How to call a module written using argparse in iPython notebook

Question

I am trying to pass BioPython sequences to Ilya Stepanov to implement the Ukkonen suffix tree algorithm in iPython notebook environment. I am tripping on the argparse component.

I've never had to deal with argparse directly before. How can I use this without rewriting main ()?

By the way, this entry of the Ukkonen algorithm is simply fantastic .

Answer 1

I had a similar problem before , but using optparse instead of argparse .

You do not need to change anything in the original script, just assign a new sys.argv list sys.argv this:

 if __name__ == "__main__": from Bio import SeqIO path = '/path/to/sequences.txt' sequences = [str(record.seq) for record in SeqIO.parse(path, 'fasta')] sys.argv = ['-f'] + sequences main() 

Answer 2

An alternative to using argparse on Ipython laptops is to pass a string:

args = parser.parse_args() (line 303 from the git repository you are referencing.)

There will be something like:

 parser = argparse.ArgumentParser( description='Searching longest common substring. ' 'Uses Ukkonen\ suffix tree algorithm and generalized suffix tree. ' 'Written by Ilya Stepanov (c) 2013') parser.add_argument( 'strings', metavar='STRING', nargs='*', help='String for searching', ) parser.add_argument( '-f', '--file', help='Path for input file. First line should contain number of lines to search in' ) 

and

args = parser.parse_args("AAA --file /path/to/sequences.txt".split())

Edit: works

Answer 3

I ended up using BioPython to extract the sequences and then to edit the implementation of Ilya Steanov to remove the argparse methods.

 import imp seqs = [] lcsm = imp.load_source('lcsm', '/path/to/ukkonen.py') for record in SeqIO.parse('/path/to/sequences.txt', 'fasta'): seqs.append(record) lcsm.main(seqs) 

For the algorithm, I had main() one argument, its variable strings , but this sends the algorithm a list of special BioPython Sequence objects that the re module does not need. So I had to extract the sequence string

 suffix_tree.append_string(s) 

to

 suffix_tree.append_string(str(s.seq)) 

which seems fragile, but all that I have at the moment.

Answer 4

If you use iPython for testing, converting argparse to class format can be a quick dummy solution.

 class Args: data = './data/penn' model = 'LSTM' emsize = 200 nhid = 200 args=Args() 

The Github page REPO offers a web service transformation. http://35.192.144.192:8000/arg2cls.html
I hope this will be useful for your testing. January 9/19 many bugs fixed.

Transformation scenario. Python3 required.

 python3 [arg2cls.py] [argparse_script.py] 

then copy & paste the class format to replace argparse functions.

