changeset 16:efb15a586f5e draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cravat_annotate/cravat_annotate.py	Tue Jun 12 12:05:48 2018 -0400
@@ -0,0 +1,246 @@
+"""
+A galaxy wrapper for the /rest/service/query API endpoint on Cravat.
+
+
+Notes on Mapping:
+-----------------
+The CravatQuery class uses static method 'from_array' to interpret an array of values
+into a query string for the /rest/service/query API service on the cravat server.
+This involves using a mapping dictionary to know how to associate the array's index positions
+in to query-ing attributes, such as the chromosome, position, etc. The CravatQuery
+class contains a default value ('default_mapping'); however, this could also be
+offered as a user-configurable option.
+"""
+
+
+import requests
+import json
+import sys
+import re
+
+
+class CravatQueryException(Exception):
+
+	def __init__(self, message, errors=None):	 
+		super(CravatQueryException, self).__init__(message)
+		# Support for custom error codes
+		self.errors = errors
+
+
+class CravatQuery(object):
+	"""
+	: A class for handling Cravat query strings.
+	: Args (all required):
+	:	chr - Chromosome
+	:	pos - Position
+	:	strand - Strand
+	:	ref - Reference Base
+	:	alt - Alternate Base
+	"""
+
+	# The endpoint that CravatQuerys are submitted to
+	endpoint = 'http://cravat.us/CRAVAT/rest/service/query'
+
+	# The value delimiter used in the Cravat input file to delimit values
+	delimiter = "\t"
+
+	# Defualt indices for intepretting a cravat file's row of data in to a CravatQuery
+	default_mapping = {
+		'chromosome': 1,
+		'position': 2,
+		'strand': 3,
+		'reference': 4,
+		'alternate': 5
+	}
+
+	# Defualt values. Used as backup for CravatQuery to resolve query with incomplete information
+	default_values = {
+		'strand': '+'
+	}
+
+	# The neccessary attributes neeeded to submit a query.
+	query_keys = [
+		'chromosome', 'position', 'strand', 'reference', 'alternate'
+	]
+
+	# Expected response keys from server. Ordered in list so that galaxy output has uniform column ordering run-to-run.
+	# If cravat server returns additional keys, they are appended to and included in output.
+	response_keys = [
+		"Chromosome", "Position", "Strand", "Reference base(s)", "Alternate base(s)",
+	 	"HUGO symbol", "S.O. transcript", "Sequence ontology protein change", "Sequence ontology",
+		"S.O. all transcripts", "gnomAD AF", "gnomAD AF (African)", "gnomAD AF (Amrican)",
+		"gnomAD AF (Ashkenazi Jewish)", "gnomAD AF (East Asian)", "gnomAD AF (Finnish)",
+		"gnomAD AF (Non-Finnish European)", "gnomAD AF (Other)", "gnomAD AF (South Asian)",
+		"1000 Genomes AF", "ESP6500 AF (average)", "ESP6500 AF (European American)",
+		"ESP6500 AF (African American)", "COSMIC transcript", "COSMIC protein change", 
+		"COSMIC variant count [exact nucleotide change]", "cosmic_site_nt", "CGL driver class",
+		"TARGET", "dbSNP", "cgc_role", "cgc_inheritance", "cgc_tumor_type_somatic",
+		"cgc_tumor_type_germline", "ClinVar", "ClinVar disease identifier", "ClinVar XRef",
+		"GWAS Phenotype (GRASP)", "GWAS PMID (GRASP)", "Protein 3D variant"
+	]
+
+
+	def __init__(self, _chr, pos, strand, ref, alt):
+		# '_chr' used to avoid naming confliction with python built-in 'chr'
+		self.chromosome = CravatQuery.format_chromosome(_chr)
+		self.position = pos
+		self.strand = strand
+		self.reference = ref
+		self.alternate = alt
+		self.values = [self.chromosome, self.position, self.strand, self.reference, self.alternate]
+
+
+	def __str__(self):
+		""" : Represent the CravatQuery as a valid query string for call to Cravat server """
+		return "_".join(map(lambda x: str(x), self.values))
+
+	
+	def as_query_string(self):
+		return str(self)
+
+	
+	@staticmethod
+	def from_dictionary(d):
+		"""
+		: Instantiate a CravatQuery from a dictionary representation.
