Mercurial > repos > dfornika > artic_margin_cons_medaka
changeset 5:47eb99e41bfb draft
"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_margin_cons_medaka commit cdc887baab41af2b386b1ec7239b55d474c0fff5-dirty"
| author | dfornika |
|---|---|
| date | Tue, 17 Mar 2020 21:20:38 +0000 |
| parents | eb4af87a77ff |
| children | f52f0a2778f8 |
| files | artic_margin_cons_medaka.xml github_downloaded/1005a47/margin_cons_medaka.py github_downloaded/1005a47/vcftagprimersites.py margin_cons_medaka.py |
| diffstat | 4 files changed, 1348 insertions(+), 5 deletions(-) [+] |
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--- a/artic_margin_cons_medaka.xml Wed Mar 11 02:31:04 2020 +0000 +++ b/artic_margin_cons_medaka.xml Tue Mar 17 21:20:38 2020 +0000 @@ -1,4 +1,4 @@ -<tool id="artic_margin_cons_medaka" name="ARTIC margin_cons_medaka" version="0.1.0+galaxy0"> +<tool id="artic_margin_cons_medaka" name="ARTIC margin_cons_medaka" version="0.1.0-1005a47+galaxy0"> <description>Generate consensus fasta file from a reference fasta, bam alignment and VCF file</description> <requirements> <requirement type="package" version="0.6.8">pyvcf</requirement> @@ -6,14 +6,14 @@ <requirement type="package" version="1.9">samtools</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ - ln -s '${input_alignment}' alignment.bam && - samtools index alignment.bam && + ln -s '${input_alignment}' '${input_alignment.element_identifier}' alignment.bam && + samtools index '${input_alignment.element_identifier}' && python '${__tool_directory__}/margin_cons_medaka.py' --depth '${minimum_depth}' --quality '${minimum_quality}' '${ref_fasta}' '${input_variants}' - alignment.bam + '${input_alignment.element_identifier}' > '${consensus_fasta}' 2> '${report}' ]]></command>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/github_downloaded/1005a47/margin_cons_medaka.py Tue Mar 17 21:20:38 2020 +0000 @@ -0,0 +1,149 @@ +#!/usr/bin/env python +from Bio import SeqIO +import sys +import vcf +import subprocess +from collections import defaultdict +import os.path +import operator +from .vcftagprimersites import read_bed_file +import argparse + +def collect_depths(bamfile): + if not os.path.exists(bamfile): + raise SystemExit("bamfile %s doesn't exist" % (bamfile,)) + + p = subprocess.Popen(['samtools', 'depth', bamfile], + stdout=subprocess.PIPE) + out, err = p.communicate() + depths = defaultdict(dict) + for ln in out.decode('utf-8').split("\n"): + if ln: + contig, pos, depth = ln.split("\t") + depths[contig][int(pos)] = int(depth) + return depths + +class Reporter: + def __init__(self, vcffile, depths): + self.vcffile = vcffile + self.depths = depths + + def report(self, r, status, allele): + idfile = os.path.basename(self.vcffile).split(".")[0] + print("%s\t%s\tstatus\t%s" % (idfile, r.POS, status), file=sys.stderr) + print("%s\t%s\tallele\t%s" % (idfile, r.POS, allele), file=sys.stderr) + print("%s\t%s\tref\t%s" % (idfile, r.POS, r.REF), file=sys.stderr) + print("%s\t%s\tdepth\t%s" % (idfile, r.POS, self.depths[r.CHROM][r.POS]), file=sys.stderr) + +def go(args): + MASKED_POSITIONS = defaultdict(set) + + depths = collect_depths(args.bamfile) + reporter = Reporter(args.vcffile, depths) + + seqs = dict([(rec.id, rec) for rec in SeqIO.parse(open(args.reference), "fasta")]) + cons = {} + for k in seqs.keys(): + cons[k] = list(seqs[k].seq) + + for n, c in enumerate(cons[k]): + try: + depth = depths[k][n+1] + except: + depth = 0 + + if depth < args.depth: + cons[k][n] = 'N' + + if args.masked: + for region in args.masked.split(","): + contig, positions = region.split(":") + start, end = positions.split("-") + start = int(start) + end = int(end) + for n in range(start, end): + cons[contig][n-1] = 'N' + MASKED_POSITIONS[contig].add(n-1) + + sett = set() + vcf_reader = vcf.Reader(open(args.vcffile, 'r')) + for record in vcf_reader: + if record.ALT[0] != '.': + # variant call + + if record.POS in MASKED_POSITIONS[record.CHROM]: + reporter.report(record, "masked_manual", "n") + cons[record.CHROM][record.POS-1] = 'N' + continue + + if record.num_het: + if depths[record.CHROM][record.POS] < args.depth: + reporter.report(record, "het_site_low_depth", "y") + continue + else: + reporter.report(record, "het_site", "y") + cons[record.CHROM][record.POS-1] = 'N' + continue + + if 'PRIMER' in record.INFO: + reporter.report(record, "primer_binding_site", "n") + cons[record.CHROM][record.POS-1] = 'N' + continue + + #support = float(record.INFO['SupportFraction']) + #total_reads = int(record.INFO['TotalReads']) + qual = record.QUAL + + REF = record.REF + ALT = str(record.ALT[0]) + + if len(ALT) > len(REF): + print("Skipping insertion at position: %s" % (record.POS), file=sys.stderr) + continue + + if depths[record.CHROM][record.POS] >= args.depth and record.QUAL >= args.quality: + if len(REF) > len(ALT): + print("N-masking confident deletion at %s" % (record.POS), file=sys.stderr) + for n in range(len(REF)): + cons[record.CHROM][record.POS-1+n] = 'N' + continue + + reporter.report(record, "variant", ALT) + sett.add(record.POS) + if