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vsbuffalo / findorf

ORF prediction of de novo transcriptome assemblies
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findorf giving errors #4

Open yandazeng opened 8 years ago

yandazeng commented 8 years ago

Hello Vince Buffalo,

the findorf program is very useful for me , but when i tried to use it ,it always send errors. My linux os is ubuntu biolinux 7, python version is 2.7, biopython is 1.6, Numpy is installed also xml file is from the result of Blast+,

[join] loading all contig sequences... done. [join] processing BLAST file 'Gr'... Traceback (most recent call last): File "../../Downloads/findorf-master/findorf/findorf.py", line 144, in contigs = main() File "../../Downloads/findorf-master/findorf/findorf.py", line 141, in main args.func(args) File "../../Downloads/findorf-master/findorf/findorf.py", line 41, in _join_relative_results contigs = add_blastx_results(args.ref, args.blastx) File "/home/zeng/Downloads/findorf-master/findorf/blast.py", line 93, in add_blastx_results for record in NCBIXML.parse(blast_file): File "/usr/local/lib/python2.7/dist-packages/Bio/Blast/NCBIXML.py", line 603, in parse expat_parser.Parse("", True) # End of XML record xml.parsers.expat.ExpatError: no element found: line 1734169, column 0

the line 1734169 is the end of xml file, but it always raise error from it .what should i do?

Any suggestions on what I may be doing wrong would be greatly appreciated. Thanks in advance.

yanda

vsbuffalo commented 8 years ago

It sounds like your XML is improperly formatted or truncated. Could you find a very small example XML file that still errors out in the same way and send it?

yandazeng commented 8 years ago

@vsbuffalo Thanks for your suggestion, There do have some errors during the formation of XML file. Findorf is working now when i moved the errors in XML file. Thank you very much!