Mercurial > repos > abims-sbr > mutcount

annotate scripts/S02b_study_seq_composition_nuc.py @ 1:8de21b6eb110 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
author abims-sbr
date Wed, 27 Sep 2017 10:04:08 -0400
parents 78dd6454f6f0
children 988467f963f0
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
1 #!/usr/bin/env python
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
2 ## Author: Eric FONTANILLAS
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
3 ## Date: 21.12.10
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
4 ## Object: Test for compositional bias in genome and proteome as marker of thermal adaptation (comparison between 2 "hot" species: Ap and Ps and one "cold" species: Pg)
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
5
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
6
1
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
7 import sys,os,shutil,subprocess, string
0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
8
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
9 #############
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
10 ### DEF 0 ###
1
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
11
0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
12 def simplify_fasta_name(fasta_name,LT):
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
13 for abbreviation in LT:
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
14 if abbreviation in fasta_name:
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
15 new_fasta_name = abbreviation
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
16
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
17 return(new_fasta_name)
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
18 ##########################################
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
19
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
20 ###########
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
21 ## DEF1 ##
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
22 ###########
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
23 ## Generates bash, with key = fasta name; value = sequence (WITH GAP, IF ANY, REMOVED IN THIS FUNCTION)
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
24
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
25 def dico(fasta_file,LT):
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
26
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
27 count_fastaName=0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
28 F1 = open(fasta_file, "r")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
29
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
30 bash1 = {}
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
31 while 1:
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
32 nextline = F1.readline()
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
33 #print nextline
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
34 if not nextline :
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
35 break
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
36
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
37 if nextline[0] == ">":
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
38 count_fastaName = count_fastaName + 1
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
39 fasta_name = nextline[1:-1]
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
40 nextline = F1.readline()
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
41 sequence = nextline[:-1]
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
42
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
43 if fasta_name not in bash1.keys():
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
44 fasta_name = simplify_fasta_name(fasta_name,LT) ### DEF 0 ###
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
45 bash1[fasta_name] = sequence
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
46 else:
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
47 print fasta_name
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
48
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
49 # Find alignment length
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
50 kk = bash1.keys()
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
51 key0 = kk[0]
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
52 seq0 = bash1[key0]
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
53 ln_seq = len(seq0)
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
54
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
55 F1.close()
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
56
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
57 return(bash1)
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
58 #####################################
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
59
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
60
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
61
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
62 ##################
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
63 ###### DEF2 ######
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
64 ##################
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
65 def base_composition(seq):
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
66 count_A=string.count(seq, "A") + string.count(seq, "a")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
67 count_T=string.count(seq, "T") + string.count(seq, "t")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
68 count_C=string.count(seq, "C") + string.count(seq, "c")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
69 count_G=string.count(seq, "G") + string.count(seq, "g")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
70 ## 3 ## Nucleotide proportions
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
71 ln = count_C+count_G+count_T+count_A
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
72 if (ln!=0):
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
73
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
74 CG = count_C+count_G
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
75 AT = count_T+count_A
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
76
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
77 AG = count_A+count_G
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
78 TC = count_T+count_C
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
79
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
80 ## 1 ## Search for compositional bias in genome as marker of thermal adaptation: CG vs AT
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
81 ratio_CG_AT = float(CG)/float(AT)
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
82 percent_CG = float(CG)/(float(AT) + float(CG))*100
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
83
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
84 ## 2 ## Search for compositional bias in genome as marker of thermal adaptation: AG vs TC
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
85 ratio_purine_pyrimidine=float(AG)/float(TC)
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
86 percent_purine=float(AG)/(float(AG)+float(TC))*100
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
87
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
88
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
89 prop_A = float(count_A)/float(ln)
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
90 prop_T = float(count_T)/float(ln)
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
91 prop_C = float(count_C)/float(ln)
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
92 prop_G = float(count_G)/float(ln)
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
93 else:
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
94 percent_CG=0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
95 percent_purine=0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
96 prop_A=0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
97 prop_T=0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
98 prop_C=0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
99 prop_G=0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
100
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
101 return(percent_CG, percent_purine, prop_A, prop_T, prop_C, prop_G)
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
102 ##############################################
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
103
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
104 ##################
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
105 ###### DEF3 ######
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
106 ##################
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
107 def purine_loading(seq):
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
108 count_A=string.count(seq, "A") + string.count(seq, "a")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
109 count_T=string.count(seq, "T") + string.count(seq, "t")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
110 count_C=string.count(seq, "C") + string.count(seq, "c")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
111 count_G=string.count(seq, "G") + string.count(seq, "g")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
112 ## 3 ## Nucleotide proportions
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
113 TOTAL = count_C+count_G+count_T+count_A
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
114 if (TOTAL!=0):
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
115
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
116 ## PLI : Purine loading indice (Forsdyke et al.)