len(REF) > len(ALT): + print("deletion", file=sys.stderr) + continue + + if len(ALT) > len(REF): + print("insertion", file=sys.stderr) + continue + cons[record.CHROM][record.POS-1] = str(ALT) + elif len(REF) > len(ALT): + continue + else: + if depths[record.CHROM][record.POS] < args.depth: + reporter.report(record, "low_depth_variant", "n") + else: + reporter.report(record, "low_qual_variant", "n") + #cons[record.CHROM][record.POS-1] = 'N' + continue + + #print >>sys.stderr, str(sett) + + for k in seqs.keys(): + print(">%s-%s" % (args.bamfile, k)) + print("".join(cons[k])) + +def main(): + parser = argparse.ArgumentParser() + parser.add_argument('--depth', type=int, default=5, help='minimum depth to call a variant') + parser.add_argument('--quality', type=int, default=0, help='minimum quality to call a variant') + parser.add_argument('--masked', help='Regions to mask (contig:start-end,contig:start-end)') + parser.add_argument('reference') + parser.add_argument('vcffile') + parser.add_argument('bamfile') + args = parser.parse_args() + go(args) + +if __name__ == "__main__": + main()
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text-gray-light">→</span></a></li> + <li class="edge-item-fix"><a href="/security" class="py-2 lh-condensed-ultra d-block no-underline link-gray-dark no-underline h5 Bump-link--hover" data-ga-click="(Logged out) Header, go to Security">Security <span class="Bump-link-symbol float-right text-normal text-gray-light">→</span></a></li> + </ul> + </div> + </details> + </li> + <li class="border-bottom border-lg-bottom-0 mr-0 mr-lg-3"> + <a href="/enterprise" class="HeaderMenu-link no-underline py-3 d-block d-lg-inline-block" data-ga-click="(Logged out) Header, go to Enterprise">Enterprise</a> + </li> + + <li class="d-block d-lg-flex flex-lg-nowrap flex-lg-items-center border-bottom border-lg-bottom-0 mr-0 mr-lg-3 edge-item-fix position-relative flex-wrap flex-justify-between d-flex flex-items-center "> + <details class="HeaderMenu-details details-overlay details-reset width-full"> + <summary class="HeaderMenu-summary HeaderMenu-link px-0 py-3 border-0 no-wrap d-block d-lg-inline-block"> + Explore + <svg x="0px" y="0px" viewBox="0 0 14 8" xml:space="preserve" fill="none" class="icon-chevon-down-mktg position-absolute position-lg-relative"> + <path d="M1,1l6.2,6L13,1"></path> + </svg> + </summary> + + <div class="dropdown-menu flex-auto rounded-1 bg-white px-0 pt-2 pb-0 mt-0 pb-4 p-lg-4 position-relative position-lg-absolute left-0 left-lg-n4"> + <ul class="list-style-none mb-3"> + <li class="edge-item-fix"><a href="/explore" class="py-2 lh-condensed-ultra d-block link-gray-dark no-underline h5 Bump-link--hover" data-ga-click="(Logged out) Header, go to Explore">Explore GitHub <span class="Bump-link-symbol float-right text-normal text-gray-light">→</span></a></li> + </ul> + + <h4 class="text-gray-light text-normal text-mono f5 mb-2 border-lg-top pt-lg-3">Learn & contribute</h4> + <ul class="list-style-none mb-3"> + <li class="edge-item-fix"><a href="/topics" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Topics">Topics</a></li> + <li class="edge-item-fix"><a href="/collections" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Collections">Collections</a></li> + <li class="edge-item-fix"><a href="/trending" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Trending">Trending</a></li> + <li class="edge-item-fix"><a href="https://lab.github.com/" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Learning lab">Learning Lab</a></li> + <li class="edge-item-fix"><a href="https://opensource.guide" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Open source guides">Open source guides</a></li> + </ul> + + <h4 class="text-gray-light text-normal text-mono f5 mb-2 border-lg-top pt-lg-3">Connect with others</h4> + <ul class="list-style-none mb-0"> + <li class="edge-item-fix"><a href="https://github.com/events" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Events">Events</a></li> + <li class="edge-item-fix"><a href="https://github.community" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Community forum">Community forum</a></li> + <li class="edge-item-fix"><a href="https://education.github.com" class="py-2 pb-0 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to GitHub Education">GitHub Education</a></li> + </ul> + </div> + </details> + </li> + + <li class="border-bottom border-lg-bottom-0 mr-0 mr-lg-3"> + <a href="/marketplace" class="HeaderMenu-link no-underline py-3 d-block d-lg-inline-block" data-ga-click="(Logged out) Header, go to Marketplace">Marketplace</a> + </li> + + <li class="d-block d-lg-flex flex-lg-nowrap flex-lg-items-center border-bottom border-lg-bottom-0 mr-0 mr-lg-3 edge-item-fix position-relative flex-wrap flex-justify-between d-flex flex-items-center "> + <details class="HeaderMenu-details details-overlay details-reset width-full"> + <summary class="HeaderMenu-summary HeaderMenu-link px-0 py-3 border-0 no-wrap d-block d-lg-inline-block"> + Pricing + <svg x="0px" y="0px" viewBox="0 0 14 8" xml:space="preserve" fill="none" class="icon-chevon-down-mktg