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authorDannyArends2016-03-22 23:37:13 +0100
committerPjotr Prins2016-04-20 10:17:15 +0000
commita13baa5fb98d8167e70df7008d0d07b40a05a6b9 (patch)
treeeb8a01e8073ce4ba1c250bddf9567b76b876255b
parent2cbdf59b98ae6061ef083ab29c30111d2ea1f853 (diff)
downloadgenenetwork2-a13baa5fb98d8167e70df7008d0d07b40a05a6b9.tar.gz
Adding the geno file parser from Zach
-rw-r--r--wqflask/utility/genofile_parser.py96
1 files changed, 96 insertions, 0 deletions
diff --git a/wqflask/utility/genofile_parser.py b/wqflask/utility/genofile_parser.py
new file mode 100644
index 00000000..9dd7b08b
--- /dev/null
+++ b/wqflask/utility/genofile_parser.py
@@ -0,0 +1,96 @@
+# CTL analysis for GN2
+# Author / Maintainer: Danny Arends <Danny.Arends@gmail.com>
+
+from __future__ import print_function, division, absolute_import
+import sys
+import os
+import glob
+import traceback
+import gzip
+
+import simplejson as json
+
+from pprint import pformat as pf
+
+class Marker(object):
+ def __init__(self):
+ self.name = None
+ self.chr = None
+ self.cM = None
+ self.Mb = None
+ self.genotypes = []
+
+
+class ConvertGenoFile(object):
+
+ def __init__(self, input_file):
+ self.mb_exists = False
+ self.cm_exists = False
+ self.markers = []
+
+ self.latest_row_pos = None
+ self.latest_col_pos = None
+
+ self.latest_row_value = None
+ self.latest_col_value = None
+ self.input_fh = open(input_file)
+ print("!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!")
+ self.haplotype_notation = {
+ '@mat': "3",
+ '@pat': "1",
+ '@het': "2",
+ '@unk': "NA"
+ }
+ self.configurations = {}
+
+ def process_rows(self):
+ for self.latest_row_pos, row in enumerate(self.input_fh):
+ self.latest_row_value = row
+ # Take care of headers
+ if not row.strip():
+ continue
+ if row.startswith('#'):
+ continue
+ if row.startswith('Chr'):
+ if 'Mb' in row.split():
+ self.mb_exists = True
+ if 'cM' in row.split():
+ self.cm_exists = True
+ continue
+ if row.startswith('@'):
+ key, _separater, value = row.partition(':')
+ key = key.strip()
+ value = value.strip()
+ if key in self.haplotype_notation:
+ self.configurations[value] = self.haplotype_notation[key]
+ continue
+ if not len(self.configurations):
+ raise EmptyConfigurations
+ yield row
+
+ def process_csv(self):
+ for row_count, row in enumerate(self.process_rows()):
+ row_items = row.split("\t")
+
+ this_marker = Marker()
+ this_marker.name = row_items[1]
+ this_marker.chr = row_items[0]
+ if self.cm_exists and self.mb_exists:
+ this_marker.cM = row_items[2]
+ this_marker.Mb = row_items[3]
+ genotypes = row_items[4:]
+ elif self.cm_exists:
+ this_marker.cM = row_items[2]
+ genotypes = row_items[3:]
+ elif self.mb_exists:
+ this_marker.Mb = row_items[2]
+ genotypes = row_items[3:]
+ else:
+ genotypes = row_items[2:]
+ for item_count, genotype in enumerate(genotypes):
+ if genotype.upper() in self.configurations:
+ this_marker.genotypes.append(self.configurations[genotype.upper()])
+ else:
+ this_marker.genotypes.append("NA")
+ self.markers.append(this_marker.__dict__)
+