Hallo Peter,
many many thanks it work now. But I have only a small problem. As you
see from the table the tabs are inconsistent with one another. Is there
a possibility to solve this problem?
Seqname Source feature Start End Score Strand Frame
Attributes
CP008802 GenBank gene 417 638 0,000000 1 .
locus_tag "FB03_00010"; transcript_id "FB03_00010"
CP008802 GenBank gene 814 2193 0,000000 -1 .
locus_tag "FB03_00015"; transcript_id "FB03_00015"
CP008802 GenBank gene 2407 3408 0,000000 -1 .
locus_tag "FB03_00020"; transcript_id "FB03_00020"
Am 03.06.2015 um 12:26 schrieb Peter Cock:
>
> Hello again,
>
> You are still trying to run Python command directly in the terminal
> shell, rather than within Python.
>
> When we write "$" we general mean a command to be typed at the
> terminal (Unix or Linux or Mac), e.g.
>
> $ ls -l
>
> that would mean type the letters l, s, space, minus, l, enter. This
> would give a directory listing in long mode (one file per line).
>
> In this case I was suggesting you run:
>
> $ python genbank_to_table.py
>
> (having first saved the example Python script as a file named
> genbank_to_table.py).
>
> As well as "$" to indicate the terminal prompt, you will often see
> people write ">>>" to indicate the Python prompt where you
> would type a Python command to be run inside Python.
>
> Do you know anyone in your group who knows a little Python,
> or about working at the command line? Some in-person help
> would be best. Or an introductory Python text book / tutorial?
>
> Peter
>
> On Wed, Jun 3, 2015 at 10:24 AM, Atteyet-Alla.Yassin
> <Atteyet-Alla.Yassin at ukb.uni-bonn.de> wrote:
> > Hallo peter I tried it but, unfortunately get the following and the
> output
> > file was blank:
> >
> > ukb03709 at zr1005436:~/Dokumente/idiograms$ 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
> >
> >
> >
> > _______________________________________________
> > Biopython mailing list - Biopython at mailman.open-bio.org
> > http://mailman.open-bio.org/mailman/listinfo/biopython
>
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