Open Anto007 opened 5 years ago
kblin
commented
5 years ago This is a record type I've never seen before, and it looks like Biopython doesn't like it. I'll open a bug report with Biopython to get it fixed, and then I can make sure ncbi-acc-download supports it.
Anto007
commented
5 years ago Thank you so much for your quick response. Any possible help in this regard would really make my day
kblin
commented
5 years ago I've opened a Biopython bug https://github.com/biopython/biopython/issues/2268, let's see what they think about this.
Anto007
commented
5 years ago Thanks; fingers crossed! Also, how to get the fasta file for this record on recursive mode? For example, I tried the below and I get an empty fasta file:
ncbi-acc-download --recursive NZ_AQZU00000000.1 --format fasta
ncbi-acc-download --recursive NZ_AQZU00000000.1 does appear to give me the correct .gbk file
kblin
commented
5 years ago Hm, I think I've never tried this for FASTA files. I don't think it'll work out of the box.
Anto007
commented
5 years ago Thanks again for your super-quick responses. I think I can live with .gbk files for now :-)
Anto007
commented
5 years ago Hi, I was wondering if you have managed to find any sort of fix for "ncbi-acc-download --recursive GHGH00000000.1"? My intention is certainly not to push you here but I would be very grateful for any new pointers.
kblin
commented
5 years ago This will only be fixed once Biopython 1.75 is released, as that contains a fix for the problem.
Anto007
commented
5 years ago Many thanks for your response. I will await the release of Biopython 1.75.
kblin
commented
4 years ago End of year cleaning of old issues. This one should be fixed by current Biopython versions.
Use pip install --upgrade biopython in the same virtualenv you installed ncbi-acc-download into, and you should be good to go.
Please don't hesitate to comment if the issue still exists after upgrading Biopython.
Anto007
commented
4 years ago Thank you so much for remembering to follow up with this- much appreciated! I would like to report that although there are no error messages being output now after the biopython upgrade, the command ncbi-acc-download --recursive GHGH00000000.1 merely downloads the master record gbk file and not all of the records that are covered by the master record. Unfortunately, the purpose of having 'recursive' doesn't seem to be served here.
kblin
commented
4 years ago Thanks for testing. I'll have a look at this.
kblin
commented
4 years ago Ah, shoot, it looks like there's still an issue in the Biopython support for this. 😞 We need https://github.com/biopython/biopython/pull/2432 to land and be shipped first. And I think I still need a change in ncbi-acc-download as well.
kblin
commented
4 years ago Ok, another try. Once Biopython releases 1.77, 789a34b4da52c43923ebff47c3141b4468f46892 should have fixed it. Install the 0.2.6 version of ncbi-acc-download I just to get the fix.
Anto007
commented
4 years ago Many thanks for the update; once biopython 1.77 is out, I'll give a try with ncbi-acc-download v0.2.6
I tried ncbi-acc-download --recursive GHGH00000000.1 and I got the below error message. Any help here would be very much appreciated.
Traceback (most recent call last): File "/home/user/tools/Python-3.6.2/virtualenv3/bin/ncbi-acc-download", line 10, in
sys.exit(main())
File "/home/user/tools/Python-3.6.2/virtualenv3/lib/python3.6/site-packages/ncbi_acc_download/main.py", line 54, in main
download_to_file(dl_id, config, filename, append)
File "/home/user/tools/Python-3.6.2/virtualenv3/lib/python3.6/site-packages/ncbi_acc_download/core.py", line 118, in download_to_file
_validate_and_write(r, fh, dl_id, config)
File "/home/user/tools/Python-3.6.2/virtualenv3/lib/python3.6/site-packages/ncbi_acc_download/core.py", line 162, in _validate_and_write
downloaded = download_wgs_parts(handle, config)
File "/home/user/tools/Python-3.6.2/virtualenv3/lib/python3.6/site-packages/ncbi_acc_download/wgs.py", line 107, in download_wgs_parts
records = list(SeqIO.parse(handle, config.format))
File "/home/user/tools/Python-3.6.2/virtualenv3/lib/python3.6/site-packages/Bio/SeqIO/init.py", line 655, in parse
for r in i:
File "/home/user/tools/Python-3.6.2/virtualenv3/lib/python3.6/site-packages/Bio/GenBank/Scanner.py", line 489, in parse_records
record = self.parse(handle, do_features)
File "/home/user/tools/Python-3.6.2/virtualenv3/lib/python3.6/site-packages/Bio/GenBank/Scanner.py", line 473, in parse
if self.feed(handle, consumer, do_features):
File "/home/user/tools/Python-3.6.2/virtualenv3/lib/python3.6/site-packages/Bio/GenBank/Scanner.py", line 445, in feed
self._feed_feature_table(consumer, self.parse_features(skip=False))
File "/home/user/tools/Python-3.6.2/virtualenv3/lib/python3.6/site-packages/Bio/GenBank/Scanner.py", line 171, in parse_features
raise ValueError("Premature end of features table, marker '//' found")
ValueError: Premature end of features table, marker '//' found