I create fasta file input and alignment with the MuscleCommandline I always Traceback (most recent call final): File "& lt; string>", line 244, "C: \ Python26 \ muscleIO.py" in run_nodebug file, encounter with these issues
Import sys I'm trying to import bio-import from Bio.Align.Applications, by subprocessing imported AlignIO MuscleCommandline, Kline = MuscleCommandline (input = "c: \ Python26 \ opuntia.fasta") child = subprocess.Popen (STR (kline), stdout = Subprocess.PIPE, stderr = subprocess.PIPE, shell = (sys.platform = "win32"!)) Align = AlignIO.read (child.stdout, "fasta") outfile = open ('c: \ Python26 \ opuntia Phy ',' w ') AlignIO.write ([aligned], outfile,' phylip ') outfile.close ()
, Line 11, & lt; Module & gt; Align = AlignIO.read (child.stdout, "fasta") The file "C: \ Python26 \ Lib \ site-package \ bios \ AlignIO \ __ init__.py", line 423, reading ValueError ("lift no record Not found in the handle ") ValueError: found in the handle no record
Biopython 1.54 a Fixed version of Bio Filo module was released today. I updated the document with an example pipeline to create trees. For simplicity examples, the use of clustal is to align sequences and produce trees instead of mosque and filip, but most codes are still the same or similar.
If you have already created a tree with the file (by using the .phy alignment as input), then you can use Phylo instances Can follow. Phillip creates a Nook File with the name "Nutrition" or "Foo Tree".
(Feel free to merge it with Brad's reply; I can not write any comment in that thread.)
Comments
Post a Comment