 #!/usr/bin/env python3 from collections import OrderedDict import sys import re DBG = False #add_argument(), set_defaults() only available. ListStartPatt = re.compile(r'\s*\[.*') ListStartPatt2 = re.compile(r'\).*\[.*') # list out of function scope. ListPatt = re.compile(r'(\[.*?\])') GbgPatt = re.compile(r'(.*?)\)[^\)]+') # for float('inf') cmplx. GbgPatt2 = re.compile(r'(.*?)\).*') # general gbg, ? for non greedy. LpRegex = re.compile(r'\({1,}\s{0,}') RpRegex = re.compile(r'\s{0,}\){1,}') PrRegex = re.compile(r'\((.*)(\))(?!.*\))') # from \( to last \). CmRegex = re.compile(r'\s{0,},\s{0,}') StrRegex = re.compile(r'\'(.*?)\'') # Argument dict : {arg_name : value} argDct=OrderedDict() # process 'default=' value. def default_value(tval, dtype=''): # string pattern. regres = StrRegex.match(tval) if regres and not re.search('int|float|long|bool|complex', dtype): if DBG: print('default_value: str patt found') tval = regres.group(0) return tval # typed pattern. CommaSeparated = CmRegex.split(tval)[0] if DBG: print('comma sepearated value:', CommaSeparated) if ListStartPatt.match(CommaSeparated) and not ListStartPatt2.match(CommaSeparated): lres = ListPatt.search(tval) if lres: tval = lres.group(1) if DBG: print('list patt exist tval: ', tval) else : tval = CmRegex.split(tval)[0] if DBG: print('no list format tval: ', tval) # if default value is not like - int('inf') , remove characters after ')' garbage chars. ires = RpRegex.split(tval)[0] if not (re.search('int|float|long|bool|complex', ires) and re.search(r'[az]+\(',ires)): if DBG: print('not int("inf") format. Rp removed tval : ', tval) tval = re.split(r'\s{0,}\){1,}',tval)[0] gbg = GbgPatt2.search(tval) if gbg: tval = gbg.group(1) if DBG: print('garbage exist & removed. tval : ', tval) # int('inf') patt. else: if DBG: print('type("inf") value garbaging!') gbg = GbgPatt.search(tval) if gbg: if DBG: print('garbage found, extract!') tval = gbg.group(1) return tval # Handling add_argument() def add_argument(arg_line): global argDct if DBG: print('\nin add_argument : **Pre regex: ', arg_line) ''' argument name ''' # argname = DdRegex.split(arg_line)[1] # Dash or regex for arg name. argname = re.search('\'--(.*?)\'', arg_line) if not argname: argname = re.search('\'-+(.*?)\'', arg_line) # dest= keyword handling. dest = re.search(r',\s*dest\s*=(.*)', arg_line) if dest: dval = dest.group(1) dval = default_value(dval) argname = StrRegex.search(dval) # hyphen(-) to underscore(_) if argname: argname = argname.group(1).replace('-', '_') else : # naive str argname. sres = StrRegex.match(arg_line) if sres: argname = sres.group(1) if not argname: return # no argument name ''' check for syntaxes (type=, default=, required=, action=, help=, choices=) ''' dtype = '' dres = re.search(r',\s*type\s*=\s*(.*)', arg_line) if dres: dtype = dres.group(1) dtype = CmRegex.split(dtype)[0] dfult = re.search(r',\s*default\s*=\s*(.*)', arg_line) rquird = re.search(r',\s*required\s*=\s*(.*)', arg_line) action = re.search(r',\s*action\s*=\s*(.*)', arg_line) hlp = re.search(r',\s*help\s*=\s*(.*)', arg_line) chice = re.search(r',\s*choices\s*=\s*(.*)', arg_line) # help message hlp_msg = '' if hlp: thl = hlp.group(1) if DBG: print('handling help=') hlp_msg = default_value(thl) if hlp_msg: hlp_msg = 'help='+hlp_msg # choice message choice_msg = '' if chice: tch = chice.group(1) if DBG: print('handling choices=') choice_msg = default_value(tch) if choice_msg: choice_msg = 'choices='+choice_msg+' ' ''' argument value ''' # tval: argument value. tval = '' # default exist. if dfult: tval = dfult.group(1) tval = default_value(tval, dtype) if DBG: print('value determined : ', tval) # action or required syntaxes exist. elif action or rquird: if DBG: print('in action/required handling') msg_str = '' if action: tval = action.group(1) msg_str = 'action' elif rquird: tval = rquird.group(1) msg_str = 'required' tval = default_value(tval) tval = ' ** ' + msg_str + ' '+tval+'; '+choice_msg+ hlp_msg # no default, action, required. else : argDct[argname] = ' ** default not found; '+choice_msg+ hlp_msg # value found. if tval: argDct[argname] = tval # Handling set_defaults() def set_defaults(arg_line): global argDct if DBG: print('\nin set_defaults arg_line: ', arg_line) # arguments to process. tv='' # arguments of set_default() SetPatt = re.compile(r'(.+=.+\)?)') sres = SetPatt.match(arg_line) if sres: tv = sres.group(1) if DBG: print("setPatt res: ", tv) tv = re.sub(r'\s+','', tv) if DBG: print('\nset_default values: ', tv) # one arguemnt regex. SetArgPatt = re.compile(r',?([^=]+=)[^=,]+,?') # handling multiple set_default() arguments. (may have a bug) while True: tname='' tval ='' tnv='' # func closed. if re.match(r',*\).*',tv): tv='' break if DBG: print('set_default remaining: ', tv) nres = SetArgPatt.match(tv) if nres: tname = nres.group(1) if len(tv.split(tname, 1)) > 1: tval = tv.split(tname,1)[1] tval = default_value(tval) tnv=tname+tval tname = tname.rsplit('=',1)[0] if DBG: print('set_default tnam: ', tname) print('set_default tval: ', tval) if tname: argDct[tname] = tval # split with processed argument. tv = tv.split(tnv) if len(tv) > 1: tv = tv[1] # no more value to process else: break # no arg=value pattern found. else: break # Remove empty line & Concatenate line-separated syntax. def preprocess(fname): try : with open(fname, 'r', encoding='UTF8') as f: txt = f.read() t = txt.splitlines(True) t = list( filter(None, t) ) # remove empty line t = [x for x in t if not re.match(r'\s{0,}\n',x)] # concatenate multiple lined arguments. # empl : lines to be deleted from t[]. empl = [] for i in range(len(t)-1, 0, -1): if not re.search('add_argument|set_defaults', t[i]): t[i-1] += t[i] t[i-1]=re.sub(r'\n{0,}','',t[i-1]) t[i-1]=re.sub(r'\s{1,}',' ',t[i-1]) empl.append(t[i]) for d in empl: t.remove(d) for i, line in enumerate(t): t[i] = line.replace('\"', '\'').split('parse_args()')[0] return t except IOError: print('IOError : no such file.', fname) sys.exit() def transform(fname): # t : list() contains add_argument|set_defaults lines. arg_line_list = preprocess(fname) for i, arg_line in enumerate(arg_line_list): t = PrRegex.search(arg_line) if t: t = t.group(1) # t: content of add_argument Parentheses. else : continue # nothing to parse. if re.search(r'add_argument\s*\(', arg_line): add_argument(t) elif re.search(r'set_defaults\s*\(',arg_line): set_defaults(t) else : # Nothing to parse. continue print('\nclass Args:') for i in argDct: print(' ',i, '=', argDct[i]) print() print('args=Args()') def main(): if len(sys.argv) <2: print('Usage : python arg2cls.py [target.py] [target2.py(optional)] ...') sys.exit(0) sys.argv.pop(0) #handling multiple file input. for fname in sys.argv: transform(fname) if(__name__ == "__main__"): main() 

Answer 5

I am facing a similar problem when calling argsparse, which was caused by the '-f' line. Just removing it from sys.srgv will get things done.

 import sys if __name__ == '__main__': if '-f' in sys.argv: sys.argv.remove('-f') main() 

Answer 6

Clean sys.argv

 import sys; sys.argv=['']; del sys 

https://github.com/spyder-ide/spyder/issues/3883#issuecomment-269131039