| Previous changeset 9:43815fa60f3a (2021-03-29) Next changeset 11:2bf63b38ee9b (2021-09-12) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 0faf0ade3f13d7c78d93869823ea9fdf25c21b13" |
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modified:
convert_VCF_info_fields.py macros.xml test-data/all_fasta.loc variant.xml |
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removed:
annotateVCF.py test-data/bwa-mem-mt-genome.fa test-data/bwa-mem-mt-genome.fa.fai |
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| diff -r 43815fa60f3a -r 9fb055604648 annotateVCF.py --- a/annotateVCF.py Mon Mar 29 20:05:39 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,409 +0,0 @@\n-#!/usr/bin/env python3\n-\n-# Takes in VCF file and a samtools mpileup output file\n-# Fills in annotation for the VCF file including AF, DP\n-# SB, and DP4\n-#\n-# Usage statement:\n-# python annotateVCF.py in_vcf.vcf in_mpileup.txt out_vcf.vcf\n-#\n-# Can generate in_mileup.txt with samtools mpileup (and can restrict which sites to generate pileups for with in_vcf.vcf)\n-\n-# 08/24/2020 - Nathan P. Roach, natproach@gmail.com\n-\n-import sys\n-from math import isnan, log10\n-\n-from scipy.stats import fisher_exact\n-\n-\n-def pval_to_phredqual(pval):\n- return int(round(-10. * log10(pval)))\n-\n-\n-def parseSimpleSNPpileup(fields, ref_base, alt_base):\n- base_to_idx = {\n- \'A\': 0,\n- \'a\': 0,\n- \'T\': 1,\n- \'t\': 1,\n- \'C\': 2,\n- \'c\': 2,\n- \'G\': 3,\n- \'g\': 3\n- }\n-\n- base_to_idx_stranded = {\n- \'A\': 0,\n- \'T\': 1,\n- \'C\': 2,\n- \'G\': 3,\n- \'a\': 4,\n- \'t\': 5,\n- \'c\': 6,\n- \'g\': 7\n- }\n- ref_base2 = fields[2]\n- counts = [0, 0, 0, 0]\n- stranded_counts = [0, 0, 0, 0, 0, 0, 0, 0]\n- ref_idx = base_to_idx[fields[2]]\n- dp = int(fields[3])\n- carrot_flag = False\n- ins_flag = False\n- ins_str = ""\n- ins_len = 0\n- insertion = ""\n- del_flag = False\n- del_str = ""\n- del_len = 0\n- deletion = ""\n- # dollar_flag = False\n- for base in fields[4]:\n- if carrot_flag:\n- carrot_flag = False\n- continue\n- if ins_len > 0:\n- insertion += base\n- ins_len -= 1\n- continue\n- if del_len > 0:\n- deletion += base\n- del_len -= 1\n- continue\n- if ins_flag:\n- if base.isdigit():\n- ins_str += base\n- else:\n- ins_len = int(ins_str) - 1\n- ins_str = ""\n- insertion = base\n- ins_flag = False\n- elif del_flag:\n- if base.isdigit():\n- del_str += base\n- else:\n- del_len = int(del_str) - 1\n- del_str = ""\n- deletion = base\n- del_flag = False\n- else:\n- if base == \'^\':\n- carrot_flag = True\n- continue\n- elif base == \'$\':\n- continue\n- elif base == \'+\':\n- ins_flag = True\n- elif base == \'-\':\n- del_flag = True\n- elif base == \'.