| Previous changeset 14:a28f1f52eb93 (2018-06-12) Next changeset 16:efb15a586f5e (2018-06-12) |
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Commit message:
Uploaded |
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added:
cravat_submit/cravat_submit.py cravat_submit/cravat_submit.xml |
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removed:
cravat_annotate/cravat_annotate.py cravat_annotate/cravat_annotate.xml cravat_convert/base_converter.py |
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| diff -r a28f1f52eb93 -r a46b42bda5d7 cravat_annotate/cravat_annotate.py --- a/cravat_annotate/cravat_annotate.py Tue Jun 12 12:04:45 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,246 +0,0 @@\n-"""\n-A galaxy wrapper for the /rest/service/query API endpoint on Cravat.\n-\n-\n-Notes on Mapping:\n------------------\n-The CravatQuery class uses static method \'from_array\' to interpret an array of values\n-into a query string for the /rest/service/query API service on the cravat server.\n-This involves using a mapping dictionary to know how to associate the array\'s index positions\n-in to query-ing attributes, such as the chromosome, position, etc. The CravatQuery\n-class contains a default value (\'default_mapping\'); however, this could also be\n-offered as a user-configurable option.\n-"""\n-\n-\n-import requests\n-import json\n-import sys\n-import re\n-\n-\n-class CravatQueryException(Exception):\n-\n-\tdef __init__(self, message, errors=None):\t \n-\t\tsuper(CravatQueryException, self).__init__(message)\n-\t\t# Support for custom error codes\n-\t\tself.errors = errors\n-\n-\n-class CravatQuery(object):\n-\t"""\n-\t: A class for handling Cravat query strings.\n-\t: Args (all required):\n-\t:\tchr - Chromosome\n-\t:\tpos - Position\n-\t:\tstrand - Strand\n-\t:\tref - Reference Base\n-\t:\talt - Alternate Base\n-\t"""\n-\n-\t# The endpoint that CravatQuerys are submitted to\n-\tendpoint = \'http://cravat.us/CRAVAT/rest/service/query\'\n-\n-\t# The value delimiter used in the Cravat input file to delimit values\n-\tdelimiter = "\\t"\n-\n-\t# Defualt indices for intepretting a cravat file\'s row of data in to a CravatQuery\n-\tdefault_mapping = {\n-\t\t\'chromosome\': 1,\n-\t\t\'position\': 2,\n-\t\t\'strand\': 3,\n-\t\t\'reference\': 4,\n-\t\t\'alternate\': 5\n-\t}\n-\n-\t# Defualt values. Used as backup for CravatQuery to resolve query with incomplete information\n-\tdefault_values = {\n-\t\t\'strand\': \'+\'\n-\t}\n-\n-\t# The neccessary attributes neeeded to submit a query.\n-\tquery_keys = [\n-\t\t\'chromosome\', \'position\', \'strand\', \'reference\', \'alternate\'\n-\t]\n-\n-\t# Expected response keys from server. Ordered in list so that galaxy output has uniform column ordering run-to-run.\n-\t# If cravat server returns additional keys, they are appended to and included in output.\n-\tresponse_keys = [\n-\t\t"Chromosome", "Position", "Strand", "Reference base(s)", "Alternate base(s)",\n-\t \t"HUGO symbol", "S.O. transcript", "Sequence ontology protein change", "Sequence ontology",\n-\t\t"S.O. all transcripts", "gnomAD AF", "gnomAD AF (African)", "gnomAD AF (Amrican)",\n-\t\t"gnomAD AF (Ashkenazi Jewish)", "gnomAD AF (East Asian)", "gnomAD AF (Finnish)",\n-\t\t"gnomAD AF (Non-Finnish European)", "gnomAD AF (Other)", "gnomAD AF (South Asian)",\n-\t\t"1000 Genomes AF", "ESP6500 AF (average)", "ESP6500 AF (European American)",\n-\t\t"ESP6500 AF (African American)", "COSMIC transcript", "COSMIC protein change", \n-\t\t"COSMIC variant count [exact nucleotide change]", "cosmic_site_nt", "CGL driver class",\n-\t\t"TARGET", "dbSNP", "cgc_role", "cgc_inheritance", "cgc_tumor_type_somatic",\n-\t\t"cgc_tumor_type_germline", "ClinVar", "ClinVar