build.rna_tools.rna_pdb_seq.get_parser() - Code Metrics - Inspection of "rna_tools/rna_cif2pdb.py: "file", help="", default..." - mmagnus/rna-tools - Measure and Improve Code Quality continuously with Scrutinizer

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by Marcin

created 2024-12-09 21:47 UTC

build.rna_tools.rna_pdb_seq.get_parser() A

↳ Parent: build.rna_tools.rna_pdb_seq

Complexity

Conditions

Size

Total Lines	51
Code Lines	20

Duplication

Lines	51
Ratio	100 %

Importance

Changes

Metric	Value
cc	1
eloc	20
nop	0
dl	51
loc	51
rs	9.4
c	0
b	0
f	0

How to fix Long Method

#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""

"""
from __future__ import print_function
import argparse
from icecream import ic
import textwrap
import sys
ic.configureOutput(outputFunction=lambda *a: print(*a, file=sys.stderr))
ic.configureOutput(prefix='> ')
import os

from rna_tools.rna_tools_lib import edit_pdb, add_header, get_version, \
                          collapsed_view, fetch, fetch_ba, fetch_cif, replace_chain, RNAStructure, \
                          select_pdb_fragment, sort_strings, set_chain_for_struc
from rna_tools.tools.rna_x3dna.rna_x3dna import x3DNA



def get_parser():

    parser = argparse.ArgumentParser(
        description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)

    #parser.add_argument('-', "--", help="", default="")

    parser.add_argument('--save-to-file', help='<pdb>.fa', action='store_true')

    parser.add_argument('--compact',
                        help=textwrap.dedent("""with --get-seq, get it in compact view'
$ rna_pdb_tools.py --get-seq --compact *.pdb
# 20_Bujnicki_1
ACCCGCAAGGCCGACGGCGCCGCCGCUGGUGCAAGUCCAGCCACGCUUCGGCGUGGGCGCUCAUGGGU # A:1-68
# 20_Bujnicki_2
ACCCGCAAGGCCGACGGCGCCGCCGCUGGUGCAAGUCCAGCCACGCUUCGGCGUGGGCGCUCAUGGGU # A:1-68
# 20_Bujnicki_3
ACCCGCAAGGCCGACGGCGCCGCCGCUGGUGCAAGUCCAGCCACGCUUCGGCGUGGGCGCUCAUGGGU # A:1-68
# 20_Bujnicki_4

"""), action='store_true')

    parser.add_argument('--color-seq', help='color seq, works with --get-seq', action='store_true')

    parser.add_argument('--chain-first', help="", action='store_true')

    parser.add_argument('--fasta',
                        help= textwrap.dedent("""with --get-seq, show sequences in fasta format,
can be combined with --compact (mind, chains will be separated with ' ' in one line)

$ rna_pdb_tools.py --get-seq --fasta --compact input/20_Bujnicki_1.pdb
> 20_Bujnicki_1
ACCCGCAAGGCCGACGGC GCCGCCGCUGGUGCAAGUCCAGCCACGCUUCGGCGUGGGCGCUCAUGGGU

"""), action='store_true')
    parser.add_argument('--oneline', help="", action='store_true')


    parser.add_argument('--uniq', help=textwrap.dedent("""
rna_pdb_tools.py --get-seq --uniq '[:5]' --compact --chain-first * | sort
A:1-121        ACCUUGCGCAACUGGCGAAUCCUGGGGCUGCCGCCGGCAGUACCC...CA # rp13nc3295_min.out.1
A:1-123        ACCUUGCGCGACUGGCGAAUCCUGAAGCUGCUUUGAGCGGCUUCG...AG # rp13cp0016_min.out.1
A:1-123        ACCUUGCGCGACUGGCGAAUCCUGAAGCUGCUUUGAGCGGCUUCG...AG # zcp_6537608a_ALL-000001_AA
A:1-45 57-71   GGGUCGUGACUGGCGAACAGGUGGGAAACCACCGGGGAGCGACCCGCCGCCCGCCUGGGC # solution
"""))

    parser.add_argument('--renum-atoms', help='renumber atoms, tested with --get-seq',
                         action='store_true')
    parser.add_argument("-v", "--verbose",
                        action="store_true", help="be verbose")
    parser.add_argument("file", help="", default="") # nargs='+')
    return parser


if __name__ == '__main__':
        parser = get_parser()
        args = parser.parse_args()

