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authorzsloan2016-05-18 20:06:41 +0000
committerzsloan2016-05-18 20:06:41 +0000
commitf8c89f7c24cbfcffdafd12ef2087f4de598ed4bd (patch)
treeca233c2f08151377de161a616e69031d557ff808 /wqflask/utility
parente36ffce0d972334b07ee91b817fc3f30ed3598c4 (diff)
parenta8945cc625f12e9cf733f469426bf0e4b8e83647 (diff)
downloadgenenetwork2-f8c89f7c24cbfcffdafd12ef2087f4de598ed4bd.tar.gz
Merge branch 'staging' of https://github.com/genenetwork/genenetwork2
Diffstat (limited to 'wqflask/utility')
-rw-r--r--wqflask/utility/external.py9
-rw-r--r--wqflask/utility/genofile_parser.py100
-rw-r--r--wqflask/utility/tools.py189
3 files changed, 230 insertions, 68 deletions
diff --git a/wqflask/utility/external.py b/wqflask/utility/external.py
new file mode 100644
index 00000000..50afea08
--- /dev/null
+++ b/wqflask/utility/external.py
@@ -0,0 +1,9 @@
+# Call external program
+
+import os
+import sys
+import subprocess
+
+def shell(command):
+ if subprocess.call(command, shell=True) != 0:
+ raise Exception("ERROR: failed on "+command)
diff --git a/wqflask/utility/genofile_parser.py b/wqflask/utility/genofile_parser.py
new file mode 100644
index 00000000..67b84dc9
--- /dev/null
+++ b/wqflask/utility/genofile_parser.py
@@ -0,0 +1,100 @@
+# 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("!!!!!!!!!!!!!!!!PARSER!!!!!!!!!!!!!!!!!!")
+ self.haplotype_notation = {
+ '@mat': "1",
+ '@pat': "2",
+ '@het': "-999",
+ '@unk': "-999"
+ }
+ 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
+ skip = 2 + self.cm_exists + self.mb_exists
+ self.individuals = row.split()[skip:]
+ 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().strip() in self.configurations:
+ this_marker.genotypes.append(self.configurations[genotype.upper().strip()])
+ else:
+ print("WARNING:", genotype.upper())
+ this_marker.genotypes.append("NA")
+ self.markers.append(this_marker.__dict__)
+
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index b8a41f60..dd8c4a1e 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -1,84 +1,137 @@
# Tools/paths finder resolves external paths from settings and/or environment
# variables
-#
-# Currently supported:
-#
-# PYLMM_PATH finds the root of the git repository of the pylmm_gn2 tool
import os
import sys
from wqflask import app
-def get_setting(id,default,guess,get_valid_path):
- """
- Resolve a setting from the environment or the global settings in app.config
+def get_setting(command_id,guess=None):
+ """Resolve a setting from the environment or the global settings in
+ app.config, with get_valid_path is a function checking whether the
+ path points to an expected directory and returns the full path to
+ the binary command
+
+ guess = os.environ.get('HOME')+'/pylmm'
+ get_setting('PYLMM_PATH',guess)
+
+ first tries the environment variable in +id+, next gets the Flask
+ app setting for the same +id+ and finally does an educated
+ +guess+.
+
+ In all, the environment overrides the others, next is the flask
+ setting, then the guess. A valid path to the binary command is
+ returned. If none is resolved an exception is thrown.
+
+ Note that we do not use the system path. This is on purpose
+ because it will mess up controlled (reproducible) deployment. The
+ proper way is to either use the GNU Guix defaults as listed in
+ etc/default_settings.py or override them yourself by creating a
+ different settings.py file (or setting the environment).