+		: Args:
+			: d <dictionary>: A dictionary representing a CravatQuery, containing keys: [{}] 
+		""".format(CravatQuery.query_keys)
+
+		for key in CravatQuery.query_keys:
+			if key not in d:
+				raise CravatQueryException("CravatQuery.from_dictionary requires keys: [{}], however key: '{}' was not provided "
+											.format(CravatQuery.query_keys, key))
+		return CravatQuery(d["chromosome"], d["position"], d["strand"], d["reference"], d["alternate"])
+
+
+	@staticmethod
+	def from_array(array, mapping=None):
+		"""
+		: Instantiate a CravatQuery from an array of values. Useful when translating read lines from a file.
+		: Args:
+			: fmt <str> - Either 'cr' or 'vcf', describing input format
+			: array <list> - The values to instantiate the CravatQuery from
+			: mapping <dict> - Optional. A dictionary associating cravat parameters to indicies in the array.
+								Valid values are: 'chromosome', 'position', 'strand', 'reference', 'alternate'
+		"""
+		
+		# Set the mapping value. Either recieved from user, or obtained via defualt associated to 'fmt'
+		if mapping == None:
+			mapping = CravatQuery.default_mapping
+			
+		# Build a dict of cravat querying keys to values.
+		d = {}
+		for key in CravatQuery.query_keys:
+			# Try to get index position from mapping by the key, and value from array by the index
+			if key in mapping:
+				index = mapping[key]
+				d[key] = array[index]
+			# If index not provided in mapping, check if there is a defualt value
+			elif key in CravatQuery.default_values:
+				d[key] = CravatQuery.default_values[key]
+			# Unable to get value for querying key, meaning can't construct the minimum requirements for query
+			else:
+				raise CravatQueryException("CravatQuery.from_array requires a mapping index for key: '{}', however value was not provided".format(key))
+		return CravatQuery.from_dictionary(d)
+
+
+
+	@staticmethod
+	def format_chromosome(_chr):
+		"""
+		: Format a chromosome for use as query parameter. '_chr' name used to avoid python built-in name confliction.
+		: Args:
+			: _chr - Either an interger [1,23], or 'x'/'X', or 'y'/'Y', or a string of the form
+			: 		'chr<z>' where '<z>' is one of the previously described values 
+		"""
+		inRange = lambda x: 1 <= x and x <= 23
+		_chr = _chr.lower()
+		_chr = _chr.strip('chr')
+		# Handler interger chromosomes 1 to 23
+		try:
+			_chr = int(_chr)
+			if inRange(_chr):
+				return 'chr' + str(_chr)
+			else:
+				raise CravatQueryException("Chromsomme of '{}' was out of range [1,23]".format(_chr))
+		except:
+			pass
+		# Handle chromosomes chromosomes x and y
+		if _chr == 'x' or _chr == 'y':
+			return 'chr' + _chr
+		raise CravatQueryException("Unable to resolve input: '{}' into a valid chromosome representation".format(_chr))
+
+
+	@staticmethod
+	def jump_header(in_file, out_file, headerlines=0):
+		"""
+		: Jumps over a header space of line number 'headerlines'. Sets up in_file so that
+		: the next execution of in_file.readline() will return the first non-header line.
+		"""
+		in_file.seek(0)
+		for line in range(headerlines):
+			in_file.readline()
+
+
+def main(in_path, out_path, pre_callback=None, user_mapping=None):
+	"""
+	: Read the file line by line and use data to query cravat server.
