Mercurial > repos > in_silico > cravat_annotate_mutations
changeset 20:c5b3d80c43e6 draft
Uploaded
| author | in_silico |
|---|---|
| date | Tue, 12 Jun 2018 14:06:22 -0400 |
| parents | ec55c91879e8 |
| children | 94fdd28c0dbb |
| files | cravat_annotate/cravat_annotate.py cravat_annotate/cravat_annotate.xml cravat_convert/base_converter.py cravat_convert/cravat_convert.py cravat_convert/cravat_convert.xml cravat_convert/vcf_converter.py |
| diffstat | 6 files changed, 152 insertions(+), 362 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cravat_annotate/cravat_annotate.py Tue Jun 12 14:06:22 2018 -0400 @@ -0,0 +1,127 @@ +""" +A galaxy wrapper for the /rest/service/query API endpoint on Cravat. +""" + + +import requests +import json +import sys +import re +import argparse + + +# 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 +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. +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 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 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: + 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. Respone code: '{}', Response Text: '{}'".format(call.status_code, call.text)) + json_response = json.loads(call.text) + # See if server returned additional json key-val paris not expected in response_keys + for key in json_response: + if key not in response_keys: + response_keys.append(key) + # Write key in order of response_keys to standardize order of output columns + wrote = False + for key in response_keys: + if key not in json_response: + val = None + val = json_response[key] + # Format standardization for numerics + 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") + + +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 Tue Jun 12 14:06:22 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> +
--- a/cravat_convert/base_converter.py Tue Jun 12 14:06:10 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 Tue Jun 12 14:06:10 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,77 +0,0 @@ -''' -Convert a VCF format file to Cravat format file -''' - -import os -import argparse -from vcf_converter import CravatConverter - -# File read/write configuration variables -vcf_sep = '\t' -cr_sep = '\t' -cr_newline = '\n' - -# VCF Headers mapped to their index position in a row of VCF values -vcf_mapping = { - 'CHROM': 0, - 'POS': 1, - 'ID': 2, - 'REF': 3, - 'ALT': 4, - 'QUAL': 5, - 'FILTER': 6, - 'INFO': 7, - 'FORMAT': 8, - 'NA00001': 9, - 'NA00002': 10, - 'NA00003': 11 -} - - -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 = os.path.join(os.getcwd(), "cravat_converted.txt"), - help = 'Output path to write the cravat file to') - return parser.parse_args() - - -def convert(in_path, out_path=None): - 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() - - for line in in_file: - if line.startswith("#"): - continue - line = line.strip().split(vcf_sep) - # 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() - convert(cli_args.input, cli_args.output)
--- a/cravat_convert/cravat_convert.xml Tue Jun 12 14:06:10 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 Tue Jun 12 14:06:10 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