changeset 23:f8703ba30180 draft

Uploaded
author in_silico
date Wed, 18 Jul 2018 10:25:17 -0400
parents 0ca746ab1151
children e46db72f5b74
files cravat_annotate/cravat_annotate.py cravat_annotate/cravat_annotate.xml cravat_convert/__pycache__/base_converter.cpython-36.pyc cravat_convert/__pycache__/vcf_converter.cpython-36.pyc cravat_convert/base_converter.py cravat_convert/cravat_convert.py cravat_convert/cravat_convert.xml cravat_convert/vcf_converter.py
diffstat 8 files changed, 153 insertions(+), 369 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cravat_annotate/cravat_annotate.py	Wed Jul 18 10:25:17 2018 -0400
@@ -0,0 +1,128 @@
+import requests
+import json
+import sys
+import re
+import argparse
+from __future__ import print_function
+
+
+# The endpoint that CravatQuerys are submitted to
+endpoint = 'http://www.cravat.us/CRAVAT/rest/service/query'
+
+
+# newline and delimiter values used in the output file
+delimiter = "\t"
+newline = "\n"
+
+
+# Defualt indices for intepretting a cravat file's row of data in to a CravatQuery
+cr_mapping = {
+	'chromosome': 1,
+	'position': 2,
+	'strand': 3,
+	'reference': 4,
+	'alternate': 5
+}
+
+
+# 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.
+ordered_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 get_args():
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--input',
+                            '-i',
+                            required = True,
+                            help='Input path to a cravat file for querying',)
+    parser.add_argument('--output',
+                            '-o',
+                            default = None,
+                            help = 'Output path to write results from query')
+    return parser.parse_args()
+
+
+def format_chromosome(chrom):
+	""" : Ensure chromosome entry is propely formatted for use as querying attribute. """
+	if chrom[0:3] == 'chr':
+		return chrom
+	return 'chr' + str(chrom)
+
+
+def get_query_string(row):
+	""" : From a row dict, return a query string for the Cravat server.
+		: The row dict is cravat headeres associated to their values of that row.
+	"""
+	return '_'.join([ row['chromosome'], row['position'], row['strand'], row['reference'], row['alternate'] ])
+
+
+def query(in_path, out_path):
+	""" : From a Cravat the file at in_path, query each line on the Cravat server.
+		: Write the response values to file at out_path.
+	"""
+	with open(in_path, 'r') as in_file, \
+	open(out_path, 'w') as out_file:
+		for line in in_file:
+			try:
+				line = line.strip().split('\t')
+				# row is dict of cravat col headers assioted values in this line
+				row = { header: line[index] for header, index in cr_mapping.items() }
+				row['chromosome'] = format_chromosome(row['chromosome'])
+				query_string = get_query_string(row)
+				call = requests.get(endpoint, params={ 'mutation': query_string })
+				if call.status_code != 200 or call.text == "":
+					raise requests.RequestException('Bad server response for query="{}". Respone code: "{}", Response Text: "{}"'
+						.format(query_string, call.status_code, call.text))
+				json_response = json.loads(call.text)
+				# See if server returned additional json key-vals not expected in ordered_keys
+				for key in json_response:
+					if key not in ordered_keys:
+						ordered_keys.append(key)
+				# Write key in order of ordered_keys to standardize order of output columns
+				wrote = False
+				for key in ordered_keys:
+					if key in json_response:
+						val = json_response[key]
+					else:
+						val = None
+					# Standardize format for  numeric values
+					try:
+						val = float(val)
+						val = format(val, ".4f")
+					except:
+						pass
+					if wrote:
+						out_file.write(delimiter)
+					out_file.write(str(val))
+					wrote = True
+				out_file.write(newline)		
+			except Exception as e:
+				print(e, file=sys.stderr)
+				continue
+
+
+if __name__ == "__main__":
+	cli_args = get_args()
+	if cli_args.output == None:
+		base, _ = os.path.split(cli_args.input)
+		cli_args.output = os.path.join(base, "cravat_converted.txt") 
+	query(cli_args.input, cli_args.output)
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cravat_annotate/cravat_annotate.xml	Wed Jul 18 10:25:17 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 -i $input -o $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>
+
Binary file cravat_convert/__pycache__/base_converter.cpython-36.pyc has changed
Binary file cravat_convert/__pycache__/vcf_converter.cpython-36.pyc has changed
--- a/cravat_convert/base_converter.py	Wed Jul 18 10:18:06 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,22 +0,0 @@
-class BaseConverter(object):
-    def __init__(self):
-        self.format_name = None
-    def check_format(self,*args,**kwargs):
-        err_msg = 'Converter for %s format has no method check_format' %\
-            self.format_name
-        raise NotImplementedError(err_msg)
-    def setup(self,*args,**kwargs):
-        err_msg = 'Converter for %s format has no method setup' %\
-            self.format_name
-        raise NotImplementedError(err_msg)
-    def convert_line(self,*args,**kwargs):
-        err_msg = 'Converter for %s format has no method convert_line' %\
-            self.format_name
-        raise NotImplementedError(err_msg)
-
-
-class BadFormatError(Exception):
-    def __init__(self, message, errors=None):
-        super(BadFormatError, self).__init__(message)
-        # Support for custom error codes, if added later
-        self.errors = errors
\ No newline at end of file
--- a/cravat_convert/cravat_convert.py	Wed Jul 18 10:18:06 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,84 +0,0 @@
-'''
-Convert a VCF format file to Cravat format file
-'''
-
-import os
-import argparse
-from vcf_converter import CravatConverter
-from __future__ import print_function
-
-def get_vcf_mapping():
-    """ : VCF Headers mapped to their index position in a row of VCF values.
