Mercurial > repos > cpt > cpt_sar_finder

annotate SAR_functions.py @ 2:373c8bca8a82 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
author cpt
date Fri, 05 Jan 2024 05:57:09 +0000
parents 112751823323
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1 #!/usr/bin/env python
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3 import sys
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
4 import argparse
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
5 import os
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
6 import re
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
7 from Bio import SeqIO
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
8
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
9
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
10 class CheckSequence:
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
11 """
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
12 SAR endolysin Verification class, which starts with complete FA file, and is shrunk by each function to reveal best candidates of SAR endolysin proteins
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
13 """
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
14
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
15 def __init__(self, protein_name, protein_data):
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
16 self.name = protein_name
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
17 self.seq = protein_data.seq
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
18 self.description = protein_data.description
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
19 self.size = len(self.seq)
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
20 self.store = {}
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
21
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
22 def check_sizes(self, min, max):
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
23 """check the minimum and maximum peptide lengths"""
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
24 if self.size < min:
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
25 print("too small")
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
26 elif self.size > max:
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
27 print("too large")
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
28 else:
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
29 print(f"{self.name} : {self.seq}")
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
30 return True
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
31
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
32 def check_hydrophobicity_and_charge(
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
33 self, sar_min=15, sar_max=20, perc_residues="SGAT"
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
34 ):
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
35 """verifies the existence of a hydrophobic region within the sequence"""
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
36 hydrophobic_residues = "['FIWLVMYCATGSP']" # fed through regex
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
37 hits = self.store
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
38 pos_res = "RK"
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
39 neg_res = "DE"
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
40
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
41 if self.size > 50:
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
42 seq = self.seq[0:50]
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
43 else:
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
44 seq = self.seq
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
45 for sar_size in range(sar_min, sar_max, 1):
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
46 for i in range(0, len(seq) - sar_size, 1):
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
47 sar_seq = str(seq[i : i + sar_size])
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
48 if re.search(
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
49 (hydrophobic_residues + "{" + str(sar_size) + "}"), sar_seq
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
50 ):
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
51 (
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
52 charge_seq,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
53 charge,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
54 perc_cont,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
55 sar_coords,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
56 nterm_coords,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
57 cterm_coords,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
58 sar_start,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
59 sar_end,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
60 ) = rep_funcs(
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
61 self, seq, i, pos_res, neg_res, sar_seq, perc_residues, sar_size
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
62 )
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
63 storage_dict(
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
64 self=self,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
65 sar_size=sar_size,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
66 sar_seq=sar_seq,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
67 hits=hits,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
68 charge_seq=charge_seq,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
69 charge=charge,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
70 perc_cont=perc_cont,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
71 nterm_coords=nterm_coords,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
72 sar_coords=sar_coords,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
73 cterm_coords=cterm_coords,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
74 sar_start=sar_start,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
75 sar_end=sar_end,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
76 )
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
77 # print("TMDSIZE: {}\tINDEX: {}".format(sar_size,i+1))
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
78 elif "K" in sar_seq[0] and re.search(
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
79 (hydrophobic_residues + "{" + str(sar_size - 1) + "}"), sar_seq[1:]
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
80 ): # check frontend snorkels
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
81 (
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
82 charge_seq,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
83 charge,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
84 perc_cont,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
85 sar_coords,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
86 nterm_coords,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
87 cterm_coords,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
88 sar_start,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
89 sar_end,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
90 ) = rep_funcs(
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
91 self, seq, i, pos_res, neg_res, sar_seq, perc_residues, sar_size
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
92 )
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
93 storage_dict(
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
94 self=self,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
95 sar_size=sar_size,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
96 sar_seq=sar_seq,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
97 hits=hits,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
98 charge_seq=charge_seq,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
99 charge=charge,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
100 perc_cont=perc_cont,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
101 nterm_coords=nterm_coords,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
102 sar_coords=sar_coords,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
103 cterm_coords=cterm_coords,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
104 sar_start=sar_start,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
105 sar_end=sar_end,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
106 )
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
107 # print("TMDSIZE: {}\tINDEX: {}".format(sar_size,i+1))
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
108 elif "K" in sar_seq[-1] and re.search(
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
109 (hydrophobic_residues + "{" + str(sar_size - 1) + "}"), sar_seq[:-1]
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
110 ): # check backend snorkels
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
111 (
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
112 charge_seq,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
113 charge,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
114 perc_cont,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
115 sar_coords,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
116 nterm_coords,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
117 cterm_coords,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
118 sar_start,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
119 sar_end,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
120 ) = rep_funcs(
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
121 self, seq, i, pos_res, neg_res, sar_seq, perc_residues, sar_size
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
122 )