        # quick fix - make a list on the spot
        if list != type(args.file):
            args.file = [args.file]
        ##################################
        analyzed = []
        for f in args.file:
            #####################################
            if args.uniq:
                subname = eval('f' + args.uniq)
                if subname in analyzed:
                    continue
                else:
                    analyzed.append(subname)
            ########
            s = RNAStructure(f)
            if not s.is_pdb():
                print('Error: Not a PDB file %s' % f)
                sys.exit(1)
            s.decap_gtp()
            s.std_resn()
            s.remove_hydrogen()
            s.remove_ion()
            s.remove_water()
            if args.renum_atoms:
                s.renum_atoms()
            s.fix_O_in_UC()
            s.fix_op_atoms()

            output = ''

            # with # is easier to grep this out
            if args.fasta:
                # s.fn vs s.name
                output += s.get_seq(compact=args.compact, chainfirst=args.chain_first, fasta=args.fasta, addfn=s.name, color=args.color_seq) + '\n'
            elif args.oneline:
                output += s.get_seq(compact=args.compact, chainfirst=args.chain_first, color=args.color_seq).strip() + ' # '+ os.path.basename(f.replace('.pdb', '')) + '\n'
            else:
                output += '# ' + os.path.basename(f.replace('.pdb', '')) + '\n'
                output += s.get_seq(compact=args.compact, chainfirst=args.chain_first, color=args.color_seq) + '\n'

            try:
                sys.stdout.write(output)
                sys.stdout.flush()
            except IOError:
                pass

            if args.save_to_file:
                 from rna_pdb_fetch_header import fetch_pdb_header
                 pdb_id = f.split('/')[-1].split('_')[0]
                 header_info = fetch_pdb_header(pdb_id)
                 title = header_info.get('entry', {}).get('struct', {}).get('title', 'Title not found')
                 output = '# ' + title + '\n' + output
                 with open(f.replace('.pdb', '.txt'), 'w') as out:
                    out.write(output)
                    print(output)