position-absolute position-lg-relative"> + <path d="M1,1l6.2,6L13,1"></path> + </svg> + </summary> + + <div class="dropdown-menu flex-auto rounded-1 bg-white px-0 pt-2 pb-4 mt-0 p-lg-4 position-relative position-lg-absolute left-0 left-lg-n4"> + <a href="/pricing" class="pb-2 lh-condensed-ultra d-block link-gray-dark no-underline h5 Bump-link--hover" data-ga-click="(Logged out) Header, go to Pricing">Plans <span class="Bump-link-symbol float-right text-normal text-gray-light">→</span></a> + + <ul class="list-style-none mb-3"> + <li class="edge-item-fix"><a href="/pricing#feature-comparison" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Compare plans">Compare plans</a></li> + <li class="edge-item-fix"><a href="https://enterprise.github.com/contact" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Contact Sales">Contact Sales</a></li> + </ul> + + <ul class="list-style-none mb-0 border-lg-top pt-lg-3"> + <li class="edge-item-fix"><a href="/nonprofit" class="py-2 lh-condensed-ultra d-block no-underline link-gray-dark no-underline h5 Bump-link--hover" data-ga-click="(Logged out) Header, go to Nonprofits">Nonprofit <span class="Bump-link-symbol float-right text-normal text-gray-light">→</span></a></li> + <li class="edge-item-fix"><a href="https://education.github.com" class="py-2 pb-0 lh-condensed-ultra d-block no-underline link-gray-dark no-underline h5 Bump-link--hover" data-ga-click="(Logged out) Header, go to Education">Education <span class="Bump-link-symbol float-right text-normal text-gray-light">→</span></a></li> + </ul> + </div> + </details> + </li> + </ul> + </nav> + + <div class="d-lg-flex flex-items-center px-3 px-lg-0 text-center text-lg-left"> + <div class="d-lg-flex mb-3 mb-lg-0"> + <div class="header-search flex-self-stretch flex-lg-self-auto mr-0 mr-lg-3 mb-3 mb-lg-0 scoped-search site-scoped-search js-site-search position-relative js-jump-to" + role="combobox" + aria-owns="jump-to-results" + aria-label="Search or jump to" + aria-haspopup="listbox" + aria-expanded="false" +> + <div class="position-relative"> + <!-- '"` --><!-- </textarea></xmp> --></option></form><form class="js-site-search-form" role="search" aria-label="Site" data-scope-type="Repository" data-scope-id="122982368" data-scoped-search-url="/artic-network/fieldbioinformatics/search" data-unscoped-search-url="/search" action="/artic-network/fieldbioinformatics/search" accept-charset="UTF-8" method="get"> + <label class="form-control input-sm header-search-wrapper p-0 header-search-wrapper-jump-to position-relative d-flex flex-justify-between flex-items-center js-chromeless-input-container"> + <input type="text" + class="form-control input-sm header-search-input jump-to-field js-jump-to-field js-site-search-focus js-site-search-field is-clearable" + data-hotkey="s,/" + name="q" + value="" + placeholder="Search" + data-unscoped-placeholder="Search GitHub" + data-scoped-placeholder="Search" + autocapitalize="off" + aria-autocomplete="list" + aria-controls="jump-to-results" + aria-label="Search" + data-jump-to-suggestions-path="/_graphql/GetSuggestedNavigationDestinations" + spellcheck="false" + autocomplete="off" + > + <input type="hidden" data-csrf="true" class="js-data-jump-to-suggestions-path-csrf" value="+eJDb6Ag2p2SCsxDxFn8brqgogFywOA7HpLNNzEoodGTRTi+77WvJQNK1JUgdwRzuRtqbrMHNu9/YnHnCJfYAg==" /> + <input type="hidden" class="js-site-search-type-field" name="type" > + <img src="https://github.githubassets.com/images/search-key-slash.svg" alt="" class="mr-2 header-search-key-slash"> + + <div class="Box position-absolute overflow-hidden d-none jump-to-suggestions js-jump-to-suggestions-container"> + +<ul class="d-none js-jump-to-suggestions-template-container"> + + +<li class="d-flex flex-justify-start flex-items-center p-0 f5 navigation-item js-navigation-item js-jump-to-suggestion" role="option"> + <a tabindex="-1" class="no-underline d-flex flex-auto flex-items-center jump-to-suggestions-path js-jump-to-suggestion-path js-navigation-open p-2" href=""> + <div class="jump-to-octicon js-jump-to-octicon flex-shrink-0 mr-2 text-center d-none"> + <svg height="16" width="16" class="octicon octicon-repo flex-shrink-0 js-jump-to-octicon-repo d-none" title="Repository" aria-label="Repository" viewBox="0 0 12 16" version="1.1" role="img"><path fill-rule="evenodd" d="M4 9H3V8h1v1zm0-3H3v1h1V6zm0-2H3v1h1V4zm0-2H3v1h1V2zm8-1v12c0 .55-.45 1-1 1H6v2l-1.5-1.5L3 16v-2H1c-.55 0-1-.45-1-1V1c0-.55.45-1 1-1h10c.55 0 1 .45 1 1zm-1 10H1v2h2v-1h3v1h5v-2zm0-10H2v9h9V1z"/></svg> + <svg height="16" width="16" class="octicon octicon-project flex-shrink-0 js-jump-to-octicon-project d-none" title="Project" aria-label="Project" viewBox="0 0 15 16" version="1.1" role="img"><path fill-rule="evenodd" d="M10 12h3V2h-3v10zm-4-2h3V2H6v8zm-4 4h3V2H2v12zm-1 1h13V1H1v14zM14 0H1a1 1 0 00-1 1v14a1 1 0 001 1h13a1 1 0 001-1V1a1 1 0 00-1-1z"/></svg> + <svg height="16" width="16" class="octicon octicon-search flex-shrink-0 js-jump-to-octicon-search d-none" title="Search" aria-label="Search" viewBox="0 0 16 16" version="1.1" role="img"><path