how to run eprimer3 via terminal and through biopython? there is not a problem with the code, but rather with the eprimer3 command. Suggestions? [closed]

1

neemias @ 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 = First3Commandline ()

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

cl.set_parameter ("- outfile", "/home/neemias/Documents/google_drive/agronomy/python/out.pr3")

cl.set_parameter ("- numreturn", 1)

First3Commandline (cmd = 'eprimer3', outfile = '/ home / neemias / Documents / google_drive / agronomy / python / out.pr3', sequence = '/ home / neemias / Documents / google_drive / agronomy / python / seq1. fasta ', numreturn = 1)

print cl

eprimer3 -outfile = / home / neemias / Documents / google_drive / agronomy / python / out.pr3 -sequence = / home / neemias / Documents / google_drive / agronomy / python / seq1.fasta -numreturn = 1

import them

os.system (str (cl))

Pick PCR primers and hybridization oligos

Error: Missing SEQUENCE tag

0

quit ()

(DOES NOT WORK ON PYTHON)

neemias @ debian: / $ eprimer3 -outfile = / home / neemias / Documents / google_drive / agronomy / python / out.pr3 -sequence = / home / neemias / Documents / google_drive / agronomy / python / seq1.fasta -numreturn = 1

Pick PCR primers and hybridization oligos

Error: Missing SEQUENCE tag

(DOES NOT WORK ON THE TERMINAL)

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

Pick PCR primers and hybridization oligos

(WORKS AT TERMINAL)

    
asked by anonymous 24.07.2017 / 01:25

0 answers