\':\n- counts[ref_idx] += 1\n- stranded_counts[base_to_idx_stranded[ref_base2]] += 1\n- elif base == \',\':\n- counts[ref_idx] += 1\n- stranded_counts[base_to_idx_stranded[ref_base2.lower()]] += 1\n- elif base == \'N\' or base == \'n\':\n- continue\n- elif base == \'*\':\n- continue\n- else:\n- counts[base_to_idx[base]] += 1\n- stranded_counts[base_to_idx_stranded[base]] += 1\n- if sum(counts) == 0:\n- af = float("nan")\n- else:\n- af = float(counts[base_to_idx[alt_base]]) / float(sum(counts))\n- if float(sum(stranded_counts[0:4])) == 0:\n- faf = float("nan")\n- else:\n- faf = float(stranded_counts[base_to_idx_stranded[alt_base]]) / float(sum(stranded_counts[0:4]))\n- if float(sum(stranded_counts[4:])) == 0:\n- raf = float("nan")\n- else:\n- raf = float(stranded_counts[base_to_idx_stranded[alt_base.lower()]]) / float(sum(stranded_counts[4:]))\n- dp4 = [stranded_counts[base_to_idx_stranded[ref_base]],\n- stranded_counts[base_to_idx_stranded[ref_base.lower()]],\n- stranded_counts[base_to_idx_stranded[alt_base]],\n- stranded_counts[base_to_idx_stranded[alt_base.lower()]]]\n- return (dp, af, faf, raf, dp4)\n-\n-\n-def parseIndelPileup(fields, ref_base, alt_base):\n- counts = [0, 0, 0, 0, 0, 0, 0, 0, 0] # indel ref match, indel fwd ref match, indel rev ref match, '..b' out_vcf.write(line)\n- elif line[0] == "#":\n- out_vcf.write("##annotateVCFVersion=0.2\\n")\n- out_vcf.write("##INFO=<ID=DP,Number=1,Type=Integer,Description=\\"Raw Depth\\">\\n")\n- out_vcf.write("##INFO=<ID=AF,Number=1,Type=Float,Description=\\"Allele Frequency\\">\\n")\n- out_vcf.write("##INFO=<ID=FAF,Number=1,Type=Float,Description=\\"Forward Allele Frequency\\">\\n")\n- out_vcf.write("##INFO=<ID=RAF,Number=1,Type=Float,Description=\\"Reverse Allele Frequency\\">\\n")\n- out_vcf.write("##INFO=<ID=SB,Number=1,Type=Integer,Description=\\"Phred-scaled strand bias at this position\\">\\n")\n- out_vcf.write("##INFO=<ID=DP4,Number=4,Type=Integer,Description=\\"Counts for ref-forward bases, ref-reverse, alt-forward and alt-reverse bases\\">\\n")\n- out_vcf.write(line)\n- else:\n- fields = line.strip().split()\n- if fields[0] in to_examine:\n- to_examine[fields[0]][int(fields[1])] = (fields[3], fields[4])\n- else:\n- to_examine[fields[0]] = {int(fields[1]): (fields[3], fields[4])}\n- in_vcf.close()\n- data = {}\n-\n- # Populate data dictionary, which relates chromosome and position to the following:\n- # depth of coverage\n- # allele frequency\n- # forward strand allele frequency\n- # reverse strand allele frequency\n- # dp4 - depth of coverage of ref allele fwd strand, DOC of ref allele rev strand, DOC of alt allele fwd strand, DOC of alt allele rev strand\n- for line in in_mpileup:\n- fields = line.strip().split()\n- if fields[0] not in to_examine:\n- continue\n- if int(fields[1]) not in to_examine[fields[0]]:\n- continue\n- (ref_base, alt_base) = to_examine[fields[0]][int(fields[1])]\n- if len(ref_base.split(\',\')) > 1: # Can\'t handle multiple ref alleles\n- continue\n- if len(alt_base.split(\',\')) > 1: # Can\'t handle multiple alt alleles\n- continue\n- if len(ref_base) > 1 or len(alt_base) > 1:\n- if len(ref_base) > 1 and len(alt_base) > 1: # Can\'t handle complex indels\n- continue\n- data[(fields[0], int(fields[1]))] = parseIndelPileup(fields, ref_base, alt_base)\n- if len(ref_base) == 1 and len(alt_base) == 