fill-rule="evenodd" d="M15.7 13.3l-3.81-3.83A5.93 5.93 0 0013 6c0-3.31-2.69-6-6-6S1 2.69 1 6s2.69 6 6 6c1.3 0 2.48-.41 3.47-1.11l3.83 3.81c.19.2.45.3.7.3.25 0 .52-.09.7-.3a.996.996 0 000-1.41v.01zM7 10.7c-2.59 0-4.7-2.11-4.7-4.7 0-2.59 2.11-4.7 4.7-4.7 2.59 0 4.7 2.11 4.7 4.7 0 2.59-2.11 4.7-4.7 4.7z"/></svg> + </div> + + <img class="avatar mr-2 flex-shrink-0 js-jump-to-suggestion-avatar d-none" alt="" aria-label="Team" src="" width="28" height="28"> + + <div class="jump-to-suggestion-name js-jump-to-suggestion-name flex-auto overflow-hidden text-left no-wrap css-truncate css-truncate-target"> + </div> + + <div class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none js-jump-to-badge-search"> + <span class="js-jump-to-badge-search-text-default d-none" aria-label="in this repository"> + In this repository + </span> + <span class="js-jump-to-badge-search-text-global d-none" aria-label="in all of GitHub"> + All GitHub + </span> + <span aria-hidden="true" class="d-inline-block ml-1 v-align-middle">↵</span> + </div> + + <div aria-hidden="true" class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none d-on-nav-focus js-jump-to-badge-jump"> + Jump to + <span class="d-inline-block ml-1 v-align-middle">↵</span> + </div> + </a> +</li> + +</ul> + +<ul class="d-none js-jump-to-no-results-template-container"> + <li class="d-flex flex-justify-center flex-items-center f5 d-none js-jump-to-suggestion p-2"> + <span class="text-gray">No suggested jump to results</span> + </li> +</ul> + +<ul id="jump-to-results" role="listbox" class="p-0 m-0 js-navigation-container jump-to-suggestions-results-container js-jump-to-suggestions-results-container"> + + +<li class="d-flex flex-justify-start flex-items-center p-0 f5 navigation-item js-navigation-item js-jump-to-scoped-search d-none" role="option"> + <a tabindex="-1" class="no-underline d-flex flex-auto flex-items-center jump-to-suggestions-path js-jump-to-suggestion-path js-navigation-open p-2" href=""> + <div class="jump-to-octicon js-jump-to-octicon flex-shrink-0 mr-2 text-center d-none"> + <svg height="16" width="16" class="octicon octicon-repo flex-shrink-0 js-jump-to-octicon-repo d-none" title="Repository" aria-label="Repository" viewBox="0 0 12 16" version="1.1" role="img"><path fill-rule="evenodd" d="M4 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4.7-4.7 2.59 0 4.7 2.11 4.7 4.7 0 2.59-2.11 4.7-4.7 4.7z"/></svg> + </div> + + <img class="avatar mr-2 flex-shrink-0 js-jump-to-suggestion-avatar d-none" alt="" aria-label="Team" src="" width="28" height="28"> + + <div class="jump-to-suggestion-name js-jump-to-suggestion-name flex-auto overflow-hidden text-left no-wrap css-truncate css-truncate-target"> + </div> + + <div class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none js-jump-to-badge-search"> + <span class="js-jump-to-badge-search-text-default d-none" aria-label="in this repository"> + In this repository + </span> + <span class="js-jump-to-badge-search-text-global d-none" aria-label="in all of GitHub"> + All GitHub + </span> + <span aria-hidden="true" class="d-inline-block ml-1 v-align-middle">↵</span> + </div> + + <div aria-hidden="true" class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none d-on-nav-focus js-jump-to-badge-jump"> + Jump to + <span class="d-inline-block ml-1 v-align-middle">↵</span> + </div> + </a> +</li> + + + +<li class="d-flex flex-justify-start flex-items-center p-0 f5 navigation-item js-navigation-item js-jump-to-global-search d-none" role="option"> + <a tabindex="-1" class="no-underline d-flex flex-auto flex-items-center jump-to-suggestions-path js-jump-to-suggestion-path js-navigation-open p-2" href=""> + <div class="jump-to-octicon js-jump-to-octicon flex-shrink-0 mr-2 text-center d-none"> + <svg height="16" width="16" class="octicon octicon-repo flex-shrink-0 js-jump-to-octicon-repo d-none" title="Repository" aria-label="Repository" viewBox="0 0 12 16" version="1.1" role="img"><path fill-rule="evenodd" d="M4 9H3V8h1v1zm0-3H3v1h1V6zm0-2H3v1h1V4zm0-2H3v1h1V2zm8-1v12c0 .55-.45 1-1 1H6v2l-1.5-1.5L3 16v-2H1c-.55 0-1-.45-1-1V1c0-.55.45-1 1-1h10c.55 0 1 .45 1 1zm-1 10H1v2h2v-1h3v1h5v-2zm0-10H2v9h9V1z"/></svg> + <svg height="16" width="16" class="octicon octicon-project flex-shrink-0 js-jump-to-octicon-project d-none" title="Project" aria-label="Project" viewBox="0 0 15 16" version="1.1" role="img"><path fill-rule="evenodd" d="M10 12h3V2h-3v10zm-4-2h3V2H6v8zm-4 4h3V2H2v12zm-1 1h13V1H1v14zM14 0H1a1 1 0 00-1 1v14a1 1 0 001 1h13a1 1 0 001-1V1a1 1 0 00-1-1z"/></svg> + <svg height="16" width="16" class="octicon octicon-search flex-shrink-0 js-jump-to-octicon-search d-none" title="Search" aria-label="Search" viewBox="0 0 16 16" version="1.1" role="img"><path fill-rule="evenodd" d="M15.7 13.3l-3.81-3.83A5.93 5.93 0 0013 6c0-3.31-2.69-6-6-6S1 2.69 1 6s2.69 6 6 6c1.3 0 2.48-.41 3.47-1.11l3.83 3.81c.19.2.45.3.7.3.25 0 .52-.09.7-.3a.996.996 0 000-1.41v.01zM7 10.7c-2.59 0-4.7-2.11-4.7-4.7 0-2.59 2.11-4.7 4.7-4.7 2.59 0 4.7 2.11 4.7 4.7 0 2.59-2.11 4.7-4.7 4.7z"/></svg> + </div> + + <img class="avatar