| Next changeset 1:c13857bac2c4 (2016-03-08) |
|
Commit message:
Uploaded |
|
added:
cravat/cravat.py cravat/cravat.xml cravat/test-data/test_input.txt cravat/test-data/test_output.tsv cravat/vcf_to_cravat.py cravat/vcf_to_cravat.xml |
| b |
| diff -r 000000000000 -r 9e29dd2972ab cravat/cravat.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cravat/cravat.py Wed May 13 15:24:18 2015 -0400 |
| [ |
| @@ -0,0 +1,64 @@ +import sys +import re +import requests + +chromosome_re = re.compile('[0-9a-zA-Z_:]+\s+(chr[1-9]|chr1[0-9]|chr2[0-2]|chr[XY])\s+[0-9]+\s+[+-]\s+([ATGC]+|-)\s+([ATGC]+|-)', re.IGNORECASE) + +def is_correct_input_line (line): + if chromosome_re.match(line) != None: + return True + else: + return False + +def query (line): + url = query_url + '?mutation=' + '_'.join(line.split()) + r = requests.get(url) + annot = r.json() + return annot + +query_url = 'http://staging.cravat.us/rest/service/query' + +first_headers = ['ID', + 'Chromosome', + 'Position', + 'Strand', + 'Reference base(s)', + 'Alternate base(s)', + 'Sample'] + +input_filename = sys.argv[1] +output_filename = sys.argv[2] + +headers = [] +header_not_loaded = True + +f = open(input_filename) +wf = open(output_filename, 'w') +for line in f: + if is_correct_input_line(line) == False: + print 'Wrong format line:' + line[:-1] + continue + + toks = line[:-1].split() + uid = toks[0] + if len(toks) >= 7: + sample_id = toks[6] + else: + sample_id = 'Unknown' + annot = query(' '.join(toks[1:])) + if header_not_loaded: + headers = annot.keys() + headers.sort() + wf.write('\t'.join(first_headers)) + for header in headers: + if header not in first_headers: + wf.write('\t' + header) + wf.write('\n') + header_not_loaded = False + wf.write('\t'.join(toks[:6]) + '\t' + sample_id) + for header in headers: + if header not in first_headers: + wf.write('\t' + annot[header]) + wf.write('\n') +f.close() +wf.close() |
| b |
| diff -r 000000000000 -r 9e29dd2972ab cravat/cravat.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cravat/cravat.xml Wed May 13 15:24:18 2015 -0400 |
| b |
| @@ -0,0 +1,19 @@ +<tool id='cravat' name='CRAVAT'> + <description>CRAVAT annotation</description> + <command interpreter='python'>cravat.py $input $output</command> + <inputs> + <param format='text' name='input' type='data' label='Input file' /> + </inputs> + <outputs> + <data format='tabular' name='output' /> + </outputs> + + <tests> + <test> + <param name='input' value='test_input.txt' /> + <output name='out_file1' file='test_output.txt' /> + </test> + </tests> + + <help>This tool queries CRAVAT for variants</help> +</tool> |
| b |
| diff -r 000000000000 -r 9e29dd2972ab cravat/test-data/test_input.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cravat/test-data/test_input.txt Wed May 13 15:24:18 2015 -0400 |
| b |
| @@ -0,0 +1,5 @@ +TR1 chr22 30421786 + A T sample_1 +TR2 chr22 40814500 - A G sample_1 +TR3 chr22 25115450 + - AGG sample_2 +TR4 chr22 234234 + AGA - sample_2 +TR5 chr2 219134766 + G - sample_3 |
| b |
| diff -r 000000000000 -r 9e29dd2972ab cravat/test-data/test_output.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cravat/test-data/test_output.tsv Wed May 13 15:24:18 2015 -0400 |
| [ |
