[Biopython] gff3 file

[Atteyet-Alla.Yassin]

Hallo peter I tried it but, unfortunately get the following and the 
output file was blank:

ukb03709 at zr1005436:~/Dokumente/idiograms$ with open("CP008802.txt", "w") 
as output:
bash: Syntaxfehler beim unerwarteten Wort `('
ukb03709 at zr1005436:~/Dokumente/idiograms$ 
output.write("Seqname\tSource\tfeature\tStart\tEnd\tScore\tStrand\tFrame\tAttributes\n")
bash: Syntaxfehler beim unerwarteten Wort 
`"Seqname\tSource\tfeature\tStart\tEnd\tScore\tStrand\tFrame\tAttributes\n"'
ukb03709 at zr1005436:~/Dokumente/idiograms$     for record in 
SeqIO.parse("CP008802.gbk", "genbank"):
bash: Syntaxfehler beim unerwarteten Wort `('
ukb03709 at zr1005436:~/Dokumente/idiograms$         print("Converting %s" 
% record.name)
bash: Syntaxfehler beim unerwarteten Wort `"Converting %s"'
ukb03709 at zr1005436:~/Dokumente/idiograms$         for f in record.features:
 >             if f.type != "gene":
bash: Syntaxfehler beim unerwarteten Wort `if'
ukb03709 at zr1005436:~/Dokumente/idiograms$                 continue
bash: continue: nur in einer `for', `while' oder `until' Schleife sinnvoll.
ukb03709 at zr1005436:~/Dokumente/idiograms$             locus_tag = 
f.qualifiers["locus_tag"][0]
bash: locus_tag: Kommando nicht gefunden.
ukb03709 at zr1005436:~/Dokumente/idiograms$             if 
len(f.location.parts) > 1:
bash: Syntaxfehler beim unerwarteten Wort `f.location.parts'
ukb03709 at zr1005436:~/Dokumente/idiograms$ print("What should we do for 
%s (compound location)? %s" % (locus_tag, f.location))
bash: Syntaxfehler beim unerwarteten Wort `"What should we do for %s 
(compound location)? %s"'
ukb03709 at zr1005436:~/Dokumente/idiograms$                 continue
bash: continue: nur in einer `for', `while' oder `until' Schleife sinnvoll.
ukb03709 at zr1005436:~/Dokumente/idiograms$ 
output.write('%s\tGenBank\t%s\t%i\t%i\t0,000000\t%s\t.\tlocus_tag\t"%s"; 
transcript_id "%s"\n'
bash: Syntaxfehler beim unerwarteten Wort 
`'%s\tGenBank\t%s\t%i\t%i\t0,000000\t%s\t.\tlocus_tag\t"%s"; 
transcript_id "%s"\n''
ukb03709 at zr1005436:~/Dokumente/idiograms$                          % 
(record.name, f.type,
bash: Syntaxfehler beim unerwarteten Wort `record.name,'
ukb03709 at zr1005436:~/Dokumente/idiograms$ f.location.start + 1, 
f.location.end, f.location.strand,
bash: f.location.start: Kommando nicht gefunden.
ukb03709 at zr1005436:~/Dokumente/idiograms$ locus_tag, locus_tag))
bash: Syntaxfehler beim unerwarteten Wort `)'
ukb03709 at zr1005436:~/Dokumente/idiograms$ print("Done")

Am 02.06.2015 um 15:40 schrieb Peter Cock:
>
> On Tue, Jun 2, 2015 at 1:02 PM, Atteyet-Alla.Yassin
> <Atteyet-Alla.Yassin at ukb.uni-bonn.de> wrote:
> > Hallo Peter - Hiier are the messages. May be arised during copy and 
> paste
> > the command you sent? I work with a debian! Therfore please send the 
> command
> > as attached file:
>
> https://gist.github.com/peterjc/bf6796adbc9e7737bff6 is a Python script
> to be run inside Python, not a shell script to run at the terminal prompt.
>
> Download and save it as something like genbank_to_table.py then run
> it like this:
>
> $ python genbank_to_table.py
> Converting CP008802
> What should we do for FB03_00005 (compound location)? join{[0:6](-),
> [2158322:2159306](-)}
> Done
>
> Peter
>

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