mr-2 flex-shrink-0 js-jump-to-suggestion-avatar d-none" alt="" aria-label="Team" src="" width="28" height="28"> + + <div class="jump-to-suggestion-name js-jump-to-suggestion-name flex-auto overflow-hidden text-left no-wrap css-truncate css-truncate-target"> + </div> + + <div class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none js-jump-to-badge-search"> + <span class="js-jump-to-badge-search-text-default d-none" aria-label="in this repository"> + In this repository + </span> + <span class="js-jump-to-badge-search-text-global d-none" aria-label="in all of GitHub"> + All GitHub + </span> + <span aria-hidden="true" class="d-inline-block ml-1 v-align-middle">↵</span> + </div> + + <div aria-hidden="true" class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none d-on-nav-focus js-jump-to-badge-jump"> + Jump to + <span class="d-inline-block ml-1 v-align-middle">↵</span> + </div> + </a> +</li> + + +</ul> + + </div> + </label> +</form> </div> +</div> + + </div> + + <a href="/login?return_to=%2Fartic-network%2Ffieldbioinformatics%2Fblob%2F1005a47cce2d1cb87db8c88dbbf5cc47dde2f45c%2Fartic%2Fvcftagprimersites.py" + class="HeaderMenu-link no-underline mr-3" + data-hydro-click="{"event_type":"authentication.click","payload":{"location_in_page":"site header menu","repository_id":null,"auth_type":"SIGN_UP","originating_url":"https://github.com/artic-network/fieldbioinformatics/blob/1005a47cce2d1cb87db8c88dbbf5cc47dde2f45c/artic/vcftagprimersites.py","user_id":null}}" data-hydro-click-hmac="cf5f8a22055da3315265152e49bdf95d404c19bdcd3737101c4eed92d2c56221" + data-ga-click="(Logged out) Header, clicked Sign in, text:sign-in"> + Sign in + </a> + <a href="/join?source=header-repo&source_repo=artic-network%2Ffieldbioinformatics" + class="HeaderMenu-link d-inline-block no-underline border border-gray-dark rounded-1 px-2 py-1" + data-hydro-click="{"event_type":"authentication.click","payload":{"location_in_page":"site header menu","repository_id":null,"auth_type":"SIGN_UP","originating_url":"https://github.com/artic-network/fieldbioinformatics/blob/1005a47cce2d1cb87db8c88dbbf5cc47dde2f45c/artic/vcftagprimersites.py","user_id":null}}" data-hydro-click-hmac="cf5f8a22055da3315265152e49bdf95d404c19bdcd3737101c4eed92d2c56221" + data-ga-click="(Logged out) Header, clicked Sign up, text:sign-up"> + Sign up + </a> + </div> + </div> + </div> +</header> + + </div> + + <div id="start-of-content" class="show-on-focus"></div> + + + <div id="js-flash-container"> + +</div> + + + + + <include-fragment class="js-notification-shelf-include-fragment" data-base-src="https://github.com/notifications/beta/shelf"></include-fragment> + + + + + <div class="application-main " data-commit-hovercards-enabled> + <div itemscope itemtype="http://schema.org/SoftwareSourceCode" class=""> + <main > + + + + + + + + + + + + + + + + + + <div class="pagehead repohead hx_repohead readability-menu bg-gray-light pb-0 pt-0 pt-lg-3"> + + <div class="d-flex container-lg mb-4 p-responsive d-none d-lg-flex"> + + <div class="flex-auto min-width-0 width-fit mr-3"> + <h1 class="public d-flex flex-wrap flex-items-center break-word float-none "> + <svg 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+<table class="highlight tab-size js-file-line-container" data-tab-size="8" data-paste-markdown-skip> + <tr> + <td id="L1" class="blob-num js-line-number" data-line-number="1"></td> + <td id="LC1" class="blob-code blob-code-inner js-file-line"><span class=pl-c>#!/usr/bin/env python</span></td> + </tr> + <tr> + <td id="L2" class="blob-num js-line-number" data-line-number="2"></td> + <td id="LC2" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L3" class="blob-num js-line-number" data-line-number="3"></td> + <td id="LC3" class="blob-code blob-code-inner js-file-line"><span class=pl-k>import</span> <span class=pl-s1>vcf</span></td> + </tr> + <tr> + <td id="L4" class="blob-num js-line-number" data-line-number="4"></td> + <td id="LC4" class="blob-code blob-code-inner js-file-line"><span class=pl-k>import</span> <span class=pl-s1>sys</span></td> + </tr> + <tr> + <td id="L5" class="blob-num js-line-number" data-line-number="5"></td> + <td id="LC5" class="blob-code blob-code-inner js-file-line"><span class=pl-k>import</span> <span class=pl-s1>subprocess</span></td> + </tr> + <tr> + <td id="L6" class="blob-num js-line-number" data-line-number="6"></td> + <td id="LC6" class="blob-code blob-code-inner js-file-line"><span class=pl-k>import</span> <span class=pl-s1>csv</span></td> + </tr> + <tr> + <td id="L7" class="blob-num js-line-number" data-line-number="7"></td> + <td id="LC7" class="blob-code blob-code-inner js-file-line"><span class=pl-k>from</span> <span class=pl-s1>collections</span> <span class=pl-k>import</span> <span class=pl-s1>defaultdict</span></td> + </tr> + <tr> + <td id="L8" class="blob-num js-line-number" data-line-number="8"></td> + <td id="LC8" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L9" class="blob-num js-line-number" data-line-number="9"></td> + <td id="LC9" class="blob-code blob-code-inner js-file-line"><span