[Biopython-dev] 5/19 Stack Overflow - Biopython questions

[Feed My Inbox]

==================================================
1. Can anyone tell me why these lines are not working?
==================================================
May 18, 2010 at 7:21 AM

I am trying to generate tree with fasta file input and Alignment with MuscleCommandline

import sys,os, subprocess
from Bio import AlignIO
from Bio.Align.Applications import MuscleCommandline
cline = MuscleCommandline(input="c:\Python26\opuntia.fasta")
child= subprocess.Popen(str(cline),
                         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([align],outfile,'phylip')
outfile.close()


I always encounter with these problems

Traceback (most recent call last):
  File "<string>", line 244, in run_nodebug
  File "C:\Python26\muscleIO.py", line 11, in <module>
    align=AlignIO.read(child.stdout,"fasta")
  File "C:\Python26\Lib\site-packages\Bio\AlignIO\__init__.py", line 423, in read
    raise ValueError("No records found in handle")
ValueError: No records found in handle

http://stackoverflow.com/questions/2856697/can-anyone-tell-me-why-these-lines-are-not-working

--------------------------------------------------

==================================================
2. Subprocess fails to catch the standard output
==================================================
May 18, 2010 at 7:21 AM

I am trying to generate tree with fasta file input and Alignment with MuscleCommandline

import sys,os, subprocess
from Bio import AlignIO
from Bio.Align.Applications import MuscleCommandline
cline = MuscleCommandline(input="c:\Python26\opuntia.fasta")
child= subprocess.Popen(str(cline),
                         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([align],outfile,'phylip')
outfile.close()


I always encounter with these problems

Traceback (most recent call last):
  File "<string>", line 244, in run_nodebug
  File "C:\Python26\muscleIO.py", line 11, in <module>
    align=AlignIO.read(child.stdout,"fasta")
  File "C:\Python26\Lib\site-packages\Bio\AlignIO\__init__.py", line 423, in read
    raise ValueError("No records found in handle")
ValueError: No records found in handle

http://stackoverflow.com/questions/2856697/subprocess-fails-to-catch-the-standard-output

--------------------------------------------------

===========================================================
Source: http://stackoverflow.com/questions/tagged/?tagnames=biopython&amp;sort=active
This email was sent to biopython-dev at lists.open-bio.org.

Account Login: 
https://www.feedmyinbox.com/members/login/
Don't want to receive this feed any longer? Unsubscribe here: http://www.feedmyinbox.com/feeds/unsubscribe/311789/3e0b2a02a42e76a71e4f14abbbfad2f294f545ce/
-----------------------------------------------------------
This email was carefully delivered by FeedMyInbox.com. 
230 Franklin Road Suite 814 Franklin, TN 37064