medaka_consensus: annotateVCF.py annotate

annotate annotateVCF.py @ 6:22f6a0e7424f draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 13769e7d51b30a1d15eb62a9ba89ee2064f3ddc3"

author	iuc
date	Fri, 16 Oct 2020 17:04:35 +0000
parents	84dcccebad3d
children

rev	line source
4 84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	1 #!/usr/bin/env python3
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	2
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	3 # Takes in VCF file and a samtools mpileup output file
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	4 # Fills in annotation for the VCF file including AF, DP
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	5 # SB, and DP4
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	6 #
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	7 # Usage statement:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	8 # python annotateVCF.py in_vcf.vcf in_mpileup.txt out_vcf.vcf
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	9 #
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	10 # Can generate in_mileup.txt with samtools mpileup (and can restrict which sites to generate pileups for with in_vcf.vcf)
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	11
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	12 # 08/24/2020 - Nathan P. Roach, natproach@gmail.com
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	13
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	14 import sys
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	15 from math import isnan, log10
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	16
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	17 from scipy.stats import fisher_exact
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	18
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	19
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	20 def pval_to_phredqual(pval):
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	21 return int(round(-10. * log10(pval)))
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	22
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	23
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	24 def parseSimpleSNPpileup(fields, ref_base, alt_base):
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	25 base_to_idx = {
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	26 'A': 0,
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	27 'a': 0,
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	28 'T': 1,
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	29 't': 1,
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	30 'C': 2,
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	31 'c': 2,
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	32 'G': 3,
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	33 'g': 3
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	34 }
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	35
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	36 base_to_idx_stranded = {
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	37 'A': 0,
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	38 'T': 1,
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	39 'C': 2,
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	40 'G': 3,
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	41 'a': 4,
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	42 't': 5,
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	43 'c': 6,
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	44 'g': 7
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	45 }
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	46 ref_base2 = fields[2]
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	47 counts = [0, 0, 0, 0]
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	48 stranded_counts = [0, 0, 0, 0, 0, 0, 0, 0]
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	49 ref_idx = base_to_idx[fields[2]]
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	50 dp = int(fields[3])
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	51 carrot_flag = False
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	52 ins_flag = False
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	53 ins_str = ""
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	54 ins_len = 0
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	55 insertion = ""
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	56 del_flag = False
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	57 del_str = ""
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	58 del_len = 0
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	59 deletion = ""
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	60 # dollar_flag = False
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	61 for base in fields[4]:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	62 if carrot_flag:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	63 carrot_flag = False
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	64 continue
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	65 if ins_len > 0:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	66 insertion += base
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	67 ins_len -= 1
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	68 continue
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	69 if del_len > 0:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	70 deletion += base
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	71 del_len -= 1
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	72 continue
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	73 if ins_flag:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	74 if base.isdigit():
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	75 ins_str += base
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	76 else:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	77 ins_len = int(ins_str) - 1
6 22f6a0e7424f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 13769e7d51b30a1d15eb62a9ba89ee2064f3ddc3" iuc parents: 4 diff changeset	78 ins_str = ""
4 84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	79 insertion = base
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	80 ins_flag = False
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	81 elif del_flag:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	82 if base.isdigit():
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	83 del_str += base
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	84 else:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	85 del_len = int(del_str) - 1
6 22f6a0e7424f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 13769e7d51b30a1d15eb62a9ba89ee2064f3ddc3" iuc parents: 4 diff changeset	86 del_str = ""
4 84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	87 deletion = base
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	88 del_flag = False
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	89 else:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	90 if base == '^':
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	91 carrot_flag = True
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	92 continue
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	93 elif base == '$':
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	94 continue
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	95 elif base == '+':
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	96 ins_flag = True
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	97 elif base == '-':
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	98 del_flag = True
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	99 elif base == '.':
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	100 counts[ref_idx] += 1
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	101 stranded_counts[base_to_idx_stranded[ref_base2]] += 1
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	102 elif base == ',':
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	103 counts[ref_idx] += 1
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	104 stranded_counts[base_to_idx_stranded[ref_base2.lower()]] += 1
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	105 elif base == 'N' or base == 'n':
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	106 continue
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	107 elif base == '*':
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	108 continue
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	109 else:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	110 counts[base_to_idx[base]] += 1
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	111 stranded_counts[base_to_idx_stranded[base]] += 1