class=pl-k>def</span> <span class=pl-en>read_bed_file</span>(<span class=pl-s1>fn</span>):</td> + </tr> + <tr> + <td id="L10" class="blob-num js-line-number" data-line-number="10"></td> + <td id="LC10" class="blob-code blob-code-inner js-file-line"> <span class=pl-s1>bedfile</span> <span class=pl-c1>=</span> []</td> + </tr> + <tr> + <td id="L11" class="blob-num js-line-number" data-line-number="11"></td> + <td id="LC11" class="blob-code blob-code-inner js-file-line"> <span class=pl-k>with</span> <span class=pl-en>open</span>(<span class=pl-s1>fn</span>) <span class=pl-k>as</span> <span class=pl-s1>csvfile</span>:</td> + </tr> + <tr> + <td id="L12" class="blob-num js-line-number" data-line-number="12"></td> + <td id="LC12" class="blob-code blob-code-inner js-file-line"> <span class=pl-s1>reader</span> <span class=pl-c1>=</span> <span class=pl-s1>csv</span>.<span class=pl-en>reader</span>(<span class=pl-s1>csvfile</span>, <span class=pl-s1>dialect</span><span class=pl-c1>=</span><span class=pl-s>'excel-tab'</span>)</td> + </tr> + <tr> + <td id="L13" class="blob-num js-line-number" data-line-number="13"></td> + <td id="LC13" class="blob-code blob-code-inner js-file-line"> <span class=pl-k>for</span> <span class=pl-s1>row</span> <span class=pl-c1>in</span> <span class=pl-s1>reader</span>:</td> + </tr> + <tr> + <td id="L14" class="blob-num js-line-number" data-line-number="14"></td> + <td id="LC14" class="blob-code blob-code-inner js-file-line"> <span class=pl-s1>bedrow</span> <span class=pl-c1>=</span> {}</td> + </tr> + <tr> + <td id="L15" class="blob-num js-line-number" data-line-number="15"></td> + <td id="LC15" class="blob-code blob-code-inner js-file-line"> <span class=pl-s1>bedrow</span>[<span class=pl-s>'Primer_ID'</span>] <span class=pl-c1>=</span> <span class=pl-s1>row</span>[<span class=pl-c1>3</span>]</td> + </tr> + <tr> + <td id="L16" class="blob-num js-line-number" data-line-number="16"></td> + <td id="LC16" class="blob-code blob-code-inner js-file-line"> </td> + </tr> + <tr> + <td id="L17" class="blob-num js-line-number" data-line-number="17"></td> + <td id="LC17" class="blob-code blob-code-inner js-file-line"> <span class=pl-k>if</span> <span class=pl-en>len</span>(<span class=pl-s1>row</span>) <span class=pl-c1>>=</span> <span class=pl-c1>6</span>:</td> + </tr> + <tr> + <td id="L18" class="blob-num js-line-number" data-line-number="18"></td> + <td id="LC18" class="blob-code blob-code-inner js-file-line"> <span class=pl-c># new style bed</span></td> + </tr> + <tr> + <td id="L19" class="blob-num js-line-number" data-line-number="19"></td> + <td id="LC19" class="blob-code blob-code-inner js-file-line"> <span class=pl-s1>bedrow</span>[<span class=pl-s>'direction'</span>] <span class=pl-c1>=</span> <span class=pl-s1>row</span>[<span class=pl-c1>5</span>]</td> + </tr> + <tr> + <td id="L20" class="blob-num js-line-number" data-line-number="20"></td> + <td id="LC20" class="blob-code blob-code-inner js-file-line"> <span class=pl-k>elif</span> <span class=pl-en>len</span>(<span class=pl-s1>row</span>) <span class=pl-c1>==</span> <span class=pl-c1>5</span>:</td> + </tr> + <tr> + <td id="L21" class="blob-num js-line-number" data-line-number="21"></td> + <td id="LC21" class="blob-code blob-code-inner js-file-line"> <span class=pl-c># old style without directory</span></td> + </tr> + <tr> + <td id="L22" class="blob-num js-line-number" data-line-number="22"></td> + <td id="LC22" class="blob-code blob-code-inner js-file-line"> <span class=pl-k>if</span> <span class=pl-s>'LEFT'</span> <span class=pl-c1>in</span> <span class=pl-s1>row</span>[<span class=pl-c1>3</span>]:</td> + </tr> + <tr> + <td id="L23" class="blob-num js-line-number" data-line-number="23"></td> + <td id="LC23" class="blob-code blob-code-inner js-file-line"> <span class=pl-s1>bedrow</span>[<span class=pl-s>'direction'</span>] <span class=pl-c1>=</span> <span class=pl-s>'+'</span></td> + </tr> + <tr> + <td id="L24" class="blob-num js-line-number" data-line-number="24"></td> + <td id="LC24" class="blob-code blob-code-inner js-file-line"> <span class=pl-k>elif</span> <span class=pl-s>'RIGHT'</span> <span class=pl-c1>in</span> <span class=pl-s1>row</span>[<span class=pl-c1>3</span>]:</td> + </tr> + <tr> + <td id="L25" class="blob-num js-line-number" data-line-number="25"></td> + <td id="LC25" class="blob-code blob-code-inner js-file-line"> <span class=pl-s1>bedrow</span>[<span class=pl-s>'direction'</span>] <span class=pl-c1>=</span> <span class=pl-s>'-'</span></td> + </tr> + <tr> + <td id="L26" class="blob-num js-line-number" data-line-number="26"></td> + <td id="LC26" class="blob-code blob-code-inner js-file-line"> <span class=pl-k>else</span>:</td> + </tr> + <tr> + <td id="L27" class="blob-num js-line-number" data-line-number="27"></td> + <td id="LC27" class="blob-code blob-code-inner js-file-line"> <span class=pl-en>print</span>(<span class=pl-s>"Malformed BED file!"</span>, <span class=pl-s1>file</span><span class=pl-c1>=</span><span class=pl-s1>sys</span>.