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Commit message:
planemo upload for repository https://github.com/bvalot/galaxy commit d57c24d4b2c0c741d572af9ca0d09f8b82689640 |
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added:
primer_search.py primer_search.xml qpcr_search.py qpcr_search.xml test-data/input.fasta test-data/pcr.fasta test-data/qpcr.txt |
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| diff -r 000000000000 -r 1f4836da4a14 primer_search.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/primer_search.py Tue Jun 14 08:52:22 2022 +0000 |
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| b'@@ -0,0 +1,319 @@\n+#!/usr/bin/env python3\n+# -*- coding: utf-8 -*-\n+\n+"""Search primers on database and return result"""\n+\n+import argparse\n+import os\n+import subprocess\n+import sys\n+import tempfile\n+\n+from Bio import SeqIO\n+\n+gasst_exe = "Gassst"\n+nucleo = {\n+ "R": ("A", "G"),\n+ "Y": ("C", "T"),\n+ "S": ("G", "C"),\n+ "W": ("A", "T"),\n+ "K": ("G", "T"),\n+ "M": ("A", "C"),\n+ "B": ("C", "G", "T"),\n+ "D": ("A", "G", "T"),\n+ "H": ("A", "C", "T"),\n+ "V": ("A", "C", "G"),\n+ "N": ("A", "T", "C", "G"),\n+}\n+\n+desc = "Search primer on database and return amplicons."\n+command = argparse.ArgumentParser(\n+ prog="primer_search.py",\n+ description=desc,\n+ usage="%(prog)s [options] forward reverse database",\n+)\n+command.add_argument(\n+ "-o",\n+ "--out",\n+ nargs="?",\n+ type=argparse.FileType("w"),\n+ default=sys.stdout,\n+ help="Return amplicon on fasta file, default=stdout",\n+)\n+command.add_argument(\n+ "-d",\n+ "--debug",\n+ nargs="?",\n+ type=argparse.FileType("w+"),\n+ default=None,\n+ help="Conserve a copy of primer search, default No",\n+)\n+command.add_argument(\n+ "-e",\n+ "--error",\n+ nargs="?",\n+ type=int,\n+ default=1,\n+ help="Maximun error allowed on match, default=1",\n+)\n+command.add_argument(\n+ "-m",\n+ "--min",\n+ nargs="?",\n+ type=int,\n+ default=100,\n+ help="Min len amplicon size, default=100",\n+)\n+command.add_argument(\n+ "-M",\n+ "--max",\n+ nargs="?",\n+ type=int,\n+ default=1500,\n+ help="Max len amplicon size, default=1500",\n+)\n+command.add_argument(\n+ "-k",\n+ "--keep",\n+ action="store_true",\n+ help="Keep description instead of report PCR position",\n+)\n+command.add_argument(\n+ "-r", "--remove", action="store_true", help="Remove primer from reported amplicons"\n+)\n+command.add_argument("forward", type=str, help="Forward primer sequence")\n+command.add_argument("reverse", type=str, help="Reverse primer sequence")\n+command.add_argument(\n+ "database", type=argparse.FileType("r"), help="Database to search on fasta"\n+)\n+command.add_argument("-v", "--version", action="version", version="%(prog)s 0.3.0")\n+\n+\n+class GassstResult:\n+ """A simple Gassst class containing result\n+ rev : True indicate if reverse primers, else forward\n+ """\n+\n+ def __init__(self, line):\n+ h = line.strip().split("\\t")\n+ if len(h) != 9:\n+ raise Exception("Line seems not correspond to gassst result\\n" + line)\n+ self.primer = h[0]\n+ self.rev = h[0] != "Forward"\n+ self.match = h[1]\n+ self.strand = int(h[2])\n+ self.start = int(h[3])\n+ self.error = int(h[5])\n+ self.stop = self.start + len(h[7])\n+\n+ def __repr__(self):\n+ return (\n+ self.match\n+ + " : "\n+ + str(self.start)\n+ + " in strand:"\n+ + str(self.strand)\n+ + " in primer: "\n+ + self.primer\n+ + " with error: "\n+ + str(self.error)\n+ )\n+\n+ def __eq__(self, other):\n+ return (\n+ isinstance(other, GassstResult)\n+ and self.primer == other.primer\n+ and self.rev == other.rev\n+ and self.match == other.match\n+ and self.strand == other.strand\n+ and self.start == other.start\n+ )\n+\n+ def __ne__(self, other):\n+ return not self == other\n+\n+ def __lt__(self, other):\n+ if self != other:\n+ raise Exception("Only compare equal GassstResult")\n+ return self.error < other.error\n+\n+\n+class Amplicon:\n+ """A simple Amplicon class containing forward and reverse gassst result"""\n+\n+ def __init__(self, forw, reve):\n+ if forw.strand == reve.strand:\n+ raise Exception(\n+ "Amplicon could be in inverse strand for reverse/forwar primer\\n"\n+ + forw\n+ + reve\n+ )\n+ self.forw = forw\n+ self.reve = reve\n+ self.'..b'de):\n+ primer_fasta.write(">Forward\\n" + forward + "\\n")\n+ for reverse in degenerate_primer(reverse_de):\n+ primer_fasta.write(">Reverse\\n" + reverse + "\\n")\n+ primer_fasta.close()\n+ return primer_fasta.name\n+\n+\n+def performed_gassst(command):\n+ proc = subprocess.Popen(command, stderr=subprocess.PIPE, stdout=sys.stderr)\n+ error = ""\n+ for line in iter(proc.stderr.readline, b""):\n+ error += line.decode()\n+ if error != "":\n+ sys.stdout.write("Error during processing Gassst\\n")\n+ raise Exception(error)\n+\n+\n+def read_result(f_res, f_debug):\n+ result = {}\n+ for line in iter(f_res.readline, ""):\n+ if line[0] == "F" or line[0] == "R":\n+ if f_debug is not None:\n+ f_debug.write(line)\n+ res = GassstResult(line)\n+ other_res = result.setdefault(res.match, {}).setdefault(res.primer, [])\n+ notfound = True\n+ for i, res2 in enumerate(other_res):\n+ if res == res2:\n+ notfound = False\n+ if res < res2:\n+ other_res[i] = res\n+ # print res\n+ break\n+ if notfound:\n+ other_res.append(res)\n+ return result\n+\n+\n+def get_amplicons(result):\n+ """Function to get amplicon on a sequence from forward / reverse result"""\n+ for forw in result["Forward"]:\n+ for reve in result["Reverse"]:\n+ if forw.strand != reve.strand:\n+ amp = Amplicon(forw, reve)\n+ if amp.get_start() < amp.get_stop(): # must be side by side\n+ yield amp\n+ else:\n+ del amp\n+\n+\n+if __name__ == "__main__":\n+ """Performed job on execution script"""\n+ args = command.parse_args()\n+ primer_fasta = write_primer_fasta(args.forward, args.reverse)\n+ output_result = tempfile.NamedTemporaryFile(delete=False, mode="w+")\n+ identity = int(\n+ 100 - args.error / float(max(len(args.forward), len(args.reverse))) * 100\n+ )\n+\n+ command = [\n+ gasst_exe,\n+ "-p",\n+ str(identity),\n+ "-g",\n+ "0",\n+ "-w",\n+ "6",\n+ "-h",\n+ "0",\n+ "-i",\n+ primer_fasta,\n+ "-d",\n+ args.database.name,\n+ "-o",\n+ output_result.name,\n+ ]\n+ performed_gassst(command)\n+ result = read_result(output_result, args.debug)\n+\n+ # load amplicons\n+ sys.stderr.write("Search amplicons : ")\n+ amplicons = {}\n+ for seq in result.keys():\n+ if len(result[seq]) == 2:\n+ # print "Search amplicon on seq: " + seq\n+ for amplicon in get_amplicons(result[seq]):\n+ if len(amplicon) > args.min and len(amplicon) < args.max:\n+ amplicons.setdefault(seq, []).append(amplicon)\n+ else:\n+ del amplicon\n+ # print "Find amplicons : " + str(len(amplicons[seq]))\n+ sys.stderr.write(str(sum(map(len, amplicons.values()))) + "\\n\\n")\n+\n+ # print amplicons\n+\n+ sys.stderr.write("Write result : ")\n+ for record in SeqIO.parse(args.database, "fasta"):\n+ if record.id not in amplicons:\n+ continue\n+ for i, amplicon in enumerate(amplicons.get(record.id)):\n+ sub = record[amplicon.get_start() - 1: amplicon.get_stop() - 1]\n+ if amplicon.strand == 1:\n+ sub = sub.reverse_complement()\n+ if args.remove:\n+ sub = sub[len(args.forward): len(sub) - len(args.reverse)]\n+ if args.keep:\n+ sub.id = record.id\n+ sub.description = record.description\n+ else:\n+ sub.id = record.id + "_ampli_" + str(i)\n+ sub.description = str(amplicon)\n+ SeqIO.write