| Previous changeset 4:93864b5201b6 (2018-06-12) Next changeset 6:4b0bee4d9a15 (2018-06-12) |
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Commit message:
Uploaded |
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added:
cravat_convert/cravat_convert.py cravat_convert/cravat_convert.xml |
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removed:
cravat_convert/vcf_converter.py |
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| diff -r 93864b5201b6 -r 7048ccf0ff7b cravat_convert/cravat_convert.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cravat_convert/cravat_convert.py Tue Jun 12 11:27:06 2018 -0400 |
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| @@ -0,0 +1,77 @@ +''' +Convert a VCF format file to Cravat format file +''' + +import os +import argparse +from vcf_converter import CravatConverter + +# File read/write configuration variables +vcf_sep = '\t' +cr_sep = '\t' +cr_newline = '\n' + +# VCF Headers mapped to their index position in a row of VCF values +vcf_mapping = { + 'CHROM': 0, + 'POS': 1, + 'ID': 2, + 'REF': 3, + 'ALT': 4, + 'QUAL': 5, + 'FILTER': 6, + 'INFO': 7, + 'FORMAT': 8, + 'NA00001': 9, + 'NA00002': 10, + 'NA00003': 11 +} + + +def get_args(): + parser = argparse.ArgumentParser() + parser.add_argument('--input', + '-i', + required = True, + help='Input path to a VCF file for conversion',) + parser.add_argument('--output', + '-o', + default = os.path.join(os.getcwd(), "cravat_converted.txt"), + help = 'Output path to write the cravat file to') + return parser.parse_args() + + +def convert(in_path, out_path=None): + if not out_path: + base, _ = os.path.split(in_path) + out_path = os.path.join(base, "cravat_converted.txt") + + with open(in_path, 'r') as in_file, \ + open(out_path, 'w') as out_file: + + # cr_count will be used to generate the 'TR' field of the cravat rows (first header) + cr_count = 0 + # VCF lines are always assumed to be '+' strand, as VCF doesn't specify that attribute + strand = '+' + # VCF converter. Adjusts position, reference, and alternate for Cravat formatting. + converter = CravatConverter() + + for line in in_file: + if line.startswith("#"): + continue + line = line.strip().split(vcf_sep) + # row is dict of VCF headers mapped to corresponding values of this line + row = { header: line[index] for header, index in vcf_mapping.items() } + for alt in row["ALT"].split(","): + new_pos, new_ref, new_alt = converter.extract_vcf_variant(strand, row["POS"], row["REF"], alt) + new_pos, new_ref, new_alt = str(new_pos), str(new_ref), str(new_alt) + cr_line = cr_sep.join([ + 'TR' + str(cr_count), row['CHROM'], new_pos, strand, new_ref, new_alt, row['ID'] + ]) + out_file.write(cr_line + cr_newline) + cr_count += 1 + + +if __name__ == "__main__": + cli_args = get_args() + convert(cli_args.input, cli_args.output) |
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| diff -r 93864b5201b6 -r 7048ccf0ff7b cravat_convert/cravat_convert.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cravat_convert/cravat_convert.xml Tue Jun 12 11:27:06 2018 -0400 |
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| @@ -0,0 +1,20 @@ +<tool id="cravat_convert" name="CRAVAT Convert" version="1.0.0"> + <description>Converts a VCF format file to a Cravat format file</description> + <command interpreter="python">cravat_convert.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></tests> --> + + <help> + Converts a VCF format file to a Cravat format file + </help> + +</tool> + |