<span class=pl-s1>stderr</span>) </td> + </tr> + <tr> + <td id="L28" class="blob-num js-line-number" data-line-number="28"></td> + <td id="LC28" class="blob-code blob-code-inner js-file-line"> <span class=pl-k>raise</span> <span class=pl-v>SystemExit</span></td> + </tr> + <tr> + <td id="L29" class="blob-num js-line-number" data-line-number="29"></td> + <td id="LC29" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L30" class="blob-num js-line-number" data-line-number="30"></td> + <td id="LC30" class="blob-code blob-code-inner js-file-line"> <span class=pl-k>if</span> <span class=pl-s1>bedrow</span>[<span class=pl-s>'direction'</span>] <span class=pl-c1>==</span> <span class=pl-s>'+'</span>:</td> + </tr> + <tr> + <td id="L31" class="blob-num js-line-number" data-line-number="31"></td> + <td id="LC31" class="blob-code blob-code-inner js-file-line"> <span class=pl-s1>bedrow</span>[<span class=pl-s>'end'</span>] <span class=pl-c1>=</span> <span class=pl-en>int</span>(<span class=pl-s1>row</span>[<span class=pl-c1>2</span>])</td> + </tr> + <tr> + <td id="L32" class="blob-num js-line-number" data-line-number="32"></td> + <td id="LC32" class="blob-code blob-code-inner js-file-line"> <span class=pl-s1>bedrow</span>[<span class=pl-s>'start'</span>] <span class=pl-c1>=</span> <span class=pl-en>int</span>(<span class=pl-s1>row</span>[<span class=pl-c1>1</span>])</td> + </tr> + <tr> + <td id="L33" class="blob-num js-line-number" data-line-number="33"></td> + <td id="LC33" class="blob-code blob-code-inner js-file-line"> <span class=pl-k>else</span>:</td> + </tr> + <tr> + <td id="L34" class="blob-num js-line-number" data-line-number="34"></td> + <td id="LC34" class="blob-code blob-code-inner js-file-line"> <span class=pl-s1>bedrow</span>[<span class=pl-s>'end'</span>] <span class=pl-c1>=</span> <span class=pl-en>int</span>(<span class=pl-s1>row</span>[<span class=pl-c1>1</span>])</td> + </tr> + <tr> + <td id="L35" class="blob-num js-line-number" data-line-number="35"></td> + <td id="LC35" class="blob-code blob-code-inner js-file-line"> <span class=pl-s1>bedrow</span>[<span class=pl-s>'start'</span>] <span class=pl-c1>=</span> <span class=pl-en>int</span>(<span class=pl-s1>row</span>[<span class=pl-c1>2</span>])</td> + </tr> + <tr> + <td id="L36" class="blob-num js-line-number" data-line-number="36"></td> + <td id="LC36" class="blob-code blob-code-inner js-file-line"> <span class=pl-s1>bedfile</span>.<span class=pl-en>append</span>(<span class=pl-s1>bedrow</span>)</td> + </tr> + <tr> + <td id="L37" class="blob-num js-line-number" data-line-number="37"></td> + <td id="LC37" class="blob-code blob-code-inner js-file-line"> <span class=pl-k>return</span> <span class=pl-s1>bedfile</span></td> + </tr> + <tr> + <td id="L38" class="blob-num js-line-number" data-line-number="38"></td> + <td id="LC38" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L39" class="blob-num js-line-number" data-line-number="39"></td> + <td id="LC39" class="blob-code blob-code-inner js-file-line"><span class=pl-k>def</span> <span class=pl-en>overlaps</span>(<span class=pl-s1>coords</span>, <span class=pl-s1>pos</span>):</td> + </tr> + <tr> + <td id="L40" class="blob-num js-line-number" data-line-number="40"></td> + <td id="LC40" class="blob-code blob-code-inner js-file-line"> <span class=pl-k>for</span> <span class=pl-s1>v</span> <span class=pl-c1>in</span> <span class=pl-s1>coords</span>:</td> + </tr> + <tr> + <td id="L41" class="blob-num js-line-number" data-line-number="41"></td> + <td id="LC41" class="blob-code blob-code-inner js-file-line"> <span class=pl-k>if</span> <span class=pl-s1>pos</span> <span class=pl-c1>>=</span> <span class=pl-s1>v</span>[<span class=pl-s>'start'</span>] <span class=pl-c1>and</span> <span class=pl-s1>pos</span> <span class=pl-c1><=</span> <span class=pl-s1>v</span>[<span class=pl-s>'end'</span>]:</td> + </tr> + <tr> + <td id="L42" class="blob-num js-line-number" data-line-number="42"></td> + <td id="LC42" class="blob-code blob-code-inner js-file-line"> <span class=pl-k>return</span> <span class=pl-s1>v</span></td> + </tr> + <tr> + <td id="L43" class="blob-num js-line-number" data-line-number="43"></td> + <td id="LC43" class="blob-code blob-code-inner js-file-line"> <span class=pl-k>return</span> <span class=pl-c1>False</span></td> + </tr> + <tr> + <td id="L44" class="blob-num js-line-number" data-line-number="44"></td> + <td id="LC44" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L45" class="blob-num js-line-number" data-line-number="45"></td> + <td id="LC45" class="blob-code blob-code-inner js-file-line"><span class=pl-k>if</span> <span class=pl-s1>__name__</span> <span class=pl-c1>==</span> <span class=pl-s>"__main__"</span>:</td> + </tr> + <tr> + <td id="L46" class="blob-num js-line-number" data-line-number="46"></td> + <td id="LC46" class="blob-code blob-code-inner js-file-line"> <span class=pl-k>if</span> <span class=pl-s1>sys</span>.