# Path: inmembrane/helpers.py
# def seqid_to_filename(seqid):
#     """
#     Makes a sequence id filename friendly.
#     (eg, replaces '|' with '_')
#     """
#     return seqid.replace("|", "_")
# 
# def run(cmd, out_file=None):
#     """
#     Wrapper function to run external program so that existence
#     of binary can be checked and the output directed to a specific
#     file.
#     """
#     log_stderr("# " + cmd + " > " + out_file)
#     if os.path.isfile(out_file) and (out_file != None):
#         log_stderr("# -> skipped: %s already exists" % out_file)
#         return
#     binary = cmd.split()[0]
#     is_binary_there = False
#     if os.path.isfile(binary):
#         is_binary_there = True
#     if run_with_output('which ' + binary):
#         is_binary_there = True
#     if not is_binary_there:
#         raise IOError("Couldn't find executable binary '" + binary + "'")
#     if out_file:
#         os.system(cmd + " > " + out_file)
#     else:
#         os.system(cmd)
# 
# def write_proteins_fasta(
#         fasta_filename, proteins, seqids, width=50):
#     """
#     Creates a fasta file of the sequences of a subset of the proteins.
#     """
#     f = open(fasta_filename, "w")
#     out = proteins_to_fasta(proteins, seqids=seqids, width=width)
#     f.write(out)
#     f.close()


import os
import re
from inmembrane.helpers import seqid_to_filename, run, write_proteins_fasta
# -*- coding: utf-8 -*-

citation = {'ref': u"﻿Jones DT. Improving the accuracy of transmembrane "
                   u"protein topology prediction using evolutionary "
                   u"information. Bioinformatics (Oxford, England) "

# Path: inmembrane/helpers.py
# def seqid_to_filename(seqid):
#     """
#     Makes a sequence id filename friendly.
#     (eg, replaces '|' with '_')
#     """
#     return seqid.replace("|", "_")
# 
# def run(cmd, out_file=None):
#     """
#     Wrapper function to run external program so that existence
#     of binary can be checked and the output directed to a specific
#     file.
#     """
#     log_stderr("# " + cmd + " > " + out_file)
#     if os.path.isfile(out_file) and (out_file != None):
#         log_stderr("# -> skipped: %s already exists" % out_file)
#         return
#     binary = cmd.split()[0]
#     is_binary_there = False
#     if os.path.isfile(binary):
#         is_binary_there = True
#     if run_with_output('which ' + binary):
#         is_binary_there = True
#     if not is_binary_there:
#         raise IOError("Couldn't find executable binary '" + binary + "'")
#     if out_file:
#         os.system(cmd + " > " + out_file)
#     else:
#         os.system(cmd)
# 
# def write_proteins_fasta(
#         fasta_filename, proteins, seqids, width=50):
#     """
#     Creates a fasta file of the sequences of a subset of the proteins.
#     """
#     f = open(fasta_filename, "w")
#     out = proteins_to_fasta(proteins, seqids=seqids, width=width)
#     f.write(out)
#     f.close()


# Path: inmembrane/plugins/memsat3.py
import os
import re
from inmembrane.helpers import seqid_to_filename, run, write_proteins_fasta

# -*- coding: utf-8 -*-

citation = {'ref': u"﻿Jones DT. Improving the accuracy of transmembrane "
                   u"protein topology prediction using evolutionary "
                   u"information. Bioinformatics (Oxford, England) "

                   u"2007 Mar;23(5):538-44. \n"