+	: Args:
+		: fmt <str>: 'cr' or 'vcf'. The input format
+		: in_path <str>: Path to input file
+		: in_path <str>: Path to output file
+		: header_callback <function>: A function to handle the header space. Executed
+			before main loop. Recieves in_file, out_file, and fmt as argumnets
+	"""
+
+	with open(in_path, 'r') as in_file, \
+	open(out_path, 'w') as out_file:
+
+		# Perform any pre-processing steps, such as jumping a header space
+		if pre_callback:
+			pre_callback(in_file, out_file, fmt)
+
+		# main loop
+		for line in in_file:
+
+			# Create query from line of input data
+			line = line.strip().split('\t')
+			query = CravatQuery.from_array(line, user_mapping)
+			# Make request, and write respone data
+			call = requests.get(CravatQuery.endpoint, params={ 'mutation': query.as_query_string })
+			try:
+				if call.status_code != 200 or call.text == "":
+					raise CravatQueryException("Bad Server Response. Respone code: '{}', Response Text: '{}'".format(call.status_code, call.text))
+				json_response = json.loads(call.text)
+				wrote = False
+				for key, val in json_response.items():
+					# Set numeric values to uniform format
+					try:
+						val = float(val)
+						val = format(val, ".4f")
+					except:
+						pass
+					if wrote:
+						out_file.write("\t")
+					out_file.write(val)
+					wrote = True
+				out_file.write("\n")
+			except CravatQueryException as e:
+				print(e)
+				
+		
+
+
+if __name__ == "__main__":
+
+	# Input and output file paths, obtained form command line
+	in_path = sys.argv[1]
+	out_path = sys.argv[2]
+
+	# Possibly allow user mapping configuration thourgh here. Not fully implemented
+	if len(sys.argv) > 2:
+		user_mapping = sys.argv[3]
+
+	# Run the main operation
+	main(in_path, out_path)
\ No newline at end of file

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cravat_annotate/cravat_annotate.xml	Tue Jun 12 12:05:48 2018 -0400
@@ -0,0 +1,25 @@
+<tool id="cravat_query" name="CRAVAT Query" version="1.0.0">
+    <description>Queries CRAVAT for cancer annotation</description>
+  <command interpreter="python">cravat_annotate.py $input $output</command>
+  
+  <inputs>
+    <param format="tabular" name="input" type="data" label="Source file"/>
+  </inputs>
+  
+  <outputs>
+    <data format="tabular" name="output" />
+  </outputs>
+
+  <tests>
+    <test>
+      <param name="input" value="input_call.txt"/>
+      <output name="output" file="Galaxy23-[CRAVAT_Query_on_data_22].tabular"/>
+    </test>
+  </tests>
+
+  <help>
+    This tool queries CRAVAT for cancer annotation.
+  </help>
+
+</tool>
+

--- a/cravat_submit/cravat_submit.py	Tue Jun 12 12:05:40 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,103 +0,0 @@
-import requests
-import json
-import time
-import urllib
-import sys
-import csv
-
-input_filename = sys.argv[1]
-input_select_bar = sys.argv[2]
-output_filename = sys.argv[3]
-
-# HACK: Input args corrections. 
-if input_select_bar == "None":
-    # The server represents an analyses of None as ""; however, submitting a blank string on command line throws off arg position
-    input_select_bar = ""
-    # The server represents the "Vest and Chasm" analyses as "VEST;CHASM; however, galaxy converts the semi-colon to an 'X'. Switch it back.
