exit(load_entry_point('EMBLmyGFF3==2', 'console_scripts', 'EMBLmyGFF3')())
File "/Users/chengh1/miniconda3/lib/python3.8/site-packages/EMBLmyGFF3-2-py3.8.egg/EMBLmyGFF3/EMBLmyGFF3.py", line 1346, in main
for record in GFF.parse(infile, base_dict=seq_dict):
File "/Users/chengh1/miniconda3/lib/python3.8/site-packages/BCBio/GFF/GFFParser.py", line 745, in parse
for rec in parser.parse_in_parts(gff_files, base_dict, limit_info,
File "/Users/chengh1/miniconda3/lib/python3.8/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/chengh1/miniconda3/lib/python3.8/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/chengh1/miniconda3/lib/python3.8/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/chengh1/miniconda3/lib/python3.8/site-packages/BCBio/GFF/GFFParser.py", line 699, in _lines_to_out_info
fasta_recs = self._parse_fasta(FakeHandle(line_iter))
File "/Users/chengh1/miniconda3/lib/python3.8/site-packages/BCBio/GFF/GFFParser.py", line 560, in _parse_fasta
return list(SeqIO.parse(in_handle, "fasta"))
File "/Users/chengh1/miniconda3/lib/python3.8/site-packages/Bio/SeqIO/init.py", line 627, in parse
i = iterator_generator(handle)
File "/Users/chengh1/miniconda3/lib/python3.8/site-packages/Bio/SeqIO/FastaIO.py", line 181, in init
super().init(source, alphabet=alphabet, mode="t", fmt="Fasta")
File "/Users/chengh1/miniconda3/lib/python3.8/site-packages/Bio/SeqIO/Interfaces.py", line 46, in init
if source.read(0) != "":
TypeError: read() takes 1 positional argument but 2 were given

[Juke34]

I didn't pay attention you did not switch to python 3.7. I guess it can fix the problem.
conda install python=3.7

[Juke34]

btw did you try the included test? EMBLmyGFF3-maker-example to be sure it is not related to the provided files

[henricheng]

I'm getting a bunch of errors when I use the conda install python=3.7 command.
But when I run the other one I get this.

chengh1$ EMBLmyGFF3-maker-example
Running the following command: EMBLmyGFF3 --rg REFERENCE_GROUP -i MYLOCUSTAG -p 17285 -m "genomic DNA" -r 1 -t linear -s "Drosophila melanogaster" -x INV -o EMBLmyGFF3-maker-example.embl /Users/chengh1/miniconda3/lib/python3.8/site-packages/EMBLmyGFF3-2-py3.8.egg/examples/maker.gff3 /Users/chengh1/miniconda3/lib/python3.8/site-packages/EMBLmyGFF3-2-py3.8.egg/examples/maker.fa

#############################################################################
# EMBLmyGFF3 v2                                                             #
# NBIS - National Bioinformatics Infrastructure Sweden                      #
# Authors: Martin Norling, Niclas Jareborg, Jacques Dainat                  #
# Please visit https://github.com/NBISweden/EMBLmyGFF3 for more information #
#############################################################################

17:30:58 WARNING feature: Unknown qualifier '_AED' - skipped ]
17:30:58 WARNING feature: Unknown qualifier '_eAED' - skipped
17:30:58 WARNING feature: Unknown qualifier '_QI' - skipped
Conversion done

[Juke34]

Ok the test works. So the problem is either the command or the files you provide as input. Have you check the path and that they are in read? Are you sure there is data inside ?

[henricheng]

I downloaded it with python3.7 and made use that I was in the same directory as my input files and made sure that they contained the correct information for the files, I redownloaded it from the source just to be sure and I still get this error.