1:\n- data[(fields[0], int(fields[1]))] = parseSimpleSNPpileup(fields, ref_base, alt_base)\n- in_mpileup.close()\n- # Reopen vcf, this time, skip header, annotate all the sites for which there is an entry in data dictionary\n- # (Sites without entries have either multiple ref or alt bases, or have complex indels. Not supported (for now), and not reported as a result)\n- in_vcf = open(in_vcf_filepath, \'r\')\n- for line in in_vcf:\n- if line[0] == \'#\':\n- continue\n- fields = line.strip().split(\'\\t\')\n- if (fields[0], int(fields[1])) not in data:\n- continue\n- (dp, af, faf, raf, dp4) = data[(fields[0], int(fields[1]))]\n- dp2x2 = [[dp4[0], dp4[1]], [dp4[2], dp4[3]]]\n- _, p_val = fisher_exact(dp2x2)\n- sb = pval_to_phredqual(p_val)\n- if fields[7] == "":\n- info = []\n- else:\n- info = fields[7].split(\';\')\n- info.append("DP=%d" % (dp))\n- if isnan(af):\n- info.append("AF=NaN")\n- else:\n- info.append("AF=%.6f" % (af))\n- if isnan(faf):\n- info.append("FAF=NaN")\n- else:\n- info.append("FAF=%.6f" % (faf))\n- if isnan(raf):\n- info.append("RAF=NaN")\n- else:\n- info.append("RAF=%.6f" % (raf))\n- info.append("SB=%d" % (sb))\n- info.append("DP4=%s" % (\',\'.join([str(x) for x in dp4])))\n- new_info = \';\'.join(info)\n- fields[7] = new_info\n- out_vcf.write("%s\\n" % ("\\t".join(fields)))\n- in_vcf.close()\n- out_vcf.close()\n-\n-\n-if __name__ == "__main__":\n- annotateVCF(sys.argv[1], sys.argv[2], sys.argv[3])\n' |
| b |
| diff -r 43815fa60f3a -r 9fb055604648 convert_VCF_info_fields.py --- a/convert_VCF_info_fields.py Mon Mar 29 20:05:39 2021 +0000 +++ b/convert_VCF_info_fields.py Thu Apr 22 20:25:35 2021 +0000 |
| [ |
| @@ -11,7 +11,8 @@ from collections import OrderedDict from math import log10 -from scipy.stats import fisher_exact +import scipy +import scipy.stats def pval_to_phredqual(pval): @@ -69,7 +70,7 @@ for j, i in enumerate(range(2, len(sr_list), 2)): dp4 = (sr_list[ref_fwd], sr_list[ref_rev], sr_list[i], sr_list[i + 1]) dp2x2 = [[dp4[0], dp4[1]], [dp4[2], dp4[3]]] - _, p_val = fisher_exact(dp2x2) + _, p_val = scipy.stats.fisher_exact(dp2x2) sb = pval_to_phredqual(p_val) as_ = (sc_list[ref_fwd], sc_list[ref_rev], sc_list[i], sc_list[i + 1]) |
| b |
| diff -r 43815fa60f3a -r 9fb055604648 macros.xml --- a/macros.xml Mon Mar 29 20:05:39 2021 +0000 +++ b/macros.xml Thu Apr 22 20:25:35 2021 +0000 |
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| @@ -1,7 +1,7 @@ <?xml version="1.0"?> <macros> - <token name="@TOOL_VERSION@">1.0.3</token> - <token name="@PROFILE@">18.01</token> + <token name="@TOOL_VERSION@">1.3.2</token> + <token name="@PROFILE@">20.01</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">medaka</requirement> @@ -48,29 +48,32 @@ </xml> <xml name="model" token_argument="-m" token_label="Select model"> <param argument="@ARGUMENT@" type="select" label="@LABEL@"> - <option value="r10_min_high_g303">r10_min_high_g303</option> - <option value="r10_min_high_g340">r10_min_high_g340</option> <option value="r103_min_high_g345">r103_min_high_g345</option> <option