diff options
Diffstat (limited to 'wqflask/utility/gen_geno_ob.py')
| -rw-r--r-- | wqflask/utility/gen_geno_ob.py | 182 |
1 files changed, 0 insertions, 182 deletions
diff --git a/wqflask/utility/gen_geno_ob.py b/wqflask/utility/gen_geno_ob.py deleted file mode 100644 index c7a1ea59..00000000 --- a/wqflask/utility/gen_geno_ob.py +++ /dev/null @@ -1,182 +0,0 @@ -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") |