| Previous changeset 1:152cc8feff8a (2018-06-12) Next changeset 3:b968ba302ba6 (2018-06-12) |
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Commit message:
Uploaded |
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added:
cravat_convert/vcf_converter.py |
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removed:
cravat_convert/cravat_convert.py cravat_convert/cravat_convert.xml |
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| diff -r 152cc8feff8a -r c042835a7163 cravat_convert/cravat_convert.py --- a/cravat_convert/cravat_convert.py Tue Jun 12 11:05:27 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,80 +0,0 @@ -''' -Convert a VCF format file to Cravat format file -''' - -import os -import argparse -from vcf_converter import CravatConverter -### -import ipdb - - -# 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 152cc8feff8a -r c042835a7163 cravat_convert/cravat_convert.xml --- a/cravat_convert/cravat_convert.xml Tue Jun 12 11:05:27 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,20 +0,0 @@ -<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 152cc8feff8a -r c042835a7163 cravat_convert/vcf_converter.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cravat_convert/vcf_converter.py Tue Jun 12 11:20:00 2018 -0400 |
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| b'@@ -0,0 +1,243 @@\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' |