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| diff -r 93864b5201b6 -r 7048ccf0ff7b cravat_convert/vcf_converter.py --- a/cravat_convert/vcf_converter.py Tue Jun 12 11:26:47 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,243 +0,0 @@\n-"""\r\n-A module originally obtained from the cravat package. Modified to use in the vcf\r\n-converter galaxy tool.\r\n-\r\n-\r\n-Register of changes made (Chris Jacoby):\r\n- 1) Changed imports as galaxy tool won\'t have access to complete cravat python package\r\n- 2) Defined BadFormatError in BaseConverted file, as I didn\'t have the BadFormatError module\r\n-"""\r\n-\r\n-from base_converter import BaseConverter, BadFormatError\r\n-import re\r\n-\r\n-class CravatConverter(BaseConverter):\r\n- \r\n- def __init__(self):\r\n- self.format_name = \'vcf\'\r\n- self.samples = []\r\n- self.var_counter = 0\r\n- self.addl_cols = [{\'name\':\'phred\',\r\n- \'title\':\'Phred\',\r\n- \'type\':\'string\'},\r\n- {\'name\':\'filter\',\r\n- \'title\':\'VCF filter\',\r\n- \'type\':\'string\'},\r\n- {\'name\':\'zygosity\',\r\n- \'title\':\'Zygosity\',\r\n- \'type\':\'string\'},\r\n- {\'name\':\'alt_reads\',\r\n- \'title\':\'Alternate reads\',\r\n- \'type\':\'int\'},\r\n- {\'name\':\'tot_reads\',\r\n- \'title\':\'Total reads\',\r\n- \'type\':\'int\'},\r\n- {\'name\':\'af\',\r\n- \'title\':\'Variant allele frequency\',\r\n- \'type\':\'float\'}]\r\n- \r\n- def check_format(self, f): \r\n- return f.readline().startswith(\'##fileformat=VCF\')\r\n- \r\n- def setup(self, f):\r\n- \r\n- vcf_line_no = 0\r\n- for line in f:\r\n- vcf_line_no += 1\r\n- if len(line) < 6:\r\n- continue\r\n- if line[:6] == \'#CHROM\':\r\n- toks = re.split(\'\\s+\', line.rstrip())\r\n- if len(toks) > 8:\r\n- self.samples = toks[9:]\r\n- break\r\n- \r\n- def convert_line(self, l):\r\n- if l.startswith(\'#\'): return None\r\n- self.var_counter += 1\r\n- toks = l.strip(\'\\r\\n\').split(\'\\t\')\r\n- all_wdicts = []\r\n- if len(toks) < 8:\r\n- raise BadFormatError(\'Wrong VCF format\')\r\n- [chrom, pos, tag, ref, alts, qual, filter, info] = toks[:8]\r\n- if tag == \'\':\r\n- raise BadFormatError(\'ID column is blank\')\r\n- elif tag == \'.\':\r\n- tag = \'VAR\' + str(self.var_counter)\r\n- if chrom[:3] != \'chr\':\r\n- chrom = \'chr\' + chrom\r\n- alts = alts.split(\',\')\r\n- len_alts = len(alts)\r\n- if len(toks) == 8:\r\n- for altno in range(len_alts):\r\n- wdict = None\r\n- alt = alts[altno]\r\n- newpos, newref, newalt = self.extract_vcf_variant(\'+\', pos, ref, alt)\r\n- wdict = {\'tags\':tag,\r\n- \'chrom\':chrom,\r\n- \'pos\':newpos,\r\n- \'ref_base\':newref,\r\n- \'alt_base\':newalt,\r\n- \'sample_id\':\'no_sample\',\r\n- \'phred\': qual,\r\n- \'filter\': filter}\r\n- all_wdicts.append(wdict)\r\n- elif len(toks) > 8:\r\n- sample_datas = toks[9:]\r\n- genotype_fields = {}\r\n- genotype_field_no = 0\r\n- for genotype_field in toks[8].split(\':\'):\r\n- genotype_fields[genotype_field] = genotype_field_no\r\n- genotype_field_no += 1\r\n- if not (\'GT\' in genotype_fields):\r\n- raise BadFormatError(\'No GT Field\')\r\n- gt_field_no = genotype_fields[\'GT\']\r\n- for sample_no in range(len(sample_datas)):\r\n- sample = self.samples[sample_no]\r\n- sample_data = sample_datas[sample_no].split(\':\')\r\n- gts = {}\r\n- for gt in sample_data[gt_field_no].replace(\'/\', \'|\').split(\'|\'):\r\n- '..b'\r\n- ref_reads = sample_data[genotype_fields[\'AD\']].split(\',\')[0]\r\n- alt_reads = sample_data[genotype_fields[\'AD\']].split(\',\')[1]\r\n- elif gt == max(gts.keys()): \r\n- #if geontype has multiple alt bases, then AD will have #alt1 reads, #alt2 reads\r\n- alt_reads = sample_data[genotype_fields[\'AD\']].split(\',\')[1]\r\n- else:\r\n- alt_reads = sample_data[genotype_fields[\'AD\']].split(\',\')[0] \r\n- \r\n- if \'DP\' in genotype_fields and genotype_fields[\'DP\'] <= len(sample_data): \r\n- depth = sample_data[genotype_fields[\'DP\']] \r\n- elif alt_reads != \'\' and ref_reads != \'\':\r\n- #if DP is not present but we have alt and ref reads count, dp = ref+alt\r\n- depth = int(alt_reads) + int(ref_reads) \r\n-\r\n- if \'AF\' in genotype_fields and genotype_fields[\'AF\'] <= len(sample_data):\r\n- af = float(sample_data[genotype_fields[\'AF\']] )\r\n- elif depth != \'\' and alt_reads != \'\':\r\n- #if AF not specified, calc it from alt and ref reads\r\n- af = float(alt_reads) / float(depth)\r\n- \r\n- return depth, alt_reads, af\r\n- \r\n- def extract_vcf_variant (self, strand, pos, ref, alt):\r\n-\r\n- reflen = len(ref)\r\n- altlen = len(alt)\r\n- \r\n- # Returns without change if same single nucleotide for ref and alt. \r\n- if reflen == 1 and altlen == 1 and ref == alt:\r\n- return pos, ref, alt\r\n- \r\n- # Trimming from the start and then the end of the sequence \r\n- # where the sequences overlap with the same nucleotides\r\n- new_ref2, new_alt2, new_pos = \\\r\n- self.trimming_vcf_input(ref, alt, pos, strand)\r\n- \r\n- if new_ref2 == \'\':\r\n- new_ref2 = \'-\'\r\n- if new_alt2 == \'\':\r\n- new_alt2 = \'-\'\r\n- \r\n- return new_pos, new_ref2, new_alt2\r\n- \r\n- # This function looks at the ref and alt sequences and removes \r\n- # where the overlapping sequences contain the same nucleotide.\r\n- # This trims from the end first but does not remove the first nucleotide \r\n- # because based on the format of VCF input the \r\n- # first nucleotide of the ref and alt sequence occur \r\n- # at the position specified.\r\n- # End removed first, not the first nucleotide\r\n- # Front removed and position changed\r\n- def trimming_vcf_input(self, ref, alt, pos, strand):\r\n- pos = int(pos)\r\n- reflen = len(ref)\r\n- altlen = len(alt)\r\n- minlen = min(reflen, altlen)\r\n- new_ref = ref\r\n- new_alt = alt\r\n- new_pos = pos\r\n- # Trims from the end. Except don\'t remove the first nucleotide. \r\n- # 1:6530968 CTCA -> GTCTCA becomes C -> GTC.\r\n- for nt_pos in range(0, minlen - 1): \r\n- if ref[reflen - nt_pos - 1] == alt[altlen - nt_pos - 1]:\r\n- new_ref = ref[:reflen - nt_pos - 1]\r\n- new_alt = alt[:altlen - nt_pos - 1]\r\n- else:\r\n- break \r\n- new_ref_len = len(new_ref)\r\n- new_alt_len = len(new_alt)\r\n- minlen = min(new_ref_len, new_alt_len)\r\n- new_ref2 = new_ref\r\n- new_alt2 = new_alt\r\n- # Trims from the start. 1:6530968 G -> GT becomes 1:6530969 - -> T.\r\n- for nt_pos in range(0, minlen):\r\n- if new_ref[nt_pos] == new_alt[nt_pos]:\r\n- if strand == \'+\':\r\n- new_pos += 1\r\n- elif strand == \'-\':\r\n- new_pos -= 1\r\n- new_ref2 = new_ref[nt_pos + 1:]\r\n- new_alt2 = new_alt[nt_pos + 1:]\r\n- else:\r\n- new_ref2 = new_ref[nt_pos:]\r\n- new_alt2 = new_alt[nt_pos:]\r\n- break \r\n- return new_ref2, new_alt2, new_pos\r\n-\r\n-\r\n-if __name__ == "__main__":\r\n- c = CravatConverter()\n\\ No newline at end of file\n' |