-elif input_select_bar == "VESTXCHASM":
-    input_select_bar = "VEST;CHASM" 
-
-write_header = True
-
-#plugs in params to given URL
-submit = requests.post('http://staging.cravat.us/CRAVAT/rest/service/submit', files={'inputfile':open(input_filename)}, data={'email':'[e-mail]', 'analyses': input_select_bar})   
-#,'analysis':input_select_bar,'functionalannotation': "on"})                   
-#Makes the data a json dictionary, takes out only the job ID
-jobid = json.loads(submit.text)['jobid']
-#out_file.write(jobid)    
-submitted = json.loads(submit.text)['status']
-#out_file.write('\t' + submitted)
-
-#loops until we find a status equal to Success, then breaks
-while True:
-    check = requests.get('http://staging.cravat.us/CRAVAT/rest/service/status', params={'jobid': jobid})
-    status = json.loads(check.text)['status']
-    resultfileurl = json.loads(check.text)['resultfileurl']
-    #out_file.write(str(status) + ', ')
-    if status == 'Success':
-        #out_file.write('\t' + resultfileurl)
-        break
-    else:
-        time.sleep(2)
-        
-#out_file.write('\n')
-
-#creates three files
-file_1 = time.strftime("%H:%M") + '_Z_Variant_Result.tsv'
-file_2 = time.strftime("%H:%M") + '_Z_Additional_Details.tsv'
-file_3 = time.strftime("%H:%M") + 'Combined_Variant_Results.tsv'
-
-
-#Download the two results
-urllib.urlretrieve("http://staging.cravat.us/CRAVAT/results/" + jobid + "/" + "Variant.Result.tsv", file_1)
-urllib.urlretrieve("http://staging.cravat.us/CRAVAT/results/" + jobid + "/" + "Variant_Additional_Details.Result.tsv", file_2)
-
-headers = []
-duplicates = []
-
-#opens the Variant Result file and the Variant Additional Details file as csv readers, then opens the output file (galaxy) as a writer
-with open(file_1) as tsvin_1, open(file_2) as tsvin_2, open(output_filename, 'wb') as tsvout:
-    tsvreader_1 = csv.reader(tsvin_1, delimiter='\t')
-    tsvreader_2 = csv.reader(tsvin_2, delimiter='\t')
-    tsvout = csv.writer(tsvout, delimiter='\t')
-         
-#loops through each row in the Variant Additional Details file         
-    for row in tsvreader_2:
-        #sets row_2 equal to the same row in Variant Result file
-        row_2 = tsvreader_1.next()
-        #checks if row is empty or if the first term contains '#'
-        if row == [] or row[0][0] == '#':
-            continue
-        #checks if the row begins with input line
-        if row[0] == 'Input line':
-            #Goes through each value in the headers list in VAD
-            for value in row:   
-                #Adds each value into headers 
-                headers.append(value)
-            #Loops through the Keys in VR
-            for value in row_2:
-                #Checks if the value is already in headers
-                if value in headers:
-                    continue
-                #else adds the header to headers
-                else:
-                    headers.append(value)
-                    
-            print headers
-            tsvout.writerow(headers)
-            
-            
-        else:
-            
-            cells = []
-            #Goes through each value in the next list
-            for value in row:
-                #adds it to cells
-                cells.append(value)
-            #Goes through each value from the VR file after position 11 (After it is done repeating from VAD file)
-            for value in row_2[11:]:
-                #adds in the rest of the values to cells
-                cells.append(value)
-                
-            print  cells
-            tsvout.writerow(cells)
\ No newline at end of file

--- a/cravat_submit/cravat_submit.xml	Tue Jun 12 12:05:40 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,34 +0,0 @@
-<tool id="cravat_submit" name="CRAVAT Submit, Check, and Retrieve" version="0.1.0">
-    <description>Submits, checks for, and retrieves data for cancer annotation</description>
-  <command interpreter="python">cravat_submit.py $input $dropdown $output</command>
-  
-  
-  <inputs>
-  
-    <param format="tabular" name="input" type="data" label="Source file"> </param>
-    <param format="tabular" name="dropdown" type="select" label="Analysis Program">
-      <option value="None">None</option>
-      <option value="VEST">VEST</option>
-      <option value="CHASM">CHASM</option>
-      <option value="VEST;CHASM">VEST and CHASM</option>
-    </param>
-    
-    
-  </inputs>
-  
-  <outputs>
-    <data format="tabular" name="output" />
-  </outputs>
-
-  <tests>
-    <test>
-      <param name="input" value="fa_gc_content_input.fa"/>
-      <output name="out_file1" file="fa_gc_content_output.txt"/>
-    </test>
-  </tests>
-
-  <help>
- This tool submits, checks for, and retrieves data for cancer annotation.
-  </help>
-
-</tool>