<span class=pl-s1>argv</span>[<span class=pl-c1>1</span>] <span class=pl-c1>not</span> <span class=pl-c1>in</span> <span class=pl-s1>sets</span>:</td> + </tr> + <tr> + <td id="L47" class="blob-num js-line-number" data-line-number="47"></td> + <td id="LC47" class="blob-code blob-code-inner js-file-line"> <span class=pl-en>print</span>(<span class=pl-s>"Invalid set"</span>)</td> + </tr> + <tr> + <td id="L48" class="blob-num js-line-number" data-line-number="48"></td> + <td id="LC48" class="blob-code blob-code-inner js-file-line"> <span class=pl-k>raise</span> <span class=pl-v>SystemExit</span></td> + </tr> + <tr> + <td id="L49" class="blob-num js-line-number" data-line-number="49"></td> + <td id="LC49" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L50" class="blob-num js-line-number" data-line-number="50"></td> + <td id="LC50" class="blob-code blob-code-inner js-file-line"> <span class=pl-s1>bedfile</span> <span class=pl-c1>=</span> <span class=pl-en>read_bed_file</span>(<span class=pl-s1>sys</span>.<span class=pl-s1>argv</span>[<span class=pl-c1>1</span>])</td> + </tr> + <tr> + <td id="L51" class="blob-num js-line-number" data-line-number="51"></td> + <td id="LC51" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L52" class="blob-num js-line-number" data-line-number="52"></td> + <td id="LC52" class="blob-code blob-code-inner js-file-line"> <span class=pl-s1>vcf_reader</span> <span class=pl-c1>=</span> <span class=pl-s1>vcf</span>.<span class=pl-v>Reader</span>(<span class=pl-s1>filename</span><span class=pl-c1>=</span><span class=pl-s1>sys</span>.<span class=pl-s1>argv</span>[<span class=pl-c1>2</span>])</td> + </tr> + <tr> + <td id="L53" class="blob-num js-line-number" data-line-number="53"></td> + <td id="LC53" class="blob-code blob-code-inner js-file-line"> <span class=pl-s1>vcf_writer</span> <span class=pl-c1>=</span> <span class=pl-s1>vcf</span>.<span class=pl-v>Writer</span>(<span class=pl-s1>sys</span>.<span class=pl-s1>stdout</span>, <span class=pl-s1>vcf_reader</span>)</td> + </tr> + <tr> + <td id="L54" class="blob-num js-line-number" data-line-number="54"></td> + <td id="LC54" class="blob-code blob-code-inner js-file-line"> <span class=pl-k>for</span> <span class=pl-s1>record</span> <span class=pl-c1>in</span> <span class=pl-s1>vcf_reader</span>:</td> + </tr> + <tr> + <td id="L55" class="blob-num js-line-number" data-line-number="55"></td> + <td id="LC55" class="blob-code blob-code-inner js-file-line"> <span class=pl-s1>v</span> <span class=pl-c1>=</span> <span class=pl-en>overlaps</span>(<span class=pl-s1>bedfile</span>, <span class=pl-s1>record</span>.<span class=pl-v>POS</span>)</td> + </tr> + <tr> + <td id="L56" class="blob-num js-line-number" data-line-number="56"></td> + <td id="LC56" class="blob-code blob-code-inner js-file-line"> <span class=pl-k>if</span> <span class=pl-s1>v</span>:</td> + </tr> + <tr> + <td id="L57" class="blob-num js-line-number" data-line-number="57"></td> + <td id="LC57" class="blob-code blob-code-inner js-file-line"> <span class=pl-s1>record</span>.<span class=pl-v>INFO</span>[<span class=pl-s>'PRIMER'</span>] <span class=pl-c1>=</span> <span class=pl-s1>v</span>[<span class=pl-s>"Sequence_(5-3')"</span>]</td> + </tr> + <tr> + <td id="L58" class="blob-num js-line-number" data-line-number="58"></td> + <td id="LC58" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L59" class="blob-num js-line-number" data-line-number="59"></td> + <td id="LC59" class="blob-code blob-code-inner js-file-line"><span class=pl-c># PP = list(record.INFO)</span></td> + </tr> + <tr> + <td id="L60" class="blob-num js-line-number" data-line-number="60"></td> + <td id="LC60" class="blob-code blob-code-inner js-file-line"><span class=pl-c># record.INFO = {}</span></td> + </tr> + <tr> + <td id="L61" class="blob-num js-line-number" data-line-number="61"></td> + <td id="LC61" class="blob-code blob-code-inner js-file-line"><span class=pl-c># record.INFO['PP'] = PP</span></td> + </tr> + <tr> + <td id="L62" class="blob-num js-line-number" data-line-number="62"></td> + <td id="LC62" class="blob-code blob-code-inner js-file-line"><span class=pl-c># record.INFO['DEPTH'] = depths[record.CHROM][record.POS]</span></td> + </tr> + <tr> + <td id="L63" class="blob-num js-line-number" data-line-number="63"></td> + <td id="LC63" class="blob-code blob-code-inner js-file-line"> +</td> + </tr> + <tr> + <td id="L64" class="blob-num js-line-number" data-line-number="64"></td> + <td id="LC64" class="blob-code blob-code-inner js-file-line"> <span class=pl-s1>vcf_writer</span>.<span class=pl-en>write_record</span>(<span class=pl-s1>record</span>)</td> + </tr> +</table> + + <details class="details-reset details-overlay BlobToolbar position-absolute 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--- a/margin_cons_medaka.py Wed Mar 11 02:31:04 2020 +0000 +++ b/margin_cons_medaka.py Tue Mar 17 21:20:38 2020 +0000 @@ -2,7 +2,8 @@ # Written by Nick Loman # This file adapted from ARTICnetwork 'fieldbioinformatics' pipeline: -# https://github.com/artic-network/fieldbioinformatics +# https://github.com/artic-network/fieldbioinformatics/blob/master/artic/margin_cons_medaka.py +# https://github.com/artic-network/fieldbioinformatics/blob/master/artic/vcftagprimersites.py import argparse import operator