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
123 storage_dict(
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
124 self=self,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
125 sar_size=sar_size,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
126 sar_seq=sar_seq,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
127 hits=hits,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
128 charge_seq=charge_seq,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
129 charge=charge,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
130 perc_cont=perc_cont,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
131 nterm_coords=nterm_coords,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
132 sar_coords=sar_coords,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
133 cterm_coords=cterm_coords,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
134 sar_start=sar_start,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
135 sar_end=sar_end,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
136 )
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
137 # print("TMDSIZE: {}\tINDEX: {}".format(sar_size,i+1))
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
138 continue
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
139
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
140 return hits
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
141
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
142 def shrink_results(self, sar_min=15, sar_max=20, perc_residues="SGAT"):
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
143 """removes repetiive hits, keeps only the shortest and longest of each SAR domain"""
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
144 compare_candidates = {}
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
145 hits = self.check_hydrophobicity_and_charge(sar_min=sar_min, sar_max=sar_max)
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
146 for sar_name, data in hits.items():
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
147 # print(sar_name)
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
148 compare_candidates[sar_name] = {}
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
149 # print("\nThese are the values: {}".format(v))
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
150 # count_of_times = 0
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
151 tmd_log = []
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
152 for sar_size in range(sar_max, sar_min - 1, -1):
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
153 if "TMD_" + str(sar_size) in data:
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
154 tmd_log.append(sar_size)
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
155 # print(tmd_log)
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
156 for idx, the_data in enumerate(data["TMD_" + str(sar_size)]):
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
157 # print(the_data[7])
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
158 # print(the_data)
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
159 # print(f"This is the index: {idx}")
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
160 # print(f"This is the list of data at this index: {the_data}")
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
161 if (
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
162 the_data[7] in compare_candidates[sar_name]
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
163 ): # index to start
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
164 compare_candidates[sar_name][the_data[7]]["count"] += 1
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
165 compare_candidates[sar_name][the_data[7]]["size"].append(
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
166 sar_size
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
167 )
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
168 compare_candidates[sar_name][the_data[7]]["index"].append(
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
169 idx
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
170 )
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
171 else:
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
172 compare_candidates[sar_name][the_data[7]] = {}
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
173 compare_candidates[sar_name][the_data[7]]["count"] = 1
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
174 compare_candidates[sar_name][the_data[7]]["size"] = [
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
175 sar_size
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
176 ]
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
177 compare_candidates[sar_name][the_data[7]]["index"] = [idx]
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
178 hits[sar_name]["biggest_sar"] = tmd_log[0]
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
179 for sar_name, compare_data in compare_candidates.items():
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
180 for data in compare_data.values():
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
181 if len(data["size"]) >= 3:
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
182 # print(f"{each_size} --> {data}")
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
183 minmax = [min(data["size"]), max(data["size"])]
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
184 nonminmax = [x for x in data["size"] if x not in minmax]
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
185 nonminmax_index = []
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
186 for each_nonminmax in nonminmax:
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
187 v = data["size"].index(each_nonminmax)
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
188 x = data["index"][v]
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
189 nonminmax_index.append(x)
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
190 nons = zip(nonminmax, nonminmax_index)
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
191 for value in nons:
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
192 # hits[sar_name]["TMD_"+str(value[0])] = hits[sar_name]["TMD_"+str(value[0])].pop(value[1])
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
193 hits[sar_name]["TMD_" + str(value[0])][value[1]] = [""]
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
194
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
195 return hits
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
196
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
197
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
198 def rep_funcs(self, seq, loc, pos_res, neg_res, sar_seq, perc_residues, sar_size):
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
199 """run a set of functions together before sending the results to the storage dictionary"""
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
200
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
201 charge_seq = str(seq[:loc])
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
202 charge = charge_check(charge_seq, pos_res, neg_res)
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
203 perc_cont = percent_calc(sar_seq, perc_residues, int(sar_size))
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
204 sar_start = loc
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
205 sar_end = loc + sar_size
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
206 sar_coords = "{}..{}".format(loc, loc + sar_size)
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
207 nterm_coords = "{}..{}".format("0", loc - 1)
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
208 cterm_coords = "{}..{}".format(loc + sar_size + 1, self.size)
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
209
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
210 return (
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
211 charge_seq,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
212 charge,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
213 perc_cont,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
214 sar_coords,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
215 nterm_coords,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
216 cterm_coords,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
217 sar_start,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
218 sar_end,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
219 )
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
220
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
221
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
222 ### Extra "helper" functions
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
223 def storage_dict(
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
224 self,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
225 sar_size,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
226 sar_seq,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
227 hits,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
228 charge_seq,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
229 charge,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
230 perc_cont,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
231 nterm_coords,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
232 sar_coords,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
233 cterm_coords,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
234 sar_start,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
235 sar_end,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
236 ): # probably not good to call "self" a param here...definitley not PEP approved...
