# HG changeset patch
# User in_silico
# Date 1531923523 14400
# Node ID 326aadaa3dd97daf9dd9f382d3b96ef77c3e0b5b
# Parent c5f0a7e538ff23684ea50ea1438cda0dd8aed8a7
Uploaded
diff -r c5f0a7e538ff -r 326aadaa3dd9 cravat_annotate/cravat_annotate.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/cravat_annotate/cravat_annotate.py Wed Jul 18 10:18:43 2018 -0400
@@ -0,0 +1,132 @@
+"""
+A galaxy wrapper for the /rest/service/query API endpoint on Cravat.
+"""
+
+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)
diff -r c5f0a7e538ff -r 326aadaa3dd9 cravat_annotate/cravat_annotate.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/cravat_annotate/cravat_annotate.xml Wed Jul 18 10:18:43 2018 -0400
@@ -0,0 +1,25 @@
+
+ Queries CRAVAT for cancer annotation
+ cravat_annotate.py -i $input -o $output
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ This tool queries CRAVAT for cancer annotation.
+
+
+
+
diff -r c5f0a7e538ff -r 326aadaa3dd9 cravat_convert/__pycache__/base_converter.cpython-36.pyc
Binary file cravat_convert/__pycache__/base_converter.cpython-36.pyc has changed
diff -r c5f0a7e538ff -r 326aadaa3dd9 cravat_convert/__pycache__/vcf_converter.cpython-36.pyc
Binary file cravat_convert/__pycache__/vcf_converter.cpython-36.pyc has changed
diff -r c5f0a7e538ff -r 326aadaa3dd9 cravat_convert/base_converter.py
--- a/cravat_convert/base_converter.py Wed Jul 18 10:18:36 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
diff -r c5f0a7e538ff -r 326aadaa3dd9 cravat_convert/cravat_convert.py
--- a/cravat_convert/cravat_convert.py Wed Jul 18 10:18:36 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: path to input vcf file
- : out_path: path to output cravat file. Will defualt to cravat_converted.txt in the input directory.
- : cr_sep: the value delimiter for the output cravat file. Default value of '\\t'.
- : out_newline: 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)
diff -r c5f0a7e538ff -r 326aadaa3dd9 cravat_convert/cravat_convert.xml
--- a/cravat_convert/cravat_convert.xml Wed Jul 18 10:18:36 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,20 +0,0 @@
-
- Converts a VCF format file to a Cravat format file
- cravat_convert.py -i $input -o $output
-
-
-
-
-
-
-
-
-
-
-
-
- Converts a VCF format file to a Cravat format file
-
-
-
-
diff -r c5f0a7e538ff -r 326aadaa3dd9 cravat_convert/vcf_converter.py
--- a/cravat_convert/vcf_converter.py Wed Jul 18 10:18:36 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