value="r103_min_high_g360">r103_min_high_g360</option> <option value="r103_prom_high_g360">r103_prom_high_g360</option> <option value="r103_prom_snp_g3210">r103_prom_snp_g3210</option> <option value="r103_prom_variant_g3210">r103_prom_variant_g3210</option> + <option value="r10_min_high_g303">r10_min_high_g303</option> + <option value="r10_min_high_g340">r10_min_high_g340</option> <option value="r941_min_fast_g303">r941_min_fast_g303</option> <option value="r941_min_high_g303">r941_min_high_g303</option> <option value="r941_min_high_g330">r941_min_high_g330</option> <option value="r941_min_high_g340_rle">r941_min_high_g340_rle</option> <option value="r941_min_high_g344">r941_min_high_g344</option> <option value="r941_min_high_g351">r941_min_high_g351</option> - <option value="r941_min_high_g360">r941_min_high_g360</option> + <option value="r941_min_high_g360" selected="true">r941_min_high_g360</option> <option value="r941_prom_fast_g303">r941_prom_fast_g303</option> <option value="r941_prom_high_g303">r941_prom_high_g303</option> <option value="r941_prom_high_g330">r941_prom_high_g330</option> <option value="r941_prom_high_g344">r941_prom_high_g344</option> - <option value="r941_prom_high_g360" selected="true">r941_prom_high_g360</option> + <option value="r941_prom_high_g360">r941_prom_high_g360</option> + <option value="r941_prom_high_g4011">r941_prom_high_g4011</option> <option value="r941_prom_snp_g303">r941_prom_snp_g303</option> <option value="r941_prom_snp_g322">r941_prom_snp_g322</option> + <option value="r941_prom_snp_g360">r941_prom_snp_g360</option> <option value="r941_prom_variant_g303">r941_prom_variant_g303</option> <option value="r941_prom_variant_g322">r941_prom_variant_g322</option> + <option value="r941_prom_variant_g360">r941_prom_variant_g360</option> </param> </xml> <xml name="reference"> |
| b |
| diff -r 43815fa60f3a -r 9fb055604648 test-data/all_fasta.loc --- a/test-data/all_fasta.loc Mon Mar 29 20:05:39 2021 +0000 +++ b/test-data/all_fasta.loc Thu Apr 22 20:25:35 2021 +0000 |
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| @@ -1,1 +1,1 @@ -bwa-mem-mt-genome bwa-mem-mt-genome bwa-mem-mt-genome ${__HERE__}/bwa-mem-mt-genome.fa \ No newline at end of file +ref_fasta ref_fasta ref_fasta ${__HERE__}/ref.fasta \ No newline at end of file |
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| diff -r 43815fa60f3a -r 9fb055604648 test-data/bwa-mem-mt-genome.fa --- a/test-data/bwa-mem-mt-genome.fa Mon Mar 29 20:05:39 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,238 +0,0 @@\n->gi|251831106|ref|NC_012920.1|\n-GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGG\n-GTATGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTC\n-CTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTA\n-ATTAATTAATGCTTGTAGGACATAATAATAACAATTGAATGTCTGCACAGCCACTTTCCACACAGACATC\n-ATAACAAAAAATTTCCACCAAACCCCCCCTCCCCCGCTTCTGGCCACAGCACTTAAACACATCTCTGCCA\n-AACCCCAAAAACAAAGAACCCTAACACCAGCCTAACCAGATTTCAAATTTTATCTTTTGGCGGTATGCAC\n-TTTTAACAGTCACCCCCCAACTAACACATTATTTTCCCCTCCCACTCCCATACTACTAATCTCATCAATA\n-CAACCCCCGCCCATCCTACCCAGCACACACACACCGCTGCTAACCCCATACCCCGAACCAACCAAACCCC\n-AAAGACACCCCCCACAGTTTATGTAGCTTACCTCCTCAAAGCAATACACTGAAAATGTTTAGACGGGCTC\n-ACATCACCCCATAAACAAATAGGTTTGGTCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAA\n-GCATCCCCGTTCCAGTGAGTTCACCCTCTAAATCACCACGATCAAAAGGAACAAGCATCAAGCACGCAGC\n-AATGCAGCTCAAAACGCTTAGCCTAGCCACACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAATAA\n-ACGAAAGTTTAACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACCGCGGTCACACGA\n-TTAACCCAAGTCAATAGAAGCCGGCGTAAAGAGTGTTTTAGATCACCCCCTCCCCAATAAAGCTAAAACT\n-CACCTGAGTTGTAAAAAACTCCAGTTGACACAAAATAGACTACGAAAGTGGCTTTAACATATCTGAACAC\n-ACAATAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCCTAAACCTCAACAGTTAAATC\n-AACAAAACTGCTCGCCAGAACACTACGAGCCACAGCTTAAAACTCAAAGGACCTGGCGGTGCTTCATATC\n-CCTCTAGAGGAGCCTGTTCTGTAATCGATAAACCCCGATCAACCTCACCACCTCTTGCTCAGCCTATATA\n-CCGCCATCTTCAGCAAACCCTGATGAAGGCTACAAAGTAAGCGCAAGTACCCACGTAAAGACGTTAGGTC\n-AAGGTGTAGCCCATGAGGTGGCAAGAAATGGGCTACATTTTCTACCCCAGAAAACTACGATAGCCCTTAT\n-GAAACTTAAGGGTCGAAGGTGGATTTAGCAGTAAACTAAGAGTAGAGTGCTTAGTTGAACAGGGCCCTGA\n-AGCGCGTACACACCGCCCGTCACCCTCCTCAAGTATACTTCAAAGGACATTTAACTAAAACCCCTACGCA\n-TTTATATAGAGGAGACAAGTCGTAACATGGTAAGTGTACTGGAAAGTGCACTTGGACGAACCAGAGTGTA\n-GCTTAACACAAAGCACCCAACTTACACTTAGGAGATTTCAACTTAACTTGACCGCTCTGAGCTAAACCTA\n-GCCCCAAACCCACTCCACCTTACTACCAGACAACCTTAGCCAAACCATTTACCCAAATAAAGTATAGGCG\n-ATAGAAATTGAAACCTGGCGCAATAGATATAGTACCGCAAGGGAAAGATGAAAAATTATAACCAAGCATA\n-ATATAGCAAGGACTAACCCCTATACCTTCTGCATAATGAATTAACTAGAAATAACTTTGCAAGGAGAGCC\n-AAAGCTAAGACCCCCGAAACCAGACGAGCTACCTAAGAACAGCTAAAAGAGCACACCCGTCTATGTAGCA\n-AAATAGTGGGAAGATTTATAGGTAGAGGCGACAAACCTACCGAGCCTGGTGATAGCTGGTTGTCCAAGAT\n-AGAATCTTAGTTCAACTTTAAATTTGCCCACAGAACCCTCTAAATCCCCTTGTAAATTTAACTGTTAGTC\n-CAAAGAGGAACAGCTCTTTGGACACTAGGAAAAAACCTTGTAGAGAGAGTAAAAAATTTAACACCCATAG\n-TAGGCCTAAAAGCAGCCACCAATTAAGAAAGCGTTCAAGCTCAACACCCACTACCTAAAAAATCCCAAAC\n-ATATAACTGAACTCCTCACACCCAATTGGACCAATCTATCACCCTATAGAAGAACTAATGTTAGTATAAG\n-TAACATGAAAACATTCTCCTCCGCATAAGCCTGCGTCAGATTAAAACACTGAACTGACAATTAACAGCCC\n-AATATCTACAATCAACCAACAAGTCATTATTACCCTCACTGTCAACCCAACACAGGCATGCTCATAAGGA\n-AAGGTTAAAAAAAGTAAAAGGAACTCGGCAAATCTTACCCCGCCTGTTTACCAAAAACATCACCTCTAGC\n-ATCACCAGTATTAGAGGCACCGCCTGCCCAGTGACACATGTTTAACGGCCGCGGTACCCTAACCGTGCAA\n-AGGTAGCATAATCACTTGTTCCTTAAATAGGGACCTGTATGAATGGCTCCACGAGGGTTCAGCTGTCTCT\n-TACTTTTAACCAGTGAAATTGACCTGCCCGTGAAGAGGCGGGCATAACACAGCAAGACGAGAAGACCCTA\n-TGGAGCTTTAATTTATTAATGCAAACAGTACCTAACAAACCCACAGGTCCTAAACTACCAAACCTGCATT\n-AAAAATTTCGGTTGGGGCGACCTCGGAGCAGAACCCAACCTCCGAGCAGTACATGCTAAGACTTCACCAG\n-TCAAAGCGAACTACTATACTCAATTGATCCAATAACTTGACCAACGGAACAAGTTACCCTAGGGATAACA\n-GCGCAATCCTATTCTAGAGTCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCG\n-ATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTACGTGATCTGAGTTCAGACCGG\n-AGTAATCCAGGTCGGTTTCTATCTACNTTCAAATTCCTCCCTGTACGAAAGGACAAGAGAAATAAGGCCT\n-ACTTCACAAAGCGCCTTCCCCCGTAAATGATATCATCTCAACTTAGTATTATACCCACACCCACCCAAGA\n-ACAGGGTTTGTTAAGATGGCAGAGCCCGGTAATCGCATAAAACTTAAAACTTTACAGTCAGAGGTTCAAT\n-TCCTCTTCTTAACAACATACCCATGGCCAACCTCCTACTCCTCATTGTACCCATTCTAATCGCAATGGCA\n-TTCCTAATGCTTACCGAACGAAAAATTCTAGGCTATATACAACTACGCAAAGGCCCCAACGTTGTAGGCC\n-CCTACGGGCTACTACAACCCTTCGCTGACGCCATAAAACTCTTCACCAAAGAGCCCCTAAAACCCGCCAC\n-ATCTACCATCACCCTCTACATCACCGCCCCGACCTTAGCTCTCACCATCGCTCTTCTACTATGAACCCCC\n-CTCCCCATACCCAACCCCCTGGTCAACCTCAACCTAGGCCTCCTATTTATTCTAGCCACCTCTAGCCTAG\n-CCGTTTACTCAATCCTCTGATCAGGGTGAGCATCAAACTCAAACTACGCCCTGATCGGCGCACTGCGAGC\n-AGTAGCCCAAACAATCTCATATGAAGTCACCCTAGCCATCATTCTACTATCAACATTACTAATAAGTGGC\n-TCCTTTAACCTCTCCACCCTTATCACAACACAAGAACACCTCTGATTACTCCTGCCATCA'..b'CAGTTCTTCAAATATCTACTCATCTTCCTAATTACCATACTAATCTTAGTTACCGCTAA\n-CAACCTATTCCAACTGTTCATCGGCTGAGAGGGCGTAGGAATTATATCCTTCTTGCTCATCAGTTGATGA\n-TACGCCCGAGCAGATGCCAACACAGCAGCCATTCAAGCAATCCTATACAACCGTATCGGCGATATCGGTT\n-TCATCCTCGCCTTAGCATGATTTATCCTACACTCCAACTCATGAGACCCACAACAAATAGCCCTTCTAAA\n-CGCTAATCCAAGCCTCACCCCACTACTAGGCCTCCTCCTAGCAGCAGCAGGCAAATCAGCCCAATTAGGT\n-CTCCACCCCTGACTCCCCTCAGCCATAGAAGGCCCCACCCCAGTCTCAGCCCTACTCCACTCAAGCACTA\n-TAGTTGTAGCAGGAATCTTCTTACTCATCCGCTTCCACCCCCTAGCAGAAAATAGCCCACTAATCCAAAC\n-TCTAACACTATGCTTAGGCGCTATCACCACTCTGTTCGCAGCAGTCTGCGCCCTTACACAAAATGACATC\n-AAAAAAATCGTAGCCTTCTCCACTTCAAGTCAACTAGGACTCATAATAGTTACAATCGGCATCAACCAAC\n-CACACCTAGCATTCCTGCACATCTGTACCCACGCCTTCTTCAAAGCCATACTATTTATGTGCTCCGGGTC\n-CATCATCCACAACCTTAACAATGAACAAGATATTCGAAAAATAGGAGGACTACTCAAAACCATACCTCTC\n-ACTTCAACCTCCCTCACCATTGGCAGCCTAGCATTAGCAGGAATACCTTTCCTCACAGGTTTCTACTCCA\n-AAGACCACATCATCGAAACCGCAAACATATCATACACAAACGCCTGAGCCCTATCTATTACTCTCATCGC\n-TACCTCCCTGACAAGCGCCTATAGCACTCGAATAATTCTTCTCACCCTAACAGGTCAACCTCGCTTCCCC\n-ACCCTTACTAACATTAACGAAAATAACCCCACCCTACTAAACCCCATTAAACGCCTGGCAGCCGGAAGCC\n-TATTCGCAGGATTTCTCATTACTAACAACATTTCCCCCGCATCCCCCTTCCAAACAACAATCCCCCTCTA\n-CCTAAAACTCACAGCCCTCGCTGTCACTTTCCTAGGACTTCTAACAGCCCTAGACCTCAACTACCTAACC\n-AACAAACTTAAAATAAAATCCCCACTATGCACATTTTATTTCTCCAACATACTCGGATTCTACCCTAGCA\n-TCACACACCGCACAATCCCCTATCTAGGCCTTCTTACGAGCCAAAACCTGCCCCTACTCCTCCTAGACCT\n-AACCTGACTAGAAAAGCTATTACCTAAAACAATTTCACAGCACCAAATCTCCACCTCCATCATCACCTCA\n-ACCCAAAAAGGCATAATTAAACTTTACTTCCTCTCTTTCTTCTTCCCACTCATCCTAACCCTACTCCTAA\n-TCACATAACCTATTCCCCCGAGCAATCTCAATTACAATATATACACCAACAAACAATGTTCAACCAGTAA\n-CTACTACTAATCAACGCCCATAATCATACAAAGCCCCCGCACCAATAGGATCCTCCCGAATCAACCCTGA\n-CCCCTCTCCTTCATAAATTATTCAGCTTCCTACACTATTAAAGTTTACCACAACCACCACCCCATCATAC\n-TCTTTCACCCACAGCACCAATCCTACCTCCATCGCTAACCCCACTAAAACACTCACCAAGACCTCAACCC\n-CTGACCCCCATGCCTCAGGATACTCCTCAATAGCCATCGCTGTAGTATATCCAAAGACAACCATCATTCC\n-CCCTAAATAAATTAAAAAAACTATTAAACCCATATAACCTCCCCCAAAATTCAGAATAATAACACACCCG\n-ACCACACCGCTAACAATCAATACTAAACCCCCATAAATAGGAGAAGGCTTAGAAGAAAACCCCACAAACC\n-CCATTACTAAACCCACACTCAACAGAAACAAAGCATACATCATTATTCTCGCACGGACTACAACCACGAC\n-CAATGATATGAAAAACCATCGTTGTATTTCAACTACAAGAACACCAATGACCCCAATACGCAAAACTAAC\n-CCCCTAATAAAATTAATTAACCACTCATTCATCGACCTCCCCACCCCATCCAACATCTCCGCATGATGAA\n-ACTTCGGCTCACTCCTTGGCGCCTGCCTGATCCTCCAAATCACCACAGGACTATTCCTAGCCATGCACTA\n-CTCACCAGACGCCTCAACCGCCTTTTCATCAATCGCCCACATCACTCGAGACGTAAATTATGGCTGAATC\n-ATCCGCTACCTTCACGCCAATGGCGCCTCAATATTCTTTATCTGCCTCTTCCTACACATCGGGCGAGGCC\n-TATATTACGGATCATTTCTCTACTCAGAAACCTGAAACATCGGCATTATCCTCCTGCTTGCAACTATAGC\n-AACAGCCTTCATAGGCTATGTCCTCCCGTGAGGCCAAATATCATTCTGAGGGGCCACAGTAATTACAAAC\n-TTACTATCCGCCATCCCATACATTGGGACAGACCTAGTTCAATGAATCTGAGGAGGCTACTCAGTAGACA\n-GTCCCACCCTCACACGATTCTTTACCTTTCACTTCATCTTGCCCTTCATTATTGCAGCCCTAGCAACACT\n-CCACCTCCTATTCTTGCACGAAACGGGATCAAACAACCCCCTAGGAATCACCTCCCATTCCGATAAAATC\n-ACCTTCCACCCTTACTACACAATCAAAGACGCCCTCGGCTTACTTCTCTTCCTTCTCTCCTTAATGACAT\n-TAACACTATTCTCACCAGACCTCCTAGGCGACCCAGACAATTATACCCTAGCCAACCCCTTAAACACCCC\n-TCCCCACATCAAGCCCGAATGATATTTCCTATTCGCCTACACAATTCTCCGATCCGTCCCTAACAAACTA\n-GGAGGCGTCCTTGCCCTATTACTATCCATCCTCATCCTAGCAATAATCCCCATCCTCCATATATCCAAAC\n-AACAAAGCATAATATTTCGCCCACTAAGCCAATCACTTTATTGACTCCTAGCCGCAGACCTCCTCATTCT\n-AACCTGAATCGGAGGACAACCAGTAAGCTACCCTTTTACCATCATTGGACAAGTAGCATCCGTACTATAC\n-TTCACAACAATCCTAATCCTAATACCAACTATCTCCCTAATTGAAAACAAAATACTCAAATGGGCCTGTC\n-CTTGTAGTATAAACTAATACACCAGTCTTGTAAACCGGAGATGAAAACCTTTTTCCAAGGACAAATCAGA\n-GAAAAAGTCTTTAACTCCACCATTAGCACCCAAAGCTAAGATTCTAATTTAAACTATTCTCTGTTCTTTC\n-ATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACA\n-TTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCA\n-ATCCACATCAAAACCCCCTCCCCATGCTTACAAGCAAGTACAGCAATCAACCCTCAACTATCACACATCA\n-ACTGCAACTCCAAAGCCACCCCTCACCCACTAGGATACCAACAAACCTACCCACCCTTAACAGTACATAG\n-TACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCCCC\n-TCAGATAGGGGTCCCTTGACCACCATCCTCCGTGAAATCAATATCCCGCACAAGAGTGCTACTCTCCTCG\n-CTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTC\n-ATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATG\n' |
| b |
| diff -r 43815fa60f3a -r 9fb055604648 test-data/bwa-mem-mt-genome.fa.fai --- a/test-data/bwa-mem-mt-genome.fa.fai Mon Mar 29 20:05:39 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,1 +0,0 @@ -gi|251831106|ref|NC_012920.1| 16569 31 70 71 |
| b |
| diff -r 43815fa60f3a -r 9fb055604648 variant.xml --- a/variant.xml Mon Mar 29 20:05:39 2021 +0000 +++ b/variant.xml Thu Apr 22 20:25:35 2021 +0000 |
| [ |
| @@ -1,12 +1,10 @@ <?xml version="1.0"?> -<tool id="medaka_variant" name="medaka variant tool" version="@TOOL_VERSION@+galaxy7" profile="@PROFILE@"> +<tool id="medaka_variant" name="medaka variant tool" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> <description>Probability decoding</description> <macros> <import>macros.xml</import> </macros> - <expand macro="requirements"> - <requirement type="package" version="1.4.1">scipy</requirement> - </expand> + <expand macro="requirements"/> <expand macro="version_command"/> @@ -39,13 +37,14 @@ --regions '${regions}' #end if $verbose + ${ambig_ref} + ${gvcf} ## required reference.fa #for $current in $pool.inputs '$current' #end for '$out_result' ## output - 2>&1 | tee '$out_log' #elif $pool.pool_mode == "No": ## run @@ -56,26 +55,27 @@ --regions '${regions}' #end if $verbose + ${ambig_ref} + ${gvcf} ## required reference.fa '$pool.input' '$out_result' ##output 2>&1 | tee '$out_log' #end if - #if $out_annotated: ## medaka annotate errors out if the reference is lower case at a position it's annotating because