diff options
Diffstat (limited to 'gn2/utility/gen_geno_ob.py')
| -rw-r--r-- | gn2/utility/gen_geno_ob.py | 182 |
1 files changed, 182 insertions, 0 deletions
diff --git a/gn2/utility/gen_geno_ob.py b/gn2/utility/gen_geno_ob.py new file mode 100644 index 00000000..c7a1ea59 --- /dev/null +++ b/gn2/utility/gen_geno_ob.py @@ -0,0 +1,182 @@ +class genotype: + """ + Replacement for reaper.Dataset so we can remove qtlreaper use while still generating mapping output figure + """ + + def __init__(self, filename): + self.group = None + self.type = "riset" + self.prgy = [] + self.nprgy = 0 + self.mat = -1 + self.pat = 1 + self.het = 0 + self.unk = "U" + 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 + self.cm_column = 2 + self.mb_column = 3 + + self.chromosomes = [] + + self.read_file(filename) + + def __iter__(self): + return iter(self.chromosomes) + + def __getitem__(self, index): + return self.chromosomes[index] + + def __len__(self): + 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 + # 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 + chr_ob = None + for marker in qtl_results: + locus = Locus(self) + # 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']) + if this_chr == "20": + this_chr = "X" + chr_ob = Chr(this_chr, self) + if 'chr' in marker: + locus.chr = str(marker['chr']) + if 'name' in marker: + locus.name = marker['name'] + if 'Mb' in marker: + locus.Mb = marker['Mb'] + if 'cM' in marker: + locus.cM = marker['cM'] + chr_ob.loci.append(locus) + + self.chromosomes.append(chr_ob) + + return self + + def read_file(self, filename): + 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 + chr_ob = None + for line in lines: + if line[0] == "#": + continue + elif line[0] == "@": + label = line.split(":")[0][1:] + if label == "name": + self.group = line.split(":")[1].strip() + elif label == "filler": + if line.split(":")[1].strip() == "yes": + self.filler = True + elif label == "type": + self.type = line.split(":")[1].strip() + elif label == "mat": + self.mat = line.split(":")[1].strip() + elif label == "pat": + self.pat = line.split(":")[1].strip() + elif label == "het": + self.het = line.split(":")[1].strip() + elif label == "unk": + self.unk = line.split(":")[1].strip() + else: + continue + elif line[:3] == "Chr": + header_row = line.split("\t") + if header_row[2] == "Mb": + self.mb_exists = True + self.mb_column = 2 + self.cm_column = 3 + elif header_row[3] == "Mb": + self.mb_exists = True + self.mb_column = 3 + elif header_row[2] == "cM": + self.cm_column = 2 + + if self.mb_exists: + self.prgy = header_row[4:] + else: + self.prgy = header_row[3:] + self.nprgy = len(self.prgy) + else: + if line.split("\t")[0] != this_chr: + if this_chr != "": + self.chromosomes.append(chr_ob) + this_chr = line.split("\t")[0] + chr_ob = Chr(line.split("\t")[0], self) + chr_ob.add_marker(line.split("\t")) + + self.chromosomes.append(chr_ob) + + +class Chr: + def __init__(self, name, geno_ob): + self.name = name + self.loci = [] + self.mb_exists = geno_ob.mb_exists + self.cm_column = geno_ob.cm_column + self.mb_column = geno_ob.mb_column + self.geno_ob = geno_ob + + def __iter__(self): + return iter(self.loci) + + def __getitem__(self, index): + return self.loci[index] + + def __len__(self): + return len(self.loci) + + def add_marker(self, marker_row): + self.loci.append(Locus(self.geno_ob, marker_row)) + + +class Locus: + def __init__(self, geno_ob, marker_row=None): + self.chr = None + self.name = None + self.cM = None + self.Mb = None + self.genotype = [] + if marker_row: + self.chr = marker_row[0] + self.name = marker_row[1] + 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 + try: + self.Mb = float( + marker_row[geno_ob.mb_column]) if geno_ob.mb_exists else None + except: + self.Mb = self.cM + + geno_table = { + geno_ob.mat: -1, + geno_ob.pat: 1, + geno_ob.het: 0, + geno_ob.unk: "U" + } + + self.genotype = [] + if geno_ob.mb_exists: + start_pos = 4 + else: + start_pos = 3 + + for allele in marker_row[start_pos:]: + 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") |