| @@ -0,0 +1,6 @@ +ID Chromosome Position Strand Reference base(s) Alternate base(s) Sample 1000 Genomes allele frequency Driver Genes ESP6500 allele frequency (African American) ESP6500 allele frequency (European American) ExAC allele frequency (African/African American) ExAC allele frequency (East Asian) ExAC allele frequency (Finnish) ExAC allele frequency (Latino) ExAC allele frequency (Non-Finnish European) ExAC allele frequency (Other) ExAC allele frequency (South Asian) ExAC total allele frequency HUGO symbol Mappability Warning Occurrences in COSMIC [exact nucleotide change] Occurrences in COSMIC by primary sites [exact nucleotide change] Protein sequence change in COSMIC Sequence ontology Sequence ontology all transcripts Sequence ontology protein change Sequence ontology transcript TARGET Transcript in COSMIC +TR1 chr22 30421786 + A T sample_1 0.0077875400893390178680419921875 0.02269629947841167449951171875 0 0.0238370001316070556640625 0 0 0.001123600057326257228851318359375 0 0.0011037499643862247467041015625 0 0.0021585500799119472503662109375 MTMR3 MS NM_153051.2:N1161I(MS), NM_153050.2:N1170I(MS), ENST00000323630:N1062I(MS), ENST00000351488:N1161I(MS), ENST00000333027:N1170I(MS), ENST00000406629:N1170I(MS), ENST00000401950:N1198I(MS) N1198I NM_021090.3 +TR2 chr22 40814500 - A G sample_1 0.4832270145416259765625 0.860644996166229248046875 0.396977007389068603515625 0.871408998966217041015625 0.110581003129482269287109375 0.330637991428375244140625 0.1900829970836639404296875 0.3895820081233978271484375 0.3936649858951568603515625 0.4774529933929443359375 0.4003469944000244140625 MKL1 1 stomach(1) p.S648G (stomach 1) MS ENST00000396617:S648G(MS), ENST00000402042:S598G(MS), ENST00000407029:S648G(MS), ENST00000355630:S648G(MS) S648G NM_020831.3 ENST00000355630 +TR3 chr22 25115450 + - AGG sample_2 0 0 0 0 0 0 0 0 0 0 0 PIWIL3 II NM_001255975.1:871(II), ENST00000533313:762(II), ENST00000527701:762(II), ENST00000332271:880(II) 880 NM_001008496.3 +TR4 chr22 234234 + AGA - sample_2 0 0 0 0 0 0 0 0 0 0 0 Non-Coding +TR5 chr2 219134766 + G - sample_3 0 0 0 0.00038654799573123455047607421875 0 0 0 0.000482450588606297969818115234375 0 0 0.0002977323601953685283660888671875 AAMP 2 large_intestine(2) p.P15fs*5 (large_intestine 2) FD ENST00000248450:15(FD), ENST00000444053:15(FD) 15 NM_001087.3 ENST00000248450 |
| b |
| diff -r 000000000000 -r 9e29dd2972ab cravat/vcf_to_cravat.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cravat/vcf_to_cravat.py Wed May 13 15:24:18 2015 -0400 |
| [ |
| @@ -0,0 +1,133 @@ +import sys +import re + +def extract_vcf_variant (strand, pos, ref, alt): + pos = int(pos) + reflen = len(ref) + altlen = len(alt) + minlen = min(reflen, altlen) + new_ref = ref + new_alt = alt + + if reflen == 1 and altlen == 1 and ref == alt: + return pos, ref, alt + + for nt_pos in xrange(0, minlen): + if ref[reflen - nt_pos - 1] == alt[altlen - nt_pos - 1]: + new_ref = ref[:reflen - nt_pos - 1] + new_alt = alt[:altlen - nt_pos - 1] + else: + break + newreflen = len(new_ref) + newaltlen = len(new_alt) + + minlen = min(newreflen, newaltlen) + new_pos = pos + new_ref2 = new_ref + new_alt2 = new_alt + + for nt_pos in xrange(minlen): + if new_ref[nt_pos] == new_alt[nt_pos]: + if strand == '+': + new_pos += 1 + elif strand == '-': + new_pos -= 1 + new_ref2 = new_ref[nt_pos + 1:] + new_alt2 = new_alt[nt_pos + 1:] + else: + new_ref2 = new_ref[nt_pos:] + new_alt2 = new_alt[nt_pos:] + break + if new_ref == '': + new_ref2 = '-' + if new_alt2 == '': + new_alt2 = '-' + + return new_pos, new_ref2, new_alt2 + +input_filename = sys.argv[1] +output_filename = sys.argv[2] + +f = open(input_filename) +wf = open(output_filename, 'w') + +vcf_line_no = 0 + +for line in f: + vcf_line_no += 1 + if len(line) < 6: + continue + if line[:6] == '#CHROM': + toks = re.split('\s+', line.rstrip()) + if len(toks) > 8: + samples = toks[9] + break +no_samples = len(samples) + +for line in f: + vcf_line_no += 1 + + if line[0] == '#': + continue + + toks = re.split('\s+', line.rstrip()) + + if len(toks) < 8: + continue + + [chrom, pos, uidbase, ref, alts, dummy, dummy, dummy] = toks[:8] + reflen = len(ref) + if uidbase == '.': + uidbase = 'VAR' + str(vcf_line_no) + if chrom[:3].lower != 'chr': + chrom = 'chr' + chrom + alts = alts.split(',') + + len_alts = len(alts) + if len(toks) == 8: + for altno in xrange(len_alts): + alt = alts[altno] + if len_alts == 1: + uid = uidbase + else: + uid = uidbase + '_' + str(altno + 1) + newpos, newref, newalt = extract_vcf_variant('+', pos, ref, alt) + cravat_line = '\t'.join([uid, chrom, str(newpos), '+', newref, newalt, 'Unknown']) + wf.write(cravat_line + '\n') + elif len(toks) > 8: + sample_datas = toks[9:] + + genotype_fields = {} + genotype_field_no = 0 + for genotype_field in toks[8].split(':'): + genotype_fields[genotype_field] = genotype_field_no + + if not ('GT' in genotype_fields): + print 'No GT Field at line ' + str(vcf_line_no) + ' [' + line.strip() + ']' + continue + + gt_field_no = genotype_fields['GT'] + + for sample_no in xrange(len(sample_datas)): + sample = samples[sample_no] + sample_data = sample_datas[sample_no].split(':') + gts = {} + for gt in sample_data[gt_field_no].replace('/', '|').split('|'): + if gt == '.': + continue + else: + gts[int(gt)] = True + for gt in gts.keys(): + if gt == 0: + continue + else: + alt = alts[gt - 1] + if len_alts == 1: + uid = uidbase + else: + uid = uidbase + ':' + str(gt) + newpos, newref, newalt = extract_vcf_variant('+', pos, ref, alt) + cravat_line = '\t'.join([uid + '_' + sample, chrom, str(newpos), '+', newref, newalt, sample]) + wf.write(cravat_line + '\n') +f.close() +wf.close() |
| b |
| diff -r 000000000000 -r 9e29dd2972ab cravat/vcf_to_cravat.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cravat/vcf_to_cravat.xml Wed May 13 15:24:18 2015 -0400 |
| b |
| @@ -0,0 +1,19 @@ +<tool id='vcf_to_cravat' name='VCF to CRAVAT'> + <description>VCF to CRAVAT input format conversion</description> + <command interpreter='python'>vcf_to_cravat.py $input $output</command> + <inputs> + <param format='vcf' name='input' type='data' label='Input file' /> + </inputs> + <outputs> + <data format='tabular' name='output' /> + </outputs> + + <tests> + <test> + <param name='input' value='test_input.txt' /> + <output name='out_file1' file='test_output.txt' /> + </test> + </tests> + + <help>This tool converts a VCF format file to a CRAVAT input format file.</help> +</tool> |