$ EMBLmyGFF3 chr2.gff3 chr2.fasta

#############################################################################
# EMBLmyGFF3 v2                                                             #
# NBIS - National Bioinformatics Infrastructure Sweden                      #
# Authors: Martin Norling, Niclas Jareborg, Jacques Dainat                  #
# Please visit https://github.com/NBISweden/EMBLmyGFF3 for more information #
#############################################################################

Traceback (most recent call last):
File "/home/whitehoi/.local/lib/python3.7/site-packages/Bio/SeqIO/Interfaces.py", line 42, 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 "/home/whitehoi/.local/bin/EMBLmyGFF3", line 10, in
sys.exit(main())
File "/home/whitehoi/.local/lib/python3.7/site-packages/EMBLmyGFF3/EMBLmyGFF3.py", line 1346, in main
for record in GFF.parse(infile, base_dict=seq_dict):
File "/home/whitehoi/.local/lib/python3.7/site-packages/BCBio/GFF/GFFParser.py", line 746, in parse
target_lines):
File "/home/whitehoi/.local/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 "/home/whitehoi/.local/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 "/home/whitehoi/.local/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 "/home/whitehoi/.local/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 "/home/whitehoi/.local/lib/python3.7/site-packages/BCBio/GFF/GFFParser.py", line 560, in _parse_fasta
return list(SeqIO.parse(in_handle, "fasta"))
File "/home/whitehoi/.local/lib/python3.7/site-packages/Bio/SeqIO/init.py", line 627, in parse
i = iterator_generator(handle)
File "/home/whitehoi/.local/lib/python3.7/site-packages/Bio/SeqIO/FastaIO.py", line 181, in init
super().init(source, alphabet=alphabet, mode="t", fmt="Fasta")
File "/home/whitehoi/.local/lib/python3.7/site-packages/Bio/SeqIO/Interfaces.py", line 46, in init
if source.read(0) != "":
TypeError: read() takes 1 positional argument but 2 were given

[Juke34]

Again try the test to see if it is suppose to work: EMBLmyGFF3-maker-example
Then show me your folder ls -l

[Juke34]

I guess one of your file is not properly formated or empty

[henricheng]

$ EMBLmyGFF3-maker-example
Running the following command: EMBLmyGFF3 --rg REFERENCE_GROUP -i MYLOCUSTAG -p 17285 -m "genomic DNA" -r 1 -t linear -s "Drosophila melanogaster" -x INV -o EMBLmyGFF3-maker-example.embl /home/whitehoi/.local/lib/python3.7/site-packages/examples/maker.gff3 /home/whitehoi/.local/lib/python3.7/site-packages/examples/maker.fa

#############################################################################
# EMBLmyGFF3 v2                                                             #
# NBIS - National Bioinformatics Infrastructure Sweden                      #
# Authors: Martin Norling, Niclas Jareborg, Jacques Dainat                  #
# Please visit https://github.com/NBISweden/EMBLmyGFF3 for more information #
#############################################################################

10:24:23 WARNING feature: Unknown qualifier '_AED' - skipped ]
10:24:23 WARNING feature: Unknown qualifier '_eAED' - skipped
10:24:23 WARNING feature: Unknown qualifier '_QI' - skipped
Conversion done

$ ls -l
total 4482
-rwx------ 1 whitehoi whitehoi 826861 Oct 19 09:24 chr2.fasta
-rwx------ 1 whitehoi whitehoi 1633600 Mar 6 2020 chr2.gff3
-rwx------ 1 whitehoi whitehoi 2127177 Nov 19 10:24 EMBLmyGFF3-maker-example.embl

[henricheng]

The files I downloaded were the ones from EMBOSS for the yeast genome.

[Juke34]

Test still working so probably something with the file. Could you give me a link to the files I will give a try

[henricheng]

https://www.ncbi.nlm.nih.gov/nuccore/BK006935

Then for the fast file, I just used the standard s288c genome.

[Juke34]

I do not see any gff file at this address

[henricheng]

Yes sorry, I did it manually above the title there is a thing that says "Send to: " and I choose "Destination" then changed the "Format" to "GFF3"
chr1.gff.txt

[Juke34]

Could you give me the link to the Fasta to be sure I use the same?