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added bayesdel download & update testdata & minor changes
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213 changes: 22 additions & 191 deletions
213
src/frontend_celery/tests/data/heredivar_test_data.sql
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,101 @@ | ||
| import sys | ||
| from os import path | ||
| sys.path.append(path.dirname(path.dirname(path.abspath(__file__)))) | ||
| import argparse | ||
| from gc import collect | ||
| from ntpath import join | ||
| import common.functions as functions | ||
| from os import listdir | ||
| from os.path import isfile, join, abspath | ||
| import gzip | ||
| import pandas as pd | ||
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| parser = argparse.ArgumentParser(description="") | ||
| parser.add_argument("-i", "--input", default="", help="path to input folder") | ||
| parser.add_argument("-o", "--output", default="", help="output file path. If not given will default to stdout") | ||
| #parser.add_argument("-t", "--transcripts", default="", help="The path to the ensembl gff3 file (eg. http://ftp.ensembl.org/pub/current_gff3/homo_sapiens/Homo_sapiens.GRCh38.110.gff3.gz)") | ||
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| args = parser.parse_args() | ||
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| if args.output != "": | ||
| sys.stdout = open(args.output, 'w') | ||
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| if args.input != "": | ||
| input_path = args.input | ||
| else: | ||
| input_path = sys.stdin | ||
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| #transcript_path = args.transcripts | ||
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| info_headers = ["##INFO=<ID=BayesDEL_noAF,Number=1,Type=Float,Description=\"Missense variant functional predictions by BayesDel tool (Feng 2017) used without allele frequency. Score bigger or equal to 0.16: damaging; Score smaller than 0.16: tolerated.\">"] | ||
| functions.write_vcf_header(info_headers) | ||
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| #def read_transcripts(path): | ||
| # transcripts = [] | ||
| # with open(path, 'r') as file: | ||
| # for line in file: | ||
| # line = line.strip() | ||
| # if line.startswith('#') or line == '': | ||
| # continue | ||
| # | ||
| # parts = line.split('\t') | ||
| # biotype = parts[2] | ||
| # chrom = parts[0] | ||
| # start = int(parts[3]) | ||
| # end = int(parts[4]) | ||
| # orientation = parts[6] | ||
| # info = parts[8] | ||
| # | ||
| # if biotype in ['gene', 'ncRNA_gene', 'pseudogene']: | ||
| # transcript_id = functions.find_between(info, prefix="ID=gene:", postfix="(;|$)") | ||
| # if transcript_id is None: | ||
| # continue | ||
| # | ||
| # transcripts.append([transcript_id, orientation, chrom, start, end]) | ||
| # | ||
| # result = pd.DataFrame(transcripts, columns=['transcript', 'orientation', 'chrom', 'start', 'end']) | ||
| # return result | ||
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| #transcripts = read_transcripts(transcript_path) | ||
| #functions.eprint(transcripts) | ||
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| bayesdel_files = [abspath(join(input_path, f)) for f in listdir(input_path) if isfile(join(input_path, f))] | ||
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| functions.eprint(len(bayesdel_files)) | ||
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| for bayesdel_file in bayesdel_files: | ||
| functions.eprint(bayesdel_file) | ||
| file=gzip.open(bayesdel_file, 'rb') | ||
| for line in file: | ||
| line = line.decode('utf-8') | ||
| line = line.strip() | ||
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| if line.startswith('#') or line == '': | ||
| continue | ||
| ##CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO | ||
| parts = line.split('\t') | ||
| chrom = parts[0] | ||
| pos = parts[1] | ||
| ref = parts[2] | ||
| alt = parts[3] | ||
| #possible_transcripts = transcripts[(transcripts['chrom'] == chrom) & (transcripts['start'] <= int(pos)) & (transcripts['end'] >= int(pos))] | ||
| #if len(possible_transcripts) == 1 : | ||
| # orientation = possible_transcripts.iloc[0]['orientation'] | ||
| # if orientation == '-': | ||
| # ref = functions.reverse_seq(ref) | ||
| # alt = functions.reverse_seq(alt) | ||
| # #functions.eprint("reversed: " + str(pos)) | ||
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| vcf_parts = [chrom, pos, '.', ref, alt, '.', '.', "BayesDEL_noAF=" + str(parts[4])] | ||
| vcf_line = '\t'.join(vcf_parts) | ||
| print(vcf_line) | ||
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| file.close() | ||
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