diff options
Diffstat (limited to 'wqflask/utility/gen_geno_ob.py')
| -rw-r--r-- | wqflask/utility/gen_geno_ob.py | 41 |
1 files changed, 23 insertions, 18 deletions
diff --git a/wqflask/utility/gen_geno_ob.py b/wqflask/utility/gen_geno_ob.py index 23b0b650..e619b7b6 100644 --- a/wqflask/utility/gen_geno_ob.py +++ b/wqflask/utility/gen_geno_ob.py @@ -1,9 +1,8 @@ -from __future__ import absolute_import, division, print_function - import utility.logger -logger = utility.logger.getLogger(__name__ ) +logger = utility.logger.getLogger(__name__) + -class genotype(object): +class genotype: """ Replacement for reaper.Dataset so we can remove qtlreaper use while still generating mapping output figure """ @@ -20,7 +19,7 @@ class genotype(object): self.filler = False self.mb_exists = False - #ZS: This is because I'm not sure if some files switch the column that contains Mb/cM positions; might be unnecessary + # ZS: This is because I'm not sure if some files switch the column that contains Mb/cM positions; might be unnecessary self.cm_column = 2 self.mb_column = 3 @@ -38,14 +37,16 @@ class genotype(object): return len(self.chromosomes) def read_rdata_output(self, qtl_results): - #ZS: This is necessary because R/qtl requires centimorgan marker positions, which it normally gets from the .geno file, but that doesn't exist for HET3-ITP (which only has RData), so it needs to read in the marker cM positions from the results - self.chromosomes = [] #ZS: Overwriting since the .geno file's contents are just placeholders + # ZS: This is necessary because R/qtl requires centimorgan marker positions, which it normally gets from the .geno file, but that doesn't exist for HET3-ITP (which only has RData), so it needs to read in the marker cM positions from the results + # ZS: Overwriting since the .geno file's contents are just placeholders + self.chromosomes = [] - this_chr = "" #ZS: This is so it can track when the chromosome changes as it iterates through markers + this_chr = "" # ZS: This is so it can track when the chromosome changes as it iterates through markers chr_ob = None for marker in qtl_results: locus = Locus(self) - if (str(marker['chr']) != this_chr) and this_chr != "X": #ZS: This is really awkward but works as a temporary fix + # ZS: This is really awkward but works as a temporary fix + if (str(marker['chr']) != this_chr) and this_chr != "X": if this_chr != "": self.chromosomes.append(chr_ob) this_chr = str(marker['chr']) @@ -70,7 +71,7 @@ class genotype(object): with open(filename, 'r') as geno_file: lines = geno_file.readlines() - this_chr = "" #ZS: This is so it can track when the chromosome changes as it iterates through markers + this_chr = "" # ZS: This is so it can track when the chromosome changes as it iterates through markers chr_ob = None for line in lines: if line[0] == "#": @@ -121,7 +122,8 @@ class genotype(object): self.chromosomes.append(chr_ob) -class Chr(object): + +class Chr: def __init__(self, name, geno_ob): self.name = name self.loci = [] @@ -142,8 +144,9 @@ class Chr(object): def add_marker(self, marker_row): self.loci.append(Locus(self.geno_ob, marker_row)) -class Locus(object): - def __init__(self, geno_ob, marker_row = None): + +class Locus: + def __init__(self, geno_ob, marker_row=None): self.chr = None self.name = None self.cM = None @@ -155,9 +158,11 @@ class Locus(object): try: self.cM = float(marker_row[geno_ob.cm_column]) except: - self.cM = float(marker_row[geno_ob.mb_column]) if geno_ob.mb_exists else 0 + self.cM = float( + marker_row[geno_ob.mb_column]) if geno_ob.mb_exists else 0 try: - self.Mb = float(marker_row[geno_ob.mb_column]) if geno_ob.mb_exists else None + self.Mb = float( + marker_row[geno_ob.mb_column]) if geno_ob.mb_exists else None except: self.Mb = self.cM @@ -175,7 +180,7 @@ class Locus(object): start_pos = 3 for allele in marker_row[start_pos:]: - if allele in geno_table.keys(): + if allele in list(geno_table.keys()): self.genotype.append(geno_table[allele]) - else: #ZS: Some genotype appears that isn't specified in the metadata, make it unknown - self.genotype.append("U") \ No newline at end of file + else: # ZS: Some genotype appears that isn't specified in the metadata, make it unknown + self.genotype.append("U") |