it checks vs the ref base in the vcf && python '$convert_fasta' reference.fa upper_reference.fa && ln -s '$output_annotated.in_bam' in.bam && ln -s '$output_annotated.in_bam.metadata.bam_index' in.bai - && medaka tools annotate --pad $output_annotated.pad '$out_result' upper_reference.fa in.bam tmp.vcf - && '$__tool_directory__/convert_VCF_info_fields.py' tmp.vcf '$out_annotated' + && medaka tools annotate --dpsp --pad $output_annotated.pad '$out_result' upper_reference.fa in.bam tmp.vcf + && python '$__tool_directory__/convert_VCF_info_fields.py' tmp.vcf '$out_annotated' #end if ]]></command> <inputs> <conditional name="pool"> <param name="pool_mode" type="select" label="Are you pooling HDF5 datasets?"> - <option value="No" selected="True">No</option> + <option value="No" selected="true">No</option> <option value="Yes">Yes</option> </param> <when value="Yes"> @@ -96,6 +96,8 @@ </sanitizer> </param> <param argument="--verbose" type="boolean" truevalue="--verbose" falsevalue="" label="Populate VCF info fields?"/> + <param argument="--ambig_ref" type="boolean" truevalue="--ambig_ref" falsevalue="" label="Decode variants at ambiguous reference positions?" checked="false"/> + <param argument="--gvcf" type="boolean" truevalue="--gvcf" falsevalue="" label="Output VCF records for reference loci predicted to be non-variant?" checked="false"/> <conditional name="output_annotated"> <param name="output_annotated_select" type="select" label="Output annotated VCF?" help="Annotate allele frequency, depth of coverage, etc for each variant (requires BAM file)"> <option value="true" selected="true">Output annotated VCF</option> @@ -129,8 +131,9 @@ </conditional> <conditional name="reference_source"> <param name="reference_source_selector" value="history"/> - <param name="ref_file" value="ref.fasta"/> + <param name="ref_file" value="ref.fasta.gz"/> </conditional> + <param name="ambig_ref" value="true"/> <conditional name="output_annotated"> <param name="output_annotated_select" value="true"/> <param name="in_bam" value="medaka_test.bam"/> @@ -146,7 +149,7 @@ </output> <output name="out_annotated"> <assert_contents> - <has_n_lines n="22"/> + <has_n_lines n="23"/> <has_line line="##fileformat=VCFv4.1" /> <has_line_matching expression="##medaka_version=[0-9]+\.[0-9]+\.[0-9]+" /> <has_line_matching expression="##convert_VCF_info_fields=[0-9]+\.[0-9]+" /> @@ -168,6 +171,7 @@ <param name="reference_source_selector" value="history"/> <param name="ref_file" value="ref.fasta.gz" ftype="fasta.gz"/> </conditional> + <param name="ambig_ref" value="true"/> <conditional name="output_annotated"> <param name="output_annotated_select" value="true"/> <param name="in_bam" value="medaka_test.bam"/> @@ -183,7 +187,7 @@ </output> <output name="out_annotated"> <assert_contents> - <has_n_lines n="22"/> + <has_n_lines n="23"/> <has_line line="##fileformat=VCFv4.1" /> <has_line_matching expression="##medaka_version=[0-9]+\.[0-9]+\.[0-9]+" /> <has_line_matching expression="##convert_VCF_info_fields=[0-9]+\.[0-9]+" /> |