| Previous changeset 19:ec55c91879e8 (2018-06-12) Next changeset 21:94fdd28c0dbb (2018-06-27) |
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Commit message:
Uploaded |
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added:
cravat_annotate/cravat_annotate.py cravat_annotate/cravat_annotate.xml |
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removed:
cravat_convert/base_converter.py cravat_convert/cravat_convert.py cravat_convert/cravat_convert.xml cravat_convert/vcf_converter.py |
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| diff -r ec55c91879e8 -r c5b3d80c43e6 cravat_annotate/cravat_annotate.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cravat_annotate/cravat_annotate.py Tue Jun 12 14:06:22 2018 -0400 |
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| @@ -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) |
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| diff -r ec55c91879e8 -r c5b3d80c43e6 cravat_annotate/cravat_annotate.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cravat_annotate/cravat_annotate.xml Tue Jun 12 14:06:22 2018 -0400 |
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| @@ -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> + |
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| diff -r ec55c91879e8 -r c5b3d80c43e6 cravat_convert/base_converter.py --- a/cravat_convert/base_converter.py Tue Jun 12 14:06:10 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -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 |
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| diff -r ec55c91879e8 -r c5b3d80c43e6 cravat_convert/cravat_convert.py --- a/cravat_convert/cravat_convert.py Tue Jun 12 14:06:10 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -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) |
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| diff -r ec55c91879e8 -r c5b3d80c43e6 cravat_convert/cravat_convert.xml --- a/cravat_convert/cravat_convert.xml Tue Jun 12 14:06:10 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -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> - |
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| diff -r ec55c91879e8 -r c5b3d80c43e6 cravat_convert/vcf_converter.py --- a/cravat_convert/vcf_converter.py Tue Jun 12 14:06:10 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,243 +0,0 @@\n-"""\r\n-A module originally obtained from the cravat package. Modified to use in the vcf\r\n-converter galaxy tool.\r\n-\r\n-\r\n-Register of changes made (Chris Jacoby):\r\n- 1) Changed imports as galaxy tool won\'t have access to complete cravat python package\r\n- 2) Defined BadFormatError in BaseConverted file, as I didn\'t have the BadFormatError module\r\n-"""\r\n-\r\n-from base_converter import BaseConverter, BadFormatError\r\n-import re\r\n-\r\n-class CravatConverter(BaseConverter):\r\n- \r\n- def __init__(self):\r\n- self.format_name = \'vcf\'\r\n- self.samples = []\r\n- self.var_counter = 0\r\n- self.addl_cols = [{\'name\':\'phred\',\r\n- \'title\':\'Phred\',\r\n- \'type\':\'string\'},\r\n- {\'name\':\'filter\',\r\n- \'title\':\'VCF filter\',\r\n- \'type\':\'string\'},\r\n- {\'name\':\'zygosity\',\r\n- \'title\':\'Zygosity\',\r\n- \'type\':\'string\'},\r\n- {\'name\':\'alt_reads\',\r\n- \'title\':\'Alternate reads\',\r\n- \'type\':\'int\'},\r\n- {\'name\':\'tot_reads\',\r\n- \'title\':\'Total reads\',\r\n- \'type\':\'int\'},\r\n- {\'name\':\'af\',\r\n- \'title\':\'Variant allele frequency\',\r\n- \'type\':\'float\'}]\r\n- \r\n- def check_format(self, f): \r\n- return f.readline().startswith(\'##fileformat=VCF\')\r\n- \r\n- def setup(self, f):\r\n- \r\n- vcf_line_no = 0\r\n- for line in f:\r\n- vcf_line_no += 1\r\n- if len(line) < 6:\r\n- continue\r\n- if line[:6] == \'#CHROM\':\r\n- toks = re.split(\'\\s+\', line.rstrip())\r\n- if len(toks) > 8:\r\n- self.samples = toks[9:]\r\n- break\r\n- \r\n- def convert_line(self, l):\r\n- if l.startswith(\'#\'): return None\r\n- self.var_counter += 1\r\n- toks = l.strip(\'\\r\\n\').split(\'\\t\')\r\n- all_wdicts = []\r\n- if len(toks) < 8:\r\n- raise BadFormatError(\'Wrong VCF format\')\r\n- [chrom, pos, tag, ref, alts, qual, filter, info] = toks[:8]\r\n- if tag == \'\':\r\n- raise BadFormatError(\'ID column is blank\')\r\n- elif tag == \'.