disease identifier", "ClinVar XRef",\n-\t\t"GWAS Phenotype (GRASP)", "GWAS PMID (GRASP)", "Protein 3D variant"\n-\t]\n-\n-\n-\tdef __init__(self, _chr, pos, strand, ref, alt):\n-\t\t# \'_chr\' used to avoid naming confliction with python built-in \'chr\'\n-\t\tself.chromosome = CravatQuery.format_chromosome(_chr)\n-\t\tself.position = pos\n-\t\tself.strand = strand\n-\t\tself.reference = ref\n-\t\tself.alternate = alt\n-\t\tself.values = [self.chromosome, self.position, self.strand, self.reference, self.alternate]\n-\n-\n-\tdef __str__(self):\n-\t\t""" : Represent the CravatQuery as a valid query string for call to Cravat server """\n-\t\treturn "_".join(map(lambda x: str(x), self.values))\n-\n-\t\n-\tdef as_query_string(self):\n-\t\treturn str(self)\n-\n-\t\n-\t@staticmethod\n-\tdef from_dictionary(d):\n-\t\t"""\n-\t\t: Instantiate a CravatQuery from a dictionary representation.\n-\t\t: Args:\n-\t\t\t: d <dictionary>: A dictionary representing a CravatQuery, containing keys: [{}] \n-\t\t""".format(CravatQuery.query_keys)\n-\n-\t\tfor key in CravatQuery.query_keys:\n-\t\t\tif key not in d:\n-\t\t\t\traise CravatQueryException("CravatQuery.from_dictionary requires keys: [{}], however key: \'{}\' was not provided "\n-\t\t\t\t\t\t\t\t\t\t\t.for'..b' associated to \'fmt\'\n-\t\tif mapping == None:\n-\t\t\tmapping = CravatQuery.default_mapping\n-\t\t\t\n-\t\t# Build a dict of cravat querying keys to values.\n-\t\td = {}\n-\t\tfor key in CravatQuery.query_keys:\n-\t\t\t# Try to get index position from mapping by the key, and value from array by the index\n-\t\t\tif key in mapping:\n-\t\t\t\tindex = mapping[key]\n-\t\t\t\td[key] = array[index]\n-\t\t\t# If index not provided in mapping, check if there is a defualt value\n-\t\t\telif key in CravatQuery.default_values:\n-\t\t\t\td[key] = CravatQuery.default_values[key]\n-\t\t\t# Unable to get value for querying key, meaning can\'t construct the minimum requirements for query\n-\t\t\telse:\n-\t\t\t\traise CravatQueryException("CravatQuery.from_array requires a mapping index for key: \'{}\', however value was not provided".format(key))\n-\t\treturn CravatQuery.from_dictionary(d)\n-\n-\n-\n-\t@staticmethod\n-\tdef format_chromosome(_chr):\n-\t\t"""\n-\t\t: Format a chromosome for use as query parameter. \'_chr\' name used to avoid python built-in name confliction.\n-\t\t: Args:\n-\t\t\t: _chr - Either an interger [1,23], or \'x\'/\'X\', or \'y\'/\'Y\', or a string of the form\n-\t\t\t: \t\t\'chr<z>\' where \'<z>\' is one of the previously described values \n-\t\t"""\n-\t\tinRange = lambda x: 1 <= x and x <= 23\n-\t\t_chr = _chr.lower()\n-\t\t_chr = _chr.strip(\'chr\')\n-\t\t# Handler interger chromosomes 1 to 23\n-\t\ttry:\n-\t\t\t_chr = int(_chr)\n-\t\t\tif inRange(_chr):\n-\t\t\t\treturn \'chr\' + str(_chr)\n-\t\t\telse:\n-\t\t\t\traise CravatQueryException("Chromsomme of \'{}\' was out of range [1,23]".format(_chr))\n-\t\texcept:\n-\t\t\tpass\n-\t\t# Handle chromosomes chromosomes x and y\n-\t\tif _chr == \'x\' or _chr == \'y\':\n-\t\t\treturn \'chr\' + _chr\n-\t\traise CravatQueryException("Unable to resolve input: \'{}\' into a valid chromosome representation".format(_chr))\n-\n-\n-\t@staticmethod\n-\tdef jump_header(in_file, out_file, headerlines=0):\n-\t\t"""\n-\t\t: Jumps over a header space of line number \'headerlines\'. Sets up in_file so that\n-\t\t: the next execution of in_file.readline() will return the first non-header line.\n-\t\t"""\n-\t\tin_file.seek(0)\n-\t\tfor line in range(headerlines):\n-\t\t\tin_file.readline()\n-\n-\n-def main(in_path, out_path, pre_callback=None, user_mapping=None):\n-\t"""\n-\t: Read the file line by line and use data to query cravat server.