# HG changeset patch
# User in_silico
# Date 1531923944 14400
# Node ID a7e641d146f598874abc257f96ae8e548ca4f603
# Parent 326aadaa3dd97daf9dd9f382d3b96ef77c3e0b5b
Uploaded
diff -r 326aadaa3dd9 -r a7e641d146f5 cravat_annotate/cravat_annotate.py
--- a/cravat_annotate/cravat_annotate.py Wed Jul 18 10:18:43 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,132 +0,0 @@
-"""
-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 326aadaa3dd9 -r a7e641d146f5 cravat_annotate/cravat_annotate.xml
--- a/cravat_annotate/cravat_annotate.xml Wed Jul 18 10:18:43 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,25 +0,0 @@
-
- Queries CRAVAT for cancer annotation
- cravat_annotate.py -i $input -o $output
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- This tool queries CRAVAT for cancer annotation.
-
-
-
-
diff -r 326aadaa3dd9 -r a7e641d146f5 cravat_convert/__pycache__/base_converter.cpython-36.pyc
Binary file cravat_convert/__pycache__/base_converter.cpython-36.pyc has changed
diff -r 326aadaa3dd9 -r a7e641d146f5 cravat_convert/__pycache__/vcf_converter.cpython-36.pyc
Binary file cravat_convert/__pycache__/vcf_converter.cpython-36.pyc has changed
diff -r 326aadaa3dd9 -r a7e641d146f5 cravat_convert/base_converter.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/cravat_convert/base_converter.py Wed Jul 18 10:25:44 2018 -0400
@@ -0,0 +1,22 @@
+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 326aadaa3dd9 -r a7e641d146f5 cravat_convert/cravat_convert.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/cravat_convert/cravat_convert.py Wed Jul 18 10:25:44 2018 -0400
@@ -0,0 +1,80 @@
+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 326aadaa3dd9 -r a7e641d146f5 cravat_convert/cravat_convert.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/cravat_convert/cravat_convert.xml Wed Jul 18 10:25:44 2018 -0400
@@ -0,0 +1,20 @@
+
+ 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 326aadaa3dd9 -r a7e641d146f5 cravat_convert/vcf_converter.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/cravat_convert/vcf_converter.py Wed Jul 18 10:25:44 2018 -0400
@@ -0,0 +1,243 @@
+"""
+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