[Biopython] gff3 file

[Atteyet-Alla.Yassin]

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:

ukb03709 at zr1005436:~/Dokumente/idiograms$ from Bio import SeqIO
from: can't read /var/mail/Bio
ukb03709 at zr1005436:~/Dokumente/idiograms$ with open("bac.out", "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("bac.txt", "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 `$'"What should we do for %s 
(compound location)?\n%s"''
ukb03709 at zr1005436:~/Dokumente/idiograms$                 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 
`$'\'%s\\tGenBank\\t%s\\t%i\\t%i\\t0,000000\\t%s\\t.\\tlocus_tag\\t"%s";\ntranscript_id 
"%s"\\n\'''
ukb03709 at zr1005436:~/Dokumente/idiograms$                          % 
(record.name, f.type,
bash: Syntaxfehler beim unerwarteten Wort `record.name,'
ukb03709 at zr1005436:~/Dokumente/idiograms$ f.location.start + 1, 
f.location.end,
bash: f.location.start: Kommando nicht gefunden.
ukb03709 at zr1005436:~/Dokumente/idiograms$ f.location.strand,
bash: f.location.strand,: Kommando nicht gefunden.
ukb03709 at zr1005436:~/Dokumente/idiograms$ locus_tag, locus_tag))
bash: Syntaxfehler beim unerwarteten Wort `)'
ukb03709 at zr1005436:~/Dokumente/idiograms$ print("Done")
bash: Syntaxfehler beim unerwarteten Wort `"Done"'
ukb03709 at zr1005436:~/Dokumente/idiograms$