comparison cravatp_submit.py @ 3:a018c44dc18b draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cravatp_score_and_annotate commit d80e60ce74aabe64e131d560085af099d52b81cf-dirty

2:f3027b8f28bd

from io import BytesIO

# initializes blank parameters
chasm_classifier = ''
probed_filename = None
intersected_only = False
vcf_output = None
analysis_type = None

# # Testing Command
# python cravatp_submit.py test-data/Freebayes_two-variants.vcf GRCh38
# test-data/variant.tsv test-data/gene.tsv test-data/noncoding.tsv
# test-data/error.tsv CHASM -—classifier Breast -—proBED
# test-data/MCF7_proBed.bed
parser = argparse.ArgumentParser()
parser.add_argument('cravatInput',help='The filename of the input '
                                       'CRAVAT-formatted tabular file '
                                       '(e.g., VCF)')
parser.add_argument('GRCh', help='The name of the human reference '

parser.add_argument('--classifier', help='The cancer classifier for the'
                                         ' CHASM algorithm')
parser.add_argument('--proBED', help='The filename of the proBED file '
                                     'containing peptides with genomic '
                                     'coordinates')
parser.add_argument('--intersectOnly', help='Specifies whether to '
                                            'analyze only variants '
                                            'intersected between the '
                                            'CRAVAT input and proBED '
                                            'file')
parser.add_argument('--vcfOutput', help='The output filename of the '
                                        'intersected VCF file')

# assigns parsed arguments to appropriate variables
args = parser.parse_args()

    analysis_type = args.analysis
if args.classifier:
    chasm_classifier = args.classifier
if args.proBED:
    probed_filename = args.proBED
if args.intersectOnly:
    intersected_only = args.intersectOnly    
if args.vcfOutput:
    vcf_output = args.vcfOutput

if analysis_type and '+' in analysis_type:
    analysis_type = 'CHASM;VEST'

# Creates an VCF file that only contains variants that overlap with the
# proteogenomic input (proBED) file if the user specifies that they want
# to only include intersected variants or if they want to receive the
# intersected VCF as well.
if probed_filename and (vcf_output or intersected_only == 'true'):
    proBED = loadProBED()
    if not vcf_output:
        vcf_output = 'intersected_input.vcf'
    with open(input_filename) as tsvin, open(vcf_output, 'wb') as tsvout:
        tsvreader = csv.reader(tsvin, delimiter='\t')        

                    if (genchrom == pepchrom and
                        pepposA <= genpos and
                                   genpos <= pepposB):
                        tsvout.writerow(row)
                        break
if intersected_only == 'true':
    input_filename = vcf_output

# sets up the parameters for submission to the CRAVAT API
parameters = {'email':'[e-mail]',
              'hg19': 'on' if GRCh_build == 'GRCh37' else 'off',

3:a018c44dc18b

from io import BytesIO

# initializes blank parameters
chasm_classifier = ''
probed_filename = None
all_intersect = False
vcf_output = None
analysis_type = None

# # Testing Command
# python cravatp_submit.py test-data/Freebayes_two-variants.vcf GRCh38 test-data/variant.tsv test-data/gene.tsv test-data/noncoding.tsv test-data/error.tsv CHASM -—classifier Breast -—proBED test-data/MCF7_proBed.bed
parser = argparse.ArgumentParser()
parser.add_argument('cravatInput',help='The filename of the input '
                                       'CRAVAT-formatted tabular file '
                                       '(e.g., VCF)')
parser.add_argument('GRCh', help='The name of the human reference '

parser.add_argument('--classifier', help='The cancer classifier for the'
                                         ' CHASM algorithm')
parser.add_argument('--proBED', help='The filename of the proBED file '
                                     'containing peptides with genomic '
                                     'coordinates')
parser.add_argument('--allIntersect', help='Specifies whether to '
                                            'analyze all variants')
parser.add_argument('--vcfOutput', help='The output filename of the '
                                        'intersected VCF file')

# assigns parsed arguments to appropriate variables
args = parser.parse_args()

    analysis_type = args.analysis
if args.classifier:
    chasm_classifier = args.classifier
if args.proBED:
    probed_filename = args.proBED
if args.allIntersect:
    all_intersect = args.allIntersect    
if args.vcfOutput:
    vcf_output = args.vcfOutput

if analysis_type and '+' in analysis_type:
    analysis_type = 'CHASM;VEST'

# Creates an VCF file that only contains variants that overlap with the
# proteogenomic input (proBED) file if the user specifies that they want
# to only include intersected variants or if they want to receive the
# intersected VCF as well.
if probed_filename and (vcf_output or all_intersect == 'false'):
    proBED = loadProBED()
    if not vcf_output:
        vcf_output = 'intersected_input.vcf'
    with open(input_filename) as tsvin, open(vcf_output, 'wb') as tsvout:
        tsvreader = csv.reader(tsvin, delimiter='\t')        

                    if (genchrom == pepchrom and
                        pepposA <= genpos and
                                   genpos <= pepposB):
                        tsvout.writerow(row)
                        break
if all_intersect == 'false':
    input_filename = vcf_output

# sets up the parameters for submission to the CRAVAT API
parameters = {'email':'[e-mail]',
              'hg19': 'on' if GRCh_build == 'GRCh37' else 'off',