how to run eprimer3 via terminal and via biopython? there is no problem with the code, but rather with the eprimer3 command. Suggestions?

Question

nemias@debian:/$ python

Python 2.7.9 (default, Aug 13 2016, 16:41:35)

[GCC 4.9.2] on Linux2

Type "help", "copyright", "Credits" or "License" for more information.

import Bio

from Bio.Emboss.Applications import Primer3commandline

from Bio.Emboss import Primer3

cl = Primer3commandline()

cl.set_parameter("-Sequence", "/home/Neemias/Documents/google_drive/agronomy/python/seq1.fasta")

cl.set_parameter("-outfile", "/home/Neemias/Documents/google_drive/agronomy/python/oct.Pr3")

cl.set_parameter("-numreturn", 1)

Primer3commandline(cmd='eprimer3', outfile='/home/Neemias/Documents/google_drive/agronomy/python/oct.Pr3', Sequence='/home/Neemias/Documents/google_drive/agronomy/python/seq1.fasta', numreturn=1)

print cl

eprimer3 -outfile=/home/Neemias/Documents/google_drive/agronomy/python/oct.Pr3 -Sequence=/home/Neemias/Documents/google_drive/agronomy/python/seq1.fasta -numreturn=1

import the

os.system(str(cl))

Pick PCR primers and hybridization oligos

Error: Missing SEQUENCE tag

0

quit()

(DOESN’T WORK IN PYTHON)

neemias@debian:/$ eprimer3 -outfile=/home/Neemias/Documents/google_drive/agronomy/python/oct.Pr3 -Sequence=/home/Neemias/Documents/google_drive/agronomy/python/seq1.fasta -numreturn=1

Pick PCR primers and hybridization oligos

Error: Missing SEQUENCE tag

(DOESN’T WORK IN THE TERMINAL)

neemias@debian:/$ EMBOSS_PRIMER32_CORE=/usr/bin/primer3_core eprimer32 -Sequence /home/Neemias/Documents/google_drive/agronomy/python/seq1.fasta -stdout /home/Neemias/Documents/google_drive/agronomy/python/primer.out

Pick PCR primers and hybridization oligos

(WORKS ON THE TERMINAL)