diff options
Diffstat (limited to 'wqflask/utility/gen_geno_ob.py')
| -rw-r--r-- | wqflask/utility/gen_geno_ob.py | 106 |
1 files changed, 75 insertions, 31 deletions
diff --git a/wqflask/utility/gen_geno_ob.py b/wqflask/utility/gen_geno_ob.py index 5172369f..23b0b650 100644 --- a/wqflask/utility/gen_geno_ob.py +++ b/wqflask/utility/gen_geno_ob.py @@ -1,5 +1,8 @@ from __future__ import absolute_import, division, print_function +import utility.logger +logger = utility.logger.getLogger(__name__ ) + class genotype(object): """ Replacement for reaper.Dataset so we can remove qtlreaper use while still generating mapping output figure @@ -34,8 +37,36 @@ class genotype(object): def __len__(self): return len(self.chromosomes) - def read_file(self, filename): + 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 + + 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 + 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() @@ -47,20 +78,20 @@ class genotype(object): elif line[0] == "@": label = line.split(":")[0][1:] if label == "name": - self.group = line.split(":")[1] + self.group = line.split(":")[1].strip() elif label == "filler": - if line.split(":")[1] == "yes": + if line.split(":")[1].strip() == "yes": self.filler = True elif label == "type": - self.type = line.split(":")[1] + self.type = line.split(":")[1].strip() elif label == "mat": - self.mat = line.split(":")[1] + self.mat = line.split(":")[1].strip() elif label == "pat": - self.pat = line.split(":")[1] + self.pat = line.split(":")[1].strip() elif label == "het": - self.het = line.split(":")[1] + self.het = line.split(":")[1].strip() elif label == "unk": - self.unk = line.split(":")[1] + self.unk = line.split(":")[1].strip() else: continue elif line[:3] == "Chr": @@ -109,29 +140,42 @@ class Chr(object): return len(self.loci) def add_marker(self, marker_row): - self.loci.append(Locus(marker_row, self.geno_ob)) + self.loci.append(Locus(self.geno_ob, marker_row)) class Locus(object): - def __init__(self, marker_row, geno_ob): - self.chr = marker_row[0] - self.name = marker_row[1] - self.cM = float(marker_row[geno_ob.cm_column]) - self.Mb = float(marker_row[geno_ob.mb_column]) if geno_ob.mb_exists else None - - geno_table = { - geno_ob.mat: -1, - geno_ob.pat: 1, - geno_ob.het: 0, - geno_ob.unk: "U" - } - + def __init__(self, geno_ob, marker_row = None): + self.chr = None + self.name = None + self.cM = None + self.Mb = None self.genotype = [] - if geno_ob.mb_exists: - start_pos = 4 - else: - start_pos = 3 - for allele in marker_row[start_pos:]: - if allele in 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 + 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 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 |