-        : These are only the mandatory columns, per the VCF spec.
-    """
-    return {
-        'CHROM': 0,
-        'POS': 1,
-        'ID': 2,
-        'REF': 3,
-        'ALT': 4,
-        'QUAL': 5,
-        'FILTER': 6,
-        'INFO': 7
-    }
-
-
-def get_args():
-    parser = argparse.ArgumentParser()
-    parser.add_argument('--input',
-                            '-i',
-                            required = True,
-                            help='Input path to a VCF file for conversion',)
-    parser.add_argument('--output',
-                            '-o',
-                            default = None,
-                            help = 'Output path to write the cravat file to')
-    return parser.parse_args()
-
-
-def convert(in_path, out_path=None, cr_sep='\t', cr_newline='\n'):
-    """ : Convert a VCF file to a Cravat file.
-        : Arguments:
-            : in_path: <str> path to input vcf file
-            : out_path: <str> path to output cravat file. Will defualt to cravat_converted.txt in the input directory.
-            : cr_sep: <str> the value delimiter for the output cravat file. Default value of '\\t'.
-            : out_newline: <str> the newline delimiter in the output cravat file. Default of '\\n'
-    """
-    if not out_path:
-        base, _ = os.path.split(in_path)
-        out_path = os.path.join(base, "cravat_converted.txt")
-    
-    with open(in_path, 'r') as in_file, \
-    open(out_path, 'w') as out_file:
-
-        # cr_count will be used to generate the 'TR' field of the cravat rows (first header)
-        cr_count = 0
-        # VCF lines are always assumed to be '+' strand, as VCF doesn't specify that attribute
-        strand = '+'
-        # VCF converter. Adjusts position, reference, and alternate for Cravat formatting.
-        converter = CravatConverter()
-        # A dictionary of mandatory vcf headers mapped to their row indices
-        vcf_mapping = get_vcf_mapping()
-
-        for line in in_file:
-            if line.startswith("#"):
-                continue
-            line = line.strip().split()
-            # row is dict of VCF headers mapped to corresponding values of this line
-            row = { header: line[index] for header, index in vcf_mapping.items() }
-            for alt in row["ALT"].split(","):
-                new_pos, new_ref, new_alt = converter.extract_vcf_variant(strand, row["POS"], row["REF"], alt)
-                new_pos, new_ref, new_alt = str(new_pos), str(new_ref), str(new_alt)
-                cr_line = cr_sep.join([
-                    'TR' + str(cr_count), row['CHROM'], new_pos, strand, new_ref, new_alt, row['ID']
-                ])
-                out_file.write(cr_line + cr_newline)
-                cr_count += 1
-
-
-if __name__ == "__main__":
-    cli_args = get_args()
-    if cli_args.output == None:
-        base, _ = os.path.split(cli_args.input)
-        cli_args.output = os.path.join(base, "cravat_converted.txt") 
-    convert(in_path = cli_args.input, out_path = cli_args.output)
--- a/cravat_convert/cravat_convert.xml	Wed Jul 18 10:18:06 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,20 +0,0 @@
-<tool id="cravat_convert" name="CRAVAT Convert" version="1.0.0">
-    <description>Converts a VCF format file to a Cravat format file</description>
-    <command interpreter="python">cravat_convert.py -i $input -o $output</command>
-  
-    <inputs>
-        <param format="tabular" name="input" type="data" label="Source file"/>
-    </inputs>
-  
-    <outputs>
-        <data format="tabular" name="output" />
-    </outputs>
-
-    <!-- <tests></tests> -->
-
-    <help>
-        Converts a VCF format file to a Cravat format file
-    </help>
-
-</tool>
-
--- a/cravat_convert/vcf_converter.py	Wed Jul 18 10:18:06 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,243 +0,0 @@
-"""
-A module originally obtained from the cravat package. Modified to use in the vcf
-converter galaxy tool.