1		#!/usr/bin/env python
2		# -- coding: utf-8 --
3		"""
4
5		"""
6		from __future__ import print_function
7		import argparse
8		from icecream import ic
9		import textwrap
10		import sys
11		ic.configureOutput(outputFunction=lambda a: print(a, file=sys.stderr))
12		ic.configureOutput(prefix='> ')
13		import os
14
15		from rna_tools.rna_tools_lib import edit_pdb, add_header, get_version, \
16		collapsed_view, fetch, fetch_ba, fetch_cif, replace_chain, RNAStructure, \
17		select_pdb_fragment, sort_strings, set_chain_for_struc
18		from rna_tools.tools.rna_x3dna.rna_x3dna import x3DNA
19
20
21
22	View Code Duplication	def get_parser():
		0 ignored issues – show Duplication introduced 2024-12-09 21:50 UTC by Report Bug Copy Issue Report This code seems to be duplicated in your project. Loading history...
23		parser = argparse.ArgumentParser(
24		description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)
25
26		#parser.add_argument('-', "--", help="", default="")
27
28		parser.add_argument('--save-to-file', help='<pdb>.fa', action='store_true')
29
30		parser.add_argument('--compact',
31		help=textwrap.dedent("""with --get-seq, get it in compact view'
32		$ rna_pdb_tools.py --get-seq --compact *.pdb
33		# 20_Bujnicki_1
34		ACCCGCAAGGCCGACGGCGCCGCCGCUGGUGCAAGUCCAGCCACGCUUCGGCGUGGGCGCUCAUGGGU # A:1-68
35		# 20_Bujnicki_2
36		ACCCGCAAGGCCGACGGCGCCGCCGCUGGUGCAAGUCCAGCCACGCUUCGGCGUGGGCGCUCAUGGGU # A:1-68
37		# 20_Bujnicki_3
38		ACCCGCAAGGCCGACGGCGCCGCCGCUGGUGCAAGUCCAGCCACGCUUCGGCGUGGGCGCUCAUGGGU # A:1-68
39		# 20_Bujnicki_4
40
41		"""), action='store_true')
42
43		parser.add_argument('--color-seq', help='color seq, works with --get-seq', action='store_true')
44
45		parser.add_argument('--chain-first', help="", action='store_true')
46
47		parser.add_argument('--fasta',
48		help= textwrap.dedent("""with --get-seq, show sequences in fasta format,
49		can be combined with --compact (mind, chains will be separated with ' ' in one line)
50
51		$ rna_pdb_tools.py --get-seq --fasta --compact input/20_Bujnicki_1.pdb
52		> 20_Bujnicki_1
53		ACCCGCAAGGCCGACGGC GCCGCCGCUGGUGCAAGUCCAGCCACGCUUCGGCGUGGGCGCUCAUGGGU
54
55		"""), action='store_true')
56		parser.add_argument('--oneline', help="", action='store_true')
57
58
59		parser.add_argument('--uniq', help=textwrap.dedent("""
60		rna_pdb_tools.py --get-seq --uniq '[:5]' --compact --chain-first * \| sort
61		A:1-121 ACCUUGCGCAACUGGCGAAUCCUGGGGCUGCCGCCGGCAGUACCC...CA # rp13nc3295_min.out.1
62		A:1-123 ACCUUGCGCGACUGGCGAAUCCUGAAGCUGCUUUGAGCGGCUUCG...AG # rp13cp0016_min.out.1
63		A:1-123 ACCUUGCGCGACUGGCGAAUCCUGAAGCUGCUUUGAGCGGCUUCG...AG # zcp_6537608a_ALL-000001_AA
64		A:1-45 57-71 GGGUCGUGACUGGCGAACAGGUGGGAAACCACCGGGGAGCGACCCGCCGCCCGCCUGGGC # solution
65		"""))
66
67		parser.add_argument('--renum-atoms', help='renumber atoms, tested with --get-seq',
68		action='store_true')
69		parser.add_argument("-v", "--verbose",
70		action="store_true", help="be verbose")
71		parser.add_argument("file", help="", default="") # nargs='+')
72		return parser
73
74
75		if __name__ == '__main__':
76		parser = get_parser()
77		args = parser.parse_args()
78
79		# quick fix - make a list on the spot
80		if list != type(args.file):
81		args.file = [args.file]
82		##################################
83		analyzed = []
84		for f in args.file:
85		#####################################
86		if args.uniq:
87		subname = eval('f' + args.uniq)
88		if subname in analyzed:
89		continue
90		else:
91		analyzed.append(subname)
92		########
93		s = RNAStructure(f)
94		if not s.is_pdb():
95		print('Error: Not a PDB file %s' % f)
96		sys.exit(1)
97		s.decap_gtp()
98		s.std_resn()
99		s.remove_hydrogen()
100		s.remove_ion()
101		s.remove_water()
102		if args.renum_atoms:
103		s.renum_atoms()
104		s.fix_O_in_UC()
105		s.fix_op_atoms()
106
107		output = ''
108
109		# with # is easier to grep this out
110		if args.fasta:
111		# s.fn vs s.name
112		output += s.get_seq(compact=args.compact, chainfirst=args.chain_first, fasta=args.fasta, addfn=s.name, color=args.color_seq) + '\n'
113		elif args.oneline:
114		output += s.get_seq(compact=args.compact, chainfirst=args.chain_first, color=args.color_seq).strip() + ' # '+ os.path.basename(f.replace('.pdb', '')) + '\n'
115		else:
116		output += '# ' + os.path.basename(f.replace('.pdb', '')) + '\n'
117		output += s.get_seq(compact=args.compact, chainfirst=args.chain_first, color=args.color_seq) + '\n'
118
119		try:
120		sys.stdout.write(output)
121		sys.stdout.flush()
122		except IOError:
123		pass
124
125		if args.save_to_file:
126		from rna_pdb_fetch_header import fetch_pdb_header
127		pdb_id = f.split('/')[-1].split('_')[0]
128		header_info = fetch_pdb_header(pdb_id)
129		title = header_info.get('entry', {}).get('struct', {}).get('title', 'Title not found')
130		output = '# ' + title + '\n' + output
131		with open(f.replace('.pdb', '.txt'), 'w') as out:
132		out.write(output)
133		print(output)
134
135
136

mmagnus / rna-tools

Push — master ( 3924a5...7a6481 )

build.rna_tools.rna_pdb_seq.get_parser() A

Complexity

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Duplication

Importance

How to fix Long Method

Long Method

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