\n-\t: Args:\n-\t\t: fmt <str>: \'cr\' or \'vcf\'. The input format\n-\t\t: in_path <str>: Path to input file\n-\t\t: in_path <str>: Path to output file\n-\t\t: header_callback <function>: A function to handle the header space. Executed\n-\t\t\tbefore main loop. Recieves in_file, out_file, and fmt as argumnets\n-\t"""\n-\n-\twith open(in_path, \'r\') as in_file, \\\n-\topen(out_path, \'w\') as out_file:\n-\n-\t\t# Perform any pre-processing steps, such as jumping a header space\n-\t\tif pre_callback:\n-\t\t\tpre_callback(in_file, out_file, fmt)\n-\n-\t\t# main loop\n-\t\tfor line in in_file:\n-\n-\t\t\t# Create query from line of input data\n-\t\t\tline = line.strip().split(\'\\t\')\n-\t\t\tquery = CravatQuery.from_array(line, user_mapping)\n-\t\t\t# Make request, and write respone data\n-\t\t\tcall = requests.get(CravatQuery.endpoint, params={ \'mutation\': query.as_query_string })\n-\t\t\ttry:\n-\t\t\t\tif call.status_code != 200 or call.text == "":\n-\t\t\t\t\traise CravatQueryException("Bad Server Response. Respone code: \'{}\', Response Text: \'{}\'".format(call.status_code, call.text))\n-\t\t\t\tjson_response = json.loads(call.text)\n-\t\t\t\twrote = False\n-\t\t\t\tfor key, val in json_response.items():\n-\t\t\t\t\t# Set numeric values to uniform format\n-\t\t\t\t\ttry:\n-\t\t\t\t\t\tval = float(val)\n-\t\t\t\t\t\tval = format(val, ".4f")\n-\t\t\t\t\texcept:\n-\t\t\t\t\t\tpass\n-\t\t\t\t\tif wrote:\n-\t\t\t\t\t\tout_file.write("\\t")\n-\t\t\t\t\tout_file.write(val)\n-\t\t\t\t\twrote = True\n-\t\t\t\tout_file.write("\\n")\n-\t\t\texcept CravatQueryException as e:\n-\t\t\t\tprint(e)\n-\t\t\t\t\n-\t\t\n-\n-\n-if __name__ == "__main__":\n-\n-\t# Input and output file paths, obtained form command line\n-\tin_path = sys.argv[1]\n-\tout_path = sys.argv[2]\n-\n-\t# Possibly allow user mapping configuration thourgh here. Not fully implemented\n-\tif len(sys.argv) > 2:\n-\t\tuser_mapping = sys.argv[3]\n-\n-\t# Run the main operation\n-\tmain(in_path, out_path)\n\\ No newline at end of file\n' |
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| diff -r a28f1f52eb93 -r a46b42bda5d7 cravat_annotate/cravat_annotate.xml --- a/cravat_annotate/cravat_annotate.xml Tue Jun 12 12:04:45 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,25 +0,0 @@ -<tool id="cravat_query" name="CRAVAT Query" version="1.0.0"> - <description>Queries CRAVAT for cancer annotation</description> - <command interpreter="python">cravat_annotate.py $input $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 a28f1f52eb93 -r a46b42bda5d7 cravat_convert/base_converter.py --- a/cravat_convert/base_converter.py Tue Jun 12 12:04:45 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 a28f1f52eb93 -r a46b42bda5d7 cravat_submit/cravat_submit.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cravat_submit/cravat_submit.py Tue Jun 12 12:05:40 2018 -0400 |
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| @@ -0,0 +1,103 @@ +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://staging.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://staging.cravat.us/CRAVAT/results/" + jobid + "/" + "Variant.Result.tsv", file_1) +urllib.urlretrieve("http://staging.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 |
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| diff -r a28f1f52eb93 -r a46b42bda5d7 cravat_submit/cravat_submit.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cravat_submit/cravat_submit.xml Tue Jun 12 12:05:40 2018 -0400 |
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| @@ -0,0 +1,34 @@ +<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> |