+
"""
+ def value(command):
+ if command:
+ sys.stderr.write("Found path "+command+"\n")
+ return command
+ else:
+ return None
+
# ---- Check whether environment exists
- path = get_valid_path(os.environ.get(id))
- # ---- Check whether setting exists
- setting = app.config.get(id)
- if not path:
- path = get_valid_path(setting)
- # ---- Check whether default exists
- if not path:
- path = get_valid_path(default)
- # ---- Guess directory
- if not path:
- if not setting:
- setting = guess
- path = get_valid_path(guess)
- if not path:
- raise Exception(id+' '+setting+' path unknown or faulty (update settings.py?). '+id+' should point to the root of the git repository')
-
- return path
-
-def pylmm_command(default=None):
+ sys.stderr.write("Looking for "+command_id+"\n")
+ command = value(os.environ.get(command_id))
+ if not command:
+ # ---- Check whether setting exists in app
+ command = value(app.config.get(command_id))
+ if not command:
+ command = value(guess)
+ if not command:
+ raise Exception(command_id+' path unknown or faulty (update settings.py?). '+command_id+' should point to the path')
+ return command
+
+def valid_bin(bin):
+ if os.path.islink(bin) or valid_file(bin):
+ return bin
+ return None
+
+def valid_file(fn):
+ if os.path.isfile(fn):
+ return fn
+ return None
+
+def valid_path(dir):
+ if os.path.isdir(dir):
+ return dir
+ return None
+
+def pylmm_command(guess=None):
+ return valid_bin(get_setting("PYLMM_COMMAND",guess))
+
+def gemma_command(guess=None):
+ return valid_bin(get_setting("GEMMA_COMMAND",guess))
+
+def plink_command(guess=None):
+ return valid_bin(get_setting("PLINK_COMMAND",guess))
+
+def flat_files(subdir=None):
+ base = get_setting("GENENETWORK_FILES")
+ if subdir:
+ return assert_dir(base+"/"+subdir)
+ return assert_dir(base)
+
+def assert_dir(dir):
+ if not valid_path(dir):
+ raise Exception("ERROR: can not find directory "+dir)
+ return dir
+
+def mk_dir(dir):
+ if not valid_path(dir):
+ os.makedirs(dir)
+ return assert_dir(dir)
+
+def locate(name, subdir=None):
"""
- Return the path to the repository and the python command to call
+ Locate a static flat file in the GENENETWORK_FILES environment.
+
+ This function throws an error when the file is not found.
"""
- def get_valid_path(path):
- """Test for a valid repository"""
- if path:
- sys.stderr.write("Trying PYLMM_PATH in "+path+"\n")
- if path and os.path.isfile(path+'/pylmm_gn2/lmm.py'):
- return path
+ base = get_setting("GENENETWORK_FILES")
+ if subdir:
+ base = base+"/"+subdir
+ if valid_path(base):
+ lookfor = base + "/" + name
+ if valid_file(lookfor):
+ print("Found: file "+lookfor+"\n")
+ return lookfor
else:
- None
+ raise Exception("Can not locate "+lookfor)
+ if subdir: sys.stderr.write(subdir)
+ raise Exception("Can not locate "+name+" in "+base)
- guess = os.environ.get('HOME')+'/pylmm_gn2'
- path = get_setting('PYLMM_PATH',default,guess,get_valid_path)
- pylmm_command = 'python '+path+'/pylmm_gn2/lmm.py'
- return path,pylmm_command
-
-def plink_command(default=None):
+def locate_ignore_error(name, subdir=None):
"""
- Return the path to the repository and the python command to call
+ Locate a static flat file in the GENENETWORK_FILES environment.
+
+ This function does not throw an error when the file is not found
+ but returns None.
"""
- def get_valid_path(path):
- """Test for a valid repository"""
- if path:
- sys.stderr.write("Trying PLINK_PATH in "+path+"\n")
- if path and os.path.isfile(path+'/plink'):
- return path
- else:
- None
-
- guess = os.environ.get('HOME')+'/plink_gemma'
- path = get_setting('PLINK_PATH',default,guess,get_valid_path)
- plink_command = path+'/plink'
- return path,plink_command
-
-def gemma_command(default=None):
- def get_valid_path(path):
- """Test for a valid repository"""
- if path:
- sys.stderr.write("Trying PLINK_PATH in "+path+"\n")
- if path and os.path.isfile(path+'/plink'):
- return path
- else:
- None
+ base = get_setting("GENENETWORK_FILES")
+ if subdir:
+ base = base+"/"+subdir
+ if valid_path(base):
+ lookfor = base + "/" + name
+ if valid_file(lookfor):
+ print("Found: file "+name+"\n")
+ return lookfor
+ sys.stderr.write("WARNING: file "+name+" not found\n")
+ return None
+
+def tempdir():
+ return valid_path(get_setting("TEMPDIR","/tmp"))
- guess = os.environ.get('HOME')+'/plink'
- path = get_setting('PLINK_PATH',default,guess,get_valid_path)
- gemma_command = path+'/gemma'
- return path, gemma_command \ No newline at end of file
+
+# Cached values
+PYLMM_COMMAND = pylmm_command()
+GEMMA_COMMAND = gemma_command()
+PLINK_COMMAND = plink_command()
+FLAT_FILES = flat_files()
+TEMPDIR = tempdir()