6 22f6a0e7424f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 13769e7d51b30a1d15eb62a9ba89ee2064f3ddc3" iuc parents: 4 diff changeset	112 if sum(counts) == 0:
22f6a0e7424f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 13769e7d51b30a1d15eb62a9ba89ee2064f3ddc3" iuc parents: 4 diff changeset	113 af = float("nan")
22f6a0e7424f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 13769e7d51b30a1d15eb62a9ba89ee2064f3ddc3" iuc parents: 4 diff changeset	114 else:
22f6a0e7424f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 13769e7d51b30a1d15eb62a9ba89ee2064f3ddc3" iuc parents: 4 diff changeset	115 af = float(counts[base_to_idx[alt_base]]) / float(sum(counts))
4 84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	116 if float(sum(stranded_counts[0:4])) == 0:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	117 faf = float("nan")
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	118 else:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	119 faf = float(stranded_counts[base_to_idx_stranded[alt_base]]) / float(sum(stranded_counts[0:4]))
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	120 if float(sum(stranded_counts[4:])) == 0:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	121 raf = float("nan")
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	122 else:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	123 raf = float(stranded_counts[base_to_idx_stranded[alt_base.lower()]]) / float(sum(stranded_counts[4:]))
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	124 dp4 = [stranded_counts[base_to_idx_stranded[ref_base]],
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	125 stranded_counts[base_to_idx_stranded[ref_base.lower()]],
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	126 stranded_counts[base_to_idx_stranded[alt_base]],
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	127 stranded_counts[base_to_idx_stranded[alt_base.lower()]]]
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	128 return (dp, af, faf, raf, dp4)
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	129
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	130
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	131 def parseIndelPileup(fields, ref_base, alt_base):
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	132 counts = [0, 0, 0, 0, 0, 0, 0, 0, 0] # indel ref match, indel fwd ref match, indel rev ref match, indel alt match, indel fwd alt match, indel rev alt match, other, other fwd, other rev
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	133 ref_base2 = fields[2]
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	134
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	135 carrot_flag = False
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	136 ins_flag = False
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	137 ins_str = ""
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	138 ins_len = 0
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	139 del_flag = False
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	140 del_str = ""
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	141 del_len = 0
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	142 first_iter = True
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	143 forward_flag = False
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	144 last_seq = ""
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	145 last_seq_code = 'b'
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	146 for base in fields[4]:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	147 if ins_flag:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	148 if base.isdigit():
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	149 ins_str += base
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	150 else:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	151 ins_len = int(ins_str)
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	152 ins_flag = False
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	153 if del_flag:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	154 if base.isdigit():
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	155 del_str += base
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	156 else:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	157 del_len = int(del_str)
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	158 del_flag = False
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	159 if ins_len > 0:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	160 last_seq += base
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	161 last_seq_code = 'i'
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	162 ins_len -= 1
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	163 continue
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	164 if del_len > 0:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	165 last_seq += base
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	166 last_seq_code = 'd'
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	167 del_len -= 1
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	168 continue
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	169 if carrot_flag:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	170 carrot_flag = False
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	171 continue
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	172 if base == '.' or base == ','\
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	173 or base == 'A' or base == 'a'\
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	174 or base == 'C' or base == 'c'\
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	175 or base == 'G' or base == 'g'\
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	176 or base == 'T' or base == 't'\
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	177 or base == 'N' or base == 'n'\
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	178 or base == '>' or base == '<'\
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	179 or base == '*' or base == '#':
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	180 if first_iter:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	181 first_iter = False
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	182 else:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	183 if last_seq_code == 'i':
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	184 if last_seq.upper() == alt_base.upper():
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	185 counts[3] += 1
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	186 if forward_flag:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	187 counts[4] += 1
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	188 else:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	189 counts[5] += 1
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	190 else:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	191 counts[6] += 1
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	192 if forward_flag:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	193 counts[7] += 1
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	194 else:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	195 counts[8] += 1
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	196 elif last_seq_code == 'd':
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	197 if last_seq.upper() == ref_base.upper():
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	198 counts[3] += 1
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	199 if forward_flag:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	200 counts[4] += 1
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	201 else:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	202 counts[5] += 1
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	203 else:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	204 counts[6] += 1
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	205 if forward_flag:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	206 counts[7] += 1
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	207 else:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	208 counts[8] += 1
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	209 elif last_seq_code == 'b':
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	210 if last_seq.upper() == ref_base.upper():
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	211 counts[0] += 1
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	212 if forward_flag:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	213 counts[1] += 1
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	214 else:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	215 counts[2] += 1
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	216 elif last_seq.upper() == alt_base.upper():