-
-
-Register of changes made (Chris Jacoby):
-    1) Changed imports as galaxy tool won't have access to complete cravat python package
-    2) Defined BadFormatError in BaseConverted file, as I didn't have the BadFormatError module
-"""
-
-from base_converter import BaseConverter, BadFormatError
-import re
-
-class CravatConverter(BaseConverter):
-    
-    def __init__(self):
-        self.format_name = 'vcf'
-        self.samples = []
-        self.var_counter = 0
-        self.addl_cols = [{'name':'phred',
-                           'title':'Phred',
-                           'type':'string'},
-                          {'name':'filter',
-                           'title':'VCF filter',
-                           'type':'string'},
-                          {'name':'zygosity',
-                           'title':'Zygosity',
-                           'type':'string'},
-                          {'name':'alt_reads',
-                           'title':'Alternate reads',
-                           'type':'int'},
-                          {'name':'tot_reads',
-                           'title':'Total reads',
-                           'type':'int'},
-                          {'name':'af',
-                           'title':'Variant allele frequency',
-                           'type':'float'}]
-    
-    def check_format(self, f): 
-        return f.readline().startswith('##fileformat=VCF')
-    
-    def setup(self, f):
-        
-        vcf_line_no = 0
-        for line in f:
-            vcf_line_no += 1
-            if len(line) < 6:
-                continue
-            if line[:6] == '#CHROM':
-                toks = re.split('\s+', line.rstrip())
-                if len(toks) > 8:
-                    self.samples = toks[9:]
-                break
-    
-    def convert_line(self, l):
-        if l.startswith('#'): return None
-        self.var_counter += 1
-        toks = l.strip('\r\n').split('\t')
-        all_wdicts = []
-        if len(toks) < 8:
-            raise BadFormatError('Wrong VCF format')
-        [chrom, pos, tag, ref, alts, qual, filter, info] = toks[:8]
-        if tag == '':
-            raise BadFormatError('ID column is blank')
-        elif tag == '.':
-            tag = 'VAR' + str(self.var_counter)
-        if chrom[:3] != 'chr':
-            chrom = 'chr' + chrom
-        alts = alts.split(',')
-        len_alts = len(alts)
-        if len(toks) == 8:
-            for altno in range(len_alts):
-                wdict = None
-                alt = alts[altno]
-                newpos, newref, newalt = self.extract_vcf_variant('+', pos, ref, alt)
-                wdict = {'tags':tag,
-                         'chrom':chrom,
-                         'pos':newpos,
-                         'ref_base':newref,
-                         'alt_base':newalt,
-                         'sample_id':'no_sample',
-                         'phred': qual,
-                         'filter': filter}
-                all_wdicts.append(wdict)
-        elif len(toks) > 8:
-            sample_datas = toks[9:]
-            genotype_fields = {}
-            genotype_field_no = 0
-            for genotype_field in toks[8].split(':'):
-                genotype_fields[genotype_field] = genotype_field_no
-                genotype_field_no += 1
-            if not ('GT' in genotype_fields):
-                raise BadFormatError('No GT Field')
-            gt_field_no = genotype_fields['GT']
-            for sample_no in range(len(sample_datas)):
-                sample = self.samples[sample_no]
-                sample_data = sample_datas[sample_no].split(':')
-                gts = {}
-                for gt in sample_data[gt_field_no].replace('/', '|').split('|'):
-                    if gt == '.':
-                        continue
-                    else:
-                        gts[int(gt)] = True
-                for gt in sorted(gts.keys()):
-                    wdict = None
-                    if gt == 0:
-                        continue
-                    else:
-                        alt = alts[gt - 1]
-                        newpos, newref, newalt = self.extract_vcf_variant('+', pos, ref, alt)
-                        zyg = self.homo_hetro(sample_data[gt_field_no])
-                        depth, alt_reads, af = self.extract_read_info(sample_data, gt, gts, genotype_fields)
-                            
-                        wdict = {'tags':tag,
-                                 'chrom':chrom,
-                                 'pos':newpos,
-                                 'ref_base':newref,
-                                 'alt_base':newalt,
-                                 'sample_id':sample,
-                                 'phred': qual,
-                                 'filter': filter,
-                                 'zygosity': zyg,
-                                 'tot_reads': depth,
-                                 'alt_reads': alt_reads,
-                                 'af': af,                                
-                                 }
-                        all_wdicts.append(wdict)
-        return all_wdicts
- 
-    #The vcf genotype string has a call for each allele separated by '\' or '/'
-    #If the call is the same for all allels, return 'hom' otherwise 'het'
-    def homo_hetro(self, gt_str):
-        if '.' in gt_str:
-            return '';
-        
-        gts = gt_str.strip().replace('/', '|').split('|')
-        for gt in gts:
-            if gt != gts[0]:
-                return 'het'
-        return 'hom'            
-                        
-    #Extract read depth, allele count, and allele frequency from optional VCR information
-    def extract_read_info (self, sample_data, gt, gts, genotype_fields): 
-        depth = ''
-        alt_reads = ''
-        ref_reads = ''
-        af = ''
-        
-        #AD contains 2 values usually ref count and alt count unless there are 
-        #multiple alts then it will have alt 1 then alt 2.