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
237 """organize dictionary for hydrophobicity check"""
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
238 if self.name not in hits:
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
239 hits[self.name] = {}
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
240 hits[self.name]["description"] = str(self.description)
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
241 hits[self.name]["sequence"] = str(self.seq)
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
242 hits[self.name]["size"] = str(self.size)
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
243 # GAcont = str((str(self.seq).count("G")+str(self.seq).count("A"))/int(self.size)*100)
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
244 # hits[self.name]["GAcont"] = "{:.2f}%".format(float(GAcont))
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
245 if "TMD_" + str(sar_size) not in hits[self.name]:
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
246 hits[self.name]["TMD_" + str(sar_size)] = []
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
247 hits[self.name]["TMD_" + str(sar_size)].append(
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
248 [
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
249 sar_seq,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
250 charge_seq,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
251 charge,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
252 perc_cont,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
253 nterm_coords,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
254 sar_coords,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
255 cterm_coords,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
256 sar_start,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
257 sar_end,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
258 ]
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
259 )
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
260 else:
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
261 hits[self.name]["TMD_" + str(sar_size)].append(
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
262 [
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
263 sar_seq,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
264 charge_seq,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
265 charge,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
266 perc_cont,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
267 nterm_coords,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
268 sar_coords,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
269 cterm_coords,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
270 sar_start,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
271 sar_end,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
272 ]
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
273 )
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
274 else:
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
275 if "TMD_" + str(sar_size) not in hits[self.name]:
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
276 hits[self.name]["TMD_" + str(sar_size)] = []
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
277 hits[self.name]["TMD_" + str(sar_size)].append(
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
278 [
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
279 sar_seq,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
280 charge_seq,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
281 charge,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
282 perc_cont,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
283 nterm_coords,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
284 sar_coords,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
285 cterm_coords,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
286 sar_start,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
287 sar_end,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
288 ]
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
289 )
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
290 else:
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
291 hits[self.name]["TMD_" + str(sar_size)].append(
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
292 [
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
293 sar_seq,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
294 charge_seq,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
295 charge,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
296 perc_cont,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
297 nterm_coords,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
298 sar_coords,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
299 cterm_coords,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
300 sar_start,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
301 sar_end,
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
302 ]
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
303 )
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
304
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
305
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
306 def percent_calc(sequence, residues, size):
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
307 """Calculate the percent of a set of residues within an input sequence"""
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
308 counted = {}
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
309 for aa in sequence:
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
310 # print(aa)
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
311 if aa in counted:
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
312 counted[aa] += 1
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
313 else:
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
314 counted[aa] = 1
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
315 residue_amt = 0
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
316 my_ratios = []
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
317 for res_of_interest in residues:
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
318 try:
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
319 residue_amt = counted[res_of_interest]
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
320 except KeyError:
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
321 residue_amt = 0
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
322 ratio = residue_amt / size
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
323 my_ratios.append((round(ratio * 100, 2)))
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
324
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
325 res_rat = list(zip(residues, my_ratios))
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
326
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
327 return res_rat
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
328
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
329
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
330 def charge_check(charge_seq, pos_res, neg_res):
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
331 charge = 0
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
332 for aa in charge_seq:
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
333 if aa in pos_res:
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
334 charge += 1
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
335 if aa in neg_res:
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
336 charge -= 1
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
337 return charge
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
338
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
339
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
340 if __name__ == "__main__":
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
341 sequence = "MAGBYYYTRLCVRKLRKGGGHP"
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
342 residues = "YL"
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
343 size = len(sequence)
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
344 print(size)
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
345 v = percent_calc(sequence, residues, size)
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
346 print(v)
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
347 for i in v:
112751823323 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
348 print(i)