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	217 counts[3] += 1
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	218 if forward_flag:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	219 counts[4] += 1
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	220 else:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	221 counts[5] += 1
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	222 else:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	223 counts[6] += 1
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	224 if forward_flag:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	225 counts[7] += 1
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	226 else:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	227 counts[8] += 1
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	228 if base == '.':
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	229 last_seq = ref_base2
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	230 forward_flag = True
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	231 last_seq_code = 'b'
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	232 elif base == ',':
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	233 last_seq = ref_base2
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	234 forward_flag = False
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	235 last_seq_code = 'b'
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	236 elif base == '>' or base == '<' or base == '*' or base == '#':
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	237 continue
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	238 else:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	239 forward_flag = base.isupper()
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	240 last_seq = base.upper()
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	241 last_seq_code = 'b'
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	242 elif base == '+':
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	243 ins_flag = True
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	244 ins_str = ""
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	245 elif base == '-':
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	246 del_flag = True
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	247 del_str = ""
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	248 elif base == '^':
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	249 carrot_flag = True
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	250 elif base == '$':
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	251 continue
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	252 if first_iter:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	253 first_iter = False
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	254
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	255 if last_seq_code == 'i':
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	256 if last_seq.upper() == alt_base.upper():
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	257 counts[3] += 1
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	258 if forward_flag:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	259 counts[4] += 1
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	260 else:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	261 counts[5] += 1
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	262 else:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	263 counts[6] += 1
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	264 if forward_flag:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	265 counts[7] += 1
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	266 else:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	267 counts[8] += 1
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	268 elif last_seq_code == 'd':
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	269 if last_seq.upper() == ref_base.upper():
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	270 counts[3] += 1
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	271 if forward_flag:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	272 counts[4] += 1
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	273 else:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	274 counts[5] += 1
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	275 else:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	276 counts[6] += 1
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	277 if forward_flag:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	278 counts[7] += 1
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	279 else:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	280 counts[8] += 1
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	281 elif last_seq_code == 'b':
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	282 if last_seq.upper() == ref_base.upper():
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	283 counts[0] += 1
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	284 if forward_flag:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	285 counts[1] += 1
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	286 else:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	287 counts[2] += 1
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	288 elif last_seq.upper() == alt_base.upper():
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	289 counts[3] += 1
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	290 if forward_flag:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	291 counts[4] += 1
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	292 else:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	293 counts[5] += 1
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	294 else:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	295 counts[6] += 1
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	296 if forward_flag:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	297 counts[7] += 1
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	298 else:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	299 counts[8] += 1
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	300 dp = int(fields[3])
6 22f6a0e7424f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 13769e7d51b30a1d15eb62a9ba89ee2064f3ddc3" iuc parents: 4 diff changeset	301 if sum([counts[0], counts[3], counts[6]]) == 0:
22f6a0e7424f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 13769e7d51b30a1d15eb62a9ba89ee2064f3ddc3" iuc parents: 4 diff changeset	302 af = float("nan")
22f6a0e7424f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 13769e7d51b30a1d15eb62a9ba89ee2064f3ddc3" iuc parents: 4 diff changeset	303 else:
22f6a0e7424f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 13769e7d51b30a1d15eb62a9ba89ee2064f3ddc3" iuc parents: 4 diff changeset	304 af = float(counts[3]) / float(sum([counts[0], counts[3], counts[6]]))
4 84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	305 if sum([counts[1], counts[4], counts[7]]) == 0:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	306 faf = float("nan")
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	307 else:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	308 faf = float(counts[4]) / float(sum([counts[1], counts[4], counts[7]]))
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	309 if sum([counts[2], counts[5], counts[8]]) == 0:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	310 raf = float("nan")
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	311 else:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	312 raf = float(counts[5]) / float(sum([counts[2], counts[5], counts[8]]))
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	313 dp4 = [counts[1], counts[2], counts[4], counts[5]]
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	314 return (dp, af, faf, raf, dp4)
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	315
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	316
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	317 def annotateVCF(in_vcf_filepath, in_mpileup_filepath, out_vcf_filepath):
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	318 in_vcf = open(in_vcf_filepath, 'r')
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	319 in_mpileup = open(in_mpileup_filepath, 'r')
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	320 out_vcf = open(out_vcf_filepath, 'w')
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	321
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	322 # First pass parsing of input vcf, output headerlines + new headerlines, add VCF sites we care about to to_examine (limits memory usage for sites that don't need annotation)
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	323 to_examine = {}