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
117 # (G-C)/N * 1000 et (A-T)/N * 1000
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
118
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
119 DIFF_GC = count_G - count_C
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
120 DIFF_AT = count_A - count_T
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
121
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
122 # Per bp
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
123 PLI_GC = float(DIFF_GC)/float(TOTAL)
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
124 PLI_AT = float(DIFF_AT)/float(TOTAL)
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
125
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
126 # Per 1000 bp
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
127 PLI_GC_1000 = PLI_GC*1000
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
128 PLI_AT_1000 = PLI_AT*1000
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
129 else:
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
130 DIFF_GC=0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
131 DIFF_AT=0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
132 PLI_GC=0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
133 PLI_AT=0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
134 PLI_GC_1000=0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
135 PLI_AT_1000=0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
136
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
137 return(TOTAL, DIFF_GC, DIFF_AT,PLI_GC,PLI_AT,PLI_GC_1000,PLI_AT_1000)
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
138 ##############################################
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
139
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
140 ###################
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
141 ### RUN RUN RUN ###
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
142 ###################
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
143
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
144 ##Create specific folders
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
145 Path_IN_loci_NUC = "./IN_NUC"
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
146 outpath= "./OUT"
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
147 os.makedirs(Path_IN_loci_NUC)
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
148 os.makedirs(outpath)
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
149
1
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
150 infiles = str.split(sys.argv[1], ",")
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
151 for file in infiles:
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
152 os.system("cp %s %s" %(file, Path_IN_loci_NUC))
0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
153
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
154 ## 1 ## List taxa
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
155 LT=[]
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
156 cmd="grep '>' %s" % sys.argv[2]
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
157 result = subprocess.check_output(cmd, shell=True)
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
158 result=result.split('\n')
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
159 for i in result:
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
160 sp=i[1:]
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
161 if sp !='':
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
162 LT.append(sp)
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
163 print LT
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
164
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
165 #LT = ["Ap", "Ac", "Pg"]
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
166 #os.system("grep '>' %s" %(sys.argv[1]))
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
167
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
168 ## 2 ## PathIN
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
169 # fileIN_properties = open("01_AminoAcid_Properties2.csv", "r")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
170 Lloci_NUC = os.listdir(Path_IN_loci_NUC)
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
171
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
172
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
173 ## 3 ## PathOUT
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
174 ## 3.1 ## NUC composition
1
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
175 fileOUT_NUC=open("./OUT/nuc_compositions.csv","w")
0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
176 fileOUT_NUC.write("LOCUS,")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
177 for taxa in LT:
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
178 fileOUT_NUC.write("%s_prop_A,%s_prop_T,%s_prop_C,%s_prop_G," %(taxa,taxa,taxa,taxa))
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
179 fileOUT_NUC.write("\n")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
180
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
181 ## 3.2 ## NUC percent_GC
1
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
182 fileOUT_percent_GC=open("./OUT/percent_GC.csv","w")
0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
183 fileOUT_percent_GC.write("LOCUS,")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
184 for taxa in LT:
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
185 fileOUT_percent_GC.write("%s_percent_GC," %(taxa))
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
186 fileOUT_percent_GC.write("\n")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
187
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
188 ## 3.3 ## NUC percent_purine
1
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
189 fileOUT_percent_purine=open("./OUT/percent_purine.csv","w")
0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
190 fileOUT_percent_purine.write("LOCUS,")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
191 for taxa in LT:
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
192 fileOUT_percent_purine.write("%s_percent_purine," %(taxa))
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
193 fileOUT_percent_purine.write("\n")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
194
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
195 ## 3.4 ## Purine Load
1
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
196 fileOUT_Purine_Load=open("./OUT/Purine_Load_Indice.csv", "w")
0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
197 fileOUT_Purine_Load.write("LOCUS,")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
198 for taxa in LT:
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
199 fileOUT_Purine_Load.write("%s_TOTAL,%s_DIFF_GC,%s_DIFF_AT,%s_PLI_GC1000,%s_PLI_AT1000," %(taxa,taxa,taxa,taxa,taxa))
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
200 fileOUT_Purine_Load.write("\n")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
201
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
202 #####################
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
203 ## 4 ## Process Loci
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
204 #####################
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
205 for locus in Lloci_NUC:
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
206 print locus
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
207 path_locus = "%s/%s" %(Path_IN_loci_NUC, locus)
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
208 bash = dico(path_locus,LT)
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
209
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
210 fileOUT_NUC.write("%s," %locus)
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
211 fileOUT_percent_GC.write("%s," %locus)
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
212 fileOUT_percent_purine.write("%s," %locus)
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
213 fileOUT_Purine_Load.write("%s," %locus)
1
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
214
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
215 if taxa in bash.keys():
0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
216 seq = bash[taxa]
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
217 percent_GC, percent_purine,prop_A, prop_T, prop_C, prop_G = base_composition(seq) ### DEF2 ###
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
218 TOTAL, DIFF_GC, DIFF_AT,PLI_GC,PLI_AT,PLI_GC_1000,PLI_AT_1000 = purine_loading(seq) ### DEF3 ###
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
219 fileOUT_NUC.write("%.5f,%.5f,%.5f,%.5f," %(prop_A,prop_T,prop_C,prop_G))
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
220 fileOUT_percent_GC.write("%.5f," %percent_GC)
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
221 fileOUT_percent_purine.write("%.5f," %percent_purine)
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
222 fileOUT_Purine_Load.write("%d,%d,%d,%.5f,%.5f," %(TOTAL, DIFF_GC, DIFF_AT,PLI_GC_1000, PLI_AT_1000))
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
223 fileOUT_NUC.write("\n")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
224 fileOUT_percent_GC.write("\n")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
225 fileOUT_percent_purine.write("\n")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
226 fileOUT_Purine_Load.write("\n")
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
227 fileOUT_NUC.close()
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
228 fileOUT_percent_GC.close()
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
229 fileOUT_percent_purine.close()
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
230 fileOUT_Purine_Load.close()
1
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
231