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improve gestion of already parsed vcf for other functions

tforest 2 vuotta sitten
vanhempi
commit
856e20d46e
2 muutettua tiedostoa jossa 67 lisäystä ja 2 poistoa
  1. 61 0
      sfs_tools.py
  2. 6 2
      vcf_utils.py

+ 61 - 0
sfs_tools.py Näytä tiedosto

@@ -102,6 +102,67 @@ def sfs_from_vcf(n, vcf_file, folded = True, diploid = True, phased = False, ver
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         print("Pluriallelic sites =", count_pluriall)
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     return SFS_values, count_pluriall
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+
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+def sfs_from_parsed_vcf(n, vcf_dict, folded = True, diploid = True, phased = False, verbose = False):
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+
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+    """
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+    Generates a Site Frequency Spectrum from a gzipped VCF file format.
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+
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+    Parameters
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+    ----------
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+    n : int
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+        Nb of individuals in sample.
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+    vcf_file : str
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+        SNPs in VCF file format.
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+
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+        Used to generate a Site Frequency Spectrum (SFS) from a VCF.
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+
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+    Returns
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+    -------
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+    dict
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+        Site Frequency Spectrum (SFS)
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+
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+
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+    """
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+    
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+    if diploid and not folded:
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+        n *= 2
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+    # initiate SFS_values with a zeros dict
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+    SFS_values = dict.fromkeys(range(n),0)
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+    count_pluriall = 0
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+
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+    for CHROM in vcf_dict:
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+        for SNP in vcf_dict[CHROM]:
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+            snp_genotypes = []
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+            allele_counts = {}
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+            allele_counts_list = []
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+            print(CHROM, SNP)
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+            for sample in vcf_dict[CHROM][SNP]["SAMPLES"]:
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+                if not phased:
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+                    # for UNPHASED data
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+                    smpl_genotype = [int(a) for a in sample.split(':')[0].split('/') if a != '.']
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+                else:
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+                    # for PHASED
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+                    smpl_genotype = [int(a) for a in sample.split(':')[0].split('|') if a != '.']
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+                nb_alleles = set(smpl_genotype)
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+                snp_genotypes += smpl_genotype
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+            # skip if all individuals have the same genotype
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+            if len(set(snp_genotypes)) == 1:
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+                continue
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+            for k in set(snp_genotypes):
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+                allele_counts[snp_genotypes.count(k)] = k
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+                allele_counts_list.append(snp_genotypes.count(k))
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+            SFS_values[min(allele_counts_list)-1] += 1
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+        # sum pluriall counts for this CHR to the rest
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+        count_pluriall += vcf_dict[CHROM]['NB_PLURIALL']
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+                    
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+    if verbose:
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+        print("SFS=", SFS_values)
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+    print("Pluriallelic sites =", count_pluriall)
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+    
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+    return SFS_values, count_pluriall
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+
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+
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 def barplot_sfs(sfs, folded=True, title = "Barplot"):
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     sfs_val = []
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     n = len(sfs.values())

+ 6 - 2
vcf_utils.py Näytä tiedosto

@@ -105,6 +105,7 @@ def parse_vcf(vcf_file, phased=False, stop_at=None, chr_starts_with="*"):
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                         entries = {
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                             'POS':POS,
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                             'CHR':CHROM,
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+                            # removed to save some space
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                             #'FIELDS':FIELDS,
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                             'REF':REF,
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                             'ALT':ALT,
@@ -113,13 +114,16 @@ def parse_vcf(vcf_file, phased=False, stop_at=None, chr_starts_with="*"):
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                             'SAMPLES':SAMPLES,
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                             'QUALITY':QUALITY,
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                             'GENOTYPE':GENOTYPE,
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-                            'LIKELIHOOD':LIKELIHOOD
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+                            'LIKELIHOOD':LIKELIHOOD,
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+                            'NB_PLURIALL':pluriall_counts
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                         }
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                         if CHROM.startswith(chr_starts_with):
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                         # keep if chr name starts with filter
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                         # default : *, every chr is kept
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                             if CHROM not in chrom:
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-                                 chrom[CHROM] = {}
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+                                # resent when changing chrom
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+                                pluriall_counts = 0
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+                                chrom[CHROM] = {}
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                             chrom[CHROM][POS] = entries
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                 byte_line = inputgz.readline()
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     end = time.time()