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	324 for line in in_vcf:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	325 if line[0:2] == "##":
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	326 out_vcf.write(line)
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	327 elif line[0] == "#":
6 22f6a0e7424f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 13769e7d51b30a1d15eb62a9ba89ee2064f3ddc3" iuc parents: 4 diff changeset	328 out_vcf.write("##annotateVCFVersion=0.2\n")
4 84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	329 out_vcf.write("##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Raw Depth\">\n")
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	330 out_vcf.write("##INFO=<ID=AF,Number=1,Type=Float,Description=\"Allele Frequency\">\n")
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	331 out_vcf.write("##INFO=<ID=FAF,Number=1,Type=Float,Description=\"Forward Allele Frequency\">\n")
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	332 out_vcf.write("##INFO=<ID=RAF,Number=1,Type=Float,Description=\"Reverse Allele Frequency\">\n")
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	333 out_vcf.write("##INFO=<ID=SB,Number=1,Type=Integer,Description=\"Phred-scaled strand bias at this position\">\n")
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	334 out_vcf.write("##INFO=<ID=DP4,Number=4,Type=Integer,Description=\"Counts for ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\">\n")
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	335 out_vcf.write(line)
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	336 else:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	337 fields = line.strip().split()
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	338 if fields[0] in to_examine:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	339 to_examine[fields[0]][int(fields[1])] = (fields[3], fields[4])
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	340 else:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	341 to_examine[fields[0]] = {int(fields[1]): (fields[3], fields[4])}
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	342 in_vcf.close()
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	343 data = {}
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	344
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	345 # Populate data dictionary, which relates chromosome and position to the following:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	346 # depth of coverage
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	347 # allele frequency
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	348 # forward strand allele frequency
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	349 # reverse strand allele frequency
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	350 # dp4 - depth of coverage of ref allele fwd strand, DOC of ref allele rev strand, DOC of alt allele fwd strand, DOC of alt allele rev strand
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	351 for line in in_mpileup:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	352 fields = line.strip().split()
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	353 if fields[0] not in to_examine:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	354 continue
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	355 if int(fields[1]) not in to_examine[fields[0]]:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	356 continue
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	357 (ref_base, alt_base) = to_examine[fields[0]][int(fields[1])]
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	358 if len(ref_base.split(',')) > 1: # Can't handle multiple ref alleles
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	359 continue
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	360 if len(alt_base.split(',')) > 1: # Can't handle multiple alt alleles
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	361 continue
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	362 if len(ref_base) > 1 or len(alt_base) > 1:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	363 if len(ref_base) > 1 and len(alt_base) > 1: # Can't handle complex indels
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	364 continue
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	365 data[(fields[0], int(fields[1]))] = parseIndelPileup(fields, ref_base, alt_base)
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	366 if len(ref_base) == 1 and len(alt_base) == 1:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	367 data[(fields[0], int(fields[1]))] = parseSimpleSNPpileup(fields, ref_base, alt_base)
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	368 in_mpileup.close()
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	369 # Reopen vcf, this time, skip header, annotate all the sites for which there is an entry in data dictionary
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	370 # (Sites without entries have either multiple ref or alt bases, or have complex indels. Not supported (for now), and not reported as a result)
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	371 in_vcf = open(in_vcf_filepath, 'r')
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	372 for line in in_vcf:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	373 if line[0] == '#':
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	374 continue
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	375 fields = line.strip().split('\t')
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	376 if (fields[0], int(fields[1])) not in data:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	377 continue
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	378 (dp, af, faf, raf, dp4) = data[(fields[0], int(fields[1]))]
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	379 dp2x2 = [[dp4[0], dp4[1]], [dp4[2], dp4[3]]]
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	380 _, p_val = fisher_exact(dp2x2)
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	381 sb = pval_to_phredqual(p_val)
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	382 if fields[7] == "":
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	383 info = []
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	384 else:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	385 info = fields[7].split(';')
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	386 info.append("DP=%d" % (dp))
6 22f6a0e7424f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 13769e7d51b30a1d15eb62a9ba89ee2064f3ddc3" iuc parents: 4 diff changeset	387 if isnan(af):
22f6a0e7424f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 13769e7d51b30a1d15eb62a9ba89ee2064f3ddc3" iuc parents: 4 diff changeset	388 info.append("AF=NaN")
22f6a0e7424f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 13769e7d51b30a1d15eb62a9ba89ee2064f3ddc3" iuc parents: 4 diff changeset	389 else:
22f6a0e7424f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 13769e7d51b30a1d15eb62a9ba89ee2064f3ddc3" iuc parents: 4 diff changeset	390 info.append("AF=%.6f" % (af))
4 84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	391 if isnan(faf):
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	392 info.append("FAF=NaN")
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	393 else:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	394 info.append("FAF=%.6f" % (faf))
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	395 if isnan(raf):
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	396 info.append("RAF=NaN")
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	397 else:
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	398 info.append("RAF=%.6f" % (raf))
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	399 info.append("SB=%d" % (sb))
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	400 info.append("DP4=%s" % (','.join([str(x) for x in dp4])))
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	401 new_info = ';'.join(info)
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	402 fields[7] = new_info
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	403 out_vcf.write("%s\n" % ("\t".join(fields)))
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	404 in_vcf.close()
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	405 out_vcf.close()
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	406
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	407
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	408 if __name__ == "__main__":
84dcccebad3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44" iuc parents: diff changeset	409 annotateVCF(sys.argv[1], sys.argv[2], sys.argv[3])

Mercurial > repos > iuc > medaka_consensus

annotate annotateVCF.py @ 6:22f6a0e7424f draft