| Previous changeset 23:3404770b5b7a (2018-07-18) Next changeset 25:c5f0a7e538ff (2018-07-18) |
|
Commit message:
Uploaded |
|
added:
cravat_annotate/cravat_annotate.py cravat_annotate/cravat_annotate.xml |
|
removed:
cravat_submit/cravat_submit.py cravat_submit/cravat_submit.xml |
| b |
| diff -r 3404770b5b7a -r 2b7ba092ce34 cravat_annotate/cravat_annotate.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cravat_annotate/cravat_annotate.py Wed Jul 18 09:42:05 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 + + +# 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) |
| b |
| diff -r 3404770b5b7a -r 2b7ba092ce34 cravat_annotate/cravat_annotate.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cravat_annotate/cravat_annotate.xml Wed Jul 18 09:42:05 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> + |
| b |
| diff -r 3404770b5b7a -r 2b7ba092ce34 cravat_submit/cravat_submit.py --- a/cravat_submit/cravat_submit.py Wed Jul 18 09:41:57 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,103 +0,0 @@ -import requests -import json -import time -import urllib -import sys -import csv - -input_filename = sys.argv[1] -input_select_bar = sys.argv[2] -output_filename = sys.argv[3] - -# HACK: Input args corrections. -if input_select_bar == "None": - # The server represents an analyses of None as ""; however, submitting a blank string on command line throws off arg position - input_select_bar = "" - # The server represents the "Vest and Chasm" analyses as "VEST;CHASM; however, galaxy converts the semi-colon to an 'X'. Switch it back. -elif input_select_bar == "VESTXCHASM": - input_select_bar = "VEST;CHASM" - -write_header = True - -#plugs in params to given URL -submit = requests.post('http://cravat.us/CRAVAT/rest/service/submit', files={'inputfile':open(input_filename)}, data={'email':'znylund@insilico.us.com', 'analyses': input_select_bar}) -#,'analysis':input_select_bar,'functionalannotation': "on"}) -#Makes the data a json dictionary, takes out only the job ID -jobid = json.loads(submit.text)['jobid'] -#out_file.write(jobid) -submitted = json.loads(submit.text)['status'] -#out_file.write('\t' + submitted) - -#loops until we find a status equal to Success, then breaks -while True: - check = requests.get('http://staging.cravat.us/CRAVAT/rest/service/status', params={'jobid': jobid}) - status = json.loads(check.text)['status'] - resultfileurl = json.loads(check.text)['resultfileurl'] - #out_file.write(str(status) + ', ') - if status == 'Success': - #out_file.write('\t' + resultfileurl) - break - else: - time.sleep(2) - -#out_file.write('\n') - -#creates three files -file_1 = time.strftime("%H:%M") + '_Z_Variant_Result.tsv' -file_2 = time.strftime("%H:%M") + '_Z_Additional_Details.tsv' -file_3 = time.strftime("%H:%M") + 'Combined_Variant_Results.tsv' - - -#Download the two results -urllib.urlretrieve("http://cravat.us/CRAVAT/results/" + jobid + "/" + "Variant.Result.tsv", file_1) -urllib.urlretrieve("http://cravat.us/CRAVAT/results/" + jobid + "/" + "Variant_Additional_Details.Result.tsv", file_2) - -headers = [] -duplicates = [] - -#opens the Variant Result file and the Variant Additional Details file as csv readers, then opens the output file (galaxy) as a writer -with open(file_1) as tsvin_1, open(file_2) as tsvin_2, open(output_filename, 'wb') as tsvout: - tsvreader_1 = csv.reader(tsvin_1, delimiter='\t') - tsvreader_2 = csv.reader(tsvin_2, delimiter='\t') - tsvout = csv.writer(tsvout, delimiter='\t') - -#loops through each row in the Variant Additional Details file - for row in tsvreader_2: - #sets row_2 equal to the same row in Variant Result file - row_2 = tsvreader_1.next() - #checks if row is empty or if the first term contains '#' - if row == [] or row[0][0] == '#': - continue - #checks if the row begins with input line - if row[0] == 'Input line': - #Goes through each value in the headers list in VAD - for value in row: - #Adds each value into headers - headers.append(value) - #Loops through the Keys in VR - for value in row_2: - #Checks if the value is already in headers - if value in headers: - continue - #else adds the header to headers - else: - headers.append(value) - - print headers - tsvout.writerow(headers) - - - else: - - cells = [] - #Goes through each value in the next list - for value in row: - #adds it to cells - cells.append(value) - #Goes through each value from the VR file after position 11 (After it is done repeating from VAD file) - for value in row_2[11:]: - #adds in the rest of the values to cells - cells.append(value) - - print cells - tsvout.writerow(cells) \ No newline at end of file |
| b |
| diff -r 3404770b5b7a -r 2b7ba092ce34 cravat_submit/cravat_submit.xml --- a/cravat_submit/cravat_submit.xml Wed Jul 18 09:41:57 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,34 +0,0 @@ -<tool id="cravat_submit" name="CRAVAT Submit, Check, and Retrieve" version="0.1.0"> - <description>Submits, checks for, and retrieves data for cancer annotation</description> - <command interpreter="python">cravat_submit.py $input $dropdown $output</command> - - - <inputs> - - <param format="tabular" name="input" type="data" label="Source file"> </param> - <param format="tabular" name="dropdown" type="select" label="Analysis Program"> - <option value="None">None</option> - <option value="VEST">VEST</option> - <option value="CHASM">CHASM</option> - <option value="VEST;CHASM">VEST and CHASM</option> - </param> - - - </inputs> - - <outputs> - <data format="tabular" name="output" /> - </outputs> - - <tests> - <test> - <param name="input" value="fa_gc_content_input.fa"/> - <output name="out_file1" file="fa_gc_content_output.txt"/> - </test> - </tests> - - <help> - This tool submits, checks for, and retrieves data for cancer annotation. - </help> - -</tool> |