\':\r\n- tag = \'VAR\' + str(self.var_counter)\r\n- if chrom[:3] != \'chr\':\r\n- chrom = \'chr\' + chrom\r\n- alts = alts.split(\',\')\r\n- len_alts = len(alts)\r\n- if len(toks) == 8:\r\n- for altno in range(len_alts):\r\n- wdict = None\r\n- alt = alts[altno]\r\n- newpos, newref, newalt = self.extract_vcf_variant(\'+\', pos, ref, alt)\r\n- wdict = {\'tags\':tag,\r\n- \'chrom\':chrom,\r\n- \'pos\':newpos,\r\n- \'ref_base\':newref,\r\n- \'alt_base\':newalt,\r\n- \'sample_id\':\'no_sample\',\r\n- \'phred\': qual,\r\n- \'filter\': filter}\r\n- all_wdicts.append(wdict)\r\n- elif len(toks) > 8:\r\n- sample_datas = toks[9:]\r\n- genotype_fields = {}\r\n- genotype_field_no = 0\r\n- for genotype_field in toks[8].split(\':\'):\r\n- genotype_fields[genotype_field] = genotype_field_no\r\n- genotype_field_no += 1\r\n- if not (\'GT\' in genotype_fields):\r\n- raise BadFormatError(\'No GT Field\')\r\n- gt_field_no = genotype_fields[\'GT\']\r\n- for sample_no in range(len(sample_datas)):\r\n- sample = self.samples[sample_no]\r\n- sample_data = sample_datas[sample_no].split(\':\')\r\n- gts = {}\r\n- for gt in sample_data[gt_field_no].replace(\'/\', \'|\').split(\'|\'):\r\n- '..b'\r\n- ref_reads = sample_data[genotype_fields[\'AD\']].split(\',\')[0]\r\n- alt_reads = sample_data[genotype_fields[\'AD\']].split(\',\')[1]\r\n- elif gt == max(gts.keys()): \r\n- #if geontype has multiple alt bases, then AD will have #alt1 reads, #alt2 reads\r\n- alt_reads = sample_data[genotype_fields[\'AD\']].split(\',\')[1]\r\n- else:\r\n- alt_reads = sample_data[genotype_fields[\'AD\']].split(\',\')[0] \r\n- \r\n- if \'DP\' in genotype_fields and genotype_fields[\'DP\'] <= len(sample_data): \r\n- depth = sample_data[genotype_fields[\'DP\']] \r\n- elif alt_reads != \'\' and ref_reads != \'\':\r\n- #if DP is not present but we have alt and ref reads count, dp = ref+alt\r\n- depth = int(alt_reads) + int(ref_reads) \r\n-\r\n- if \'AF\' in genotype_fields and genotype_fields[\'AF\'] <= len(sample_data):\r\n- af = float(sample_data[genotype_fields[\'AF\']] )\r\n- elif depth != \'\' and alt_reads != \'\':\r\n- #if AF not specified, calc it from alt and ref reads\r\n- af = float(alt_reads) / float(depth)\r\n- \r\n- return depth, alt_reads, af\r\n- \r\n- def extract_vcf_variant (self, strand, pos, ref, alt):\r\n-\r\n- reflen = len(ref)\r\n- altlen = len(alt)\r\n- \r\n- # Returns without change if same single nucleotide for ref and alt. \r\n- if reflen == 1 and altlen == 1 and ref == alt:\r\n- return pos, ref, alt\r\n- \r\n- # Trimming from the start and then the end of the sequence \r\n- # where the sequences overlap with the same nucleotides\r\n- new_ref2, new_alt2, new_pos = \\\r\n- self.trimming_vcf_input(ref, alt, pos, strand)\r\n- \r\n- if new_ref2 == \'\':\r\n- new_ref2 = \'-\'\r\n- if new_alt2 == \'\':\r\n- new_alt2 = \'-\'\r\n- \r\n- return new_pos, new_ref2, new_alt2\r\n- \r\n- # This function looks at the ref and alt sequences and removes \r\n- # where the overlapping sequences contain the same nucleotide.\r\n- # This trims from the end first but does not remove the first nucleotide \r\n- # because based on the format of VCF input the \r\n- # first nucleotide of the ref and alt sequence occur \r\n- # at the position specified.\r\n- # End removed first, not the first nucleotide\r\n- # Front removed and position changed\r\n- def trimming_vcf_input(self, ref, alt, pos, strand):\r\n- pos = int(pos)\r\n- reflen = len(ref)\r\n- altlen = len(alt)\r\n- minlen = min(reflen, altlen)\r\n- new_ref = ref\r\n- new_alt = alt\r\n- new_pos = pos\r\n- # Trims from the end. Except don\'t remove the first nucleotide. \r\n- # 1:6530968 CTCA -> GTCTCA becomes C -> GTC.\r\n- for nt_pos in range(0, minlen - 1): \r\n- if ref[reflen - nt_pos - 1] == alt[altlen - nt_pos - 1]:\r\n- new_ref = ref[:reflen - nt_pos - 1]\r\n- new_alt = alt[:altlen - nt_pos - 1]\r\n- else:\r\n- break \r\n- new_ref_len = len(new_ref)\r\n- new_alt_len = len(new_alt)\r\n- minlen = min(new_ref_len, new_alt_len)\r\n- new_ref2 = new_ref\r\n- new_alt2 = new_alt\r\n- # Trims from the start. 1:6530968 G -> GT becomes 1:6530969 - -> T.\r\n- for nt_pos in range(0, minlen):\r\n- if new_ref[nt_pos] == new_alt[nt_pos]:\r\n- if strand == \'+\':\r\n- new_pos += 1\r\n- elif strand == \'-\':\r\n- new_pos -= 1\r\n- new_ref2 = new_ref[nt_pos + 1:]\r\n- new_alt2 = new_alt[nt_pos + 1:]\r\n- else:\r\n- new_ref2 = new_ref[nt_pos:]\r\n- new_alt2 = new_alt[nt_pos:]\r\n- break \r\n- return new_ref2, new_alt2, new_pos\r\n-\r\n-\r\n-if __name__ == "__main__":\r\n- c = CravatConverter()\n\\ No newline at end of file\n' |