-        if 'AD' in genotype_fields and genotype_fields['AD'] <= len(sample_data): 
-            if 0 in gts.keys():
-                #if part of the genotype is reference, then AD will have #ref reads, #alt reads
-                ref_reads = sample_data[genotype_fields['AD']].split(',')[0]
-                alt_reads = sample_data[genotype_fields['AD']].split(',')[1]
-            elif gt == max(gts.keys()):    
-                #if geontype has multiple alt bases, then AD will have #alt1 reads, #alt2 reads
-                alt_reads = sample_data[genotype_fields['AD']].split(',')[1]
-            else:
-                alt_reads = sample_data[genotype_fields['AD']].split(',')[0]                            
-                             
-        if 'DP' in genotype_fields and genotype_fields['DP'] <= len(sample_data): 
-            depth = sample_data[genotype_fields['DP']] 
-        elif alt_reads != '' and ref_reads != '':
-            #if DP is not present but we have alt and ref reads count, dp = ref+alt
-            depth = int(alt_reads) + int(ref_reads)   
-
-        if 'AF' in genotype_fields and genotype_fields['AF'] <= len(sample_data):
-            af = float(sample_data[genotype_fields['AF']] )
-        elif depth != '' and alt_reads != '':
-            #if AF not specified, calc it from alt and ref reads
-            af = float(alt_reads) / float(depth)
- 
-        return depth, alt_reads, af
-            
-    def extract_vcf_variant (self, strand, pos, ref, alt):
-
-        reflen = len(ref)
-        altlen = len(alt)
-        
-        # Returns without change if same single nucleotide for ref and alt. 
-        if reflen == 1 and altlen == 1 and ref == alt:
-            return pos, ref, alt
-        
-        # Trimming from the start and then the end of the sequence 
-        # where the sequences overlap with the same nucleotides
-        new_ref2, new_alt2, new_pos = \
-            self.trimming_vcf_input(ref, alt, pos, strand)
-                
-        if new_ref2 == '':
-            new_ref2 = '-'
-        if new_alt2 == '':
-            new_alt2 = '-'
-        
-        return new_pos, new_ref2, new_alt2
-    
-    # This function looks at the ref and alt sequences and removes 
-    # where the overlapping sequences contain the same nucleotide.
-    # This trims from the end first but does not remove the first nucleotide 
-    # because based on the format of VCF input the 
-    # first nucleotide of the ref and alt sequence occur 
-    # at the position specified.
-    #     End removed first, not the first nucleotide
-    #     Front removed and position changed
-    def trimming_vcf_input(self, ref, alt, pos, strand):
-        pos = int(pos)
-        reflen = len(ref)
-        altlen = len(alt)
-        minlen = min(reflen, altlen)
-        new_ref = ref
-        new_alt = alt
-        new_pos = pos
-        # Trims from the end. Except don't remove the first nucleotide. 
-        # 1:6530968 CTCA -> GTCTCA becomes C -> GTC.
-        for nt_pos in range(0, minlen - 1): 
-            if ref[reflen - nt_pos - 1] == alt[altlen - nt_pos - 1]:
-                new_ref = ref[:reflen - nt_pos - 1]
-                new_alt = alt[:altlen - nt_pos - 1]
-            else:
-                break    
-        new_ref_len = len(new_ref)
-        new_alt_len = len(new_alt)
-        minlen = min(new_ref_len, new_alt_len)
-        new_ref2 = new_ref
-        new_alt2 = new_alt
-        # Trims from the start. 1:6530968 G -> GT becomes 1:6530969 - -> T.
-        for nt_pos in range(0, minlen):
-            if new_ref[nt_pos] == new_alt[nt_pos]:
-                if strand == '+':
-                    new_pos += 1
-                elif strand == '-':
-                    new_pos -= 1
-                new_ref2 = new_ref[nt_pos + 1:]
-                new_alt2 = new_alt[nt_pos + 1:]
-            else:
-                new_ref2 = new_ref[nt_pos:]
-                new_alt2 = new_alt[nt_pos:]
-                break  
-        return new_ref2, new_alt2, new_pos
-
-
-if __name__ == "__main__":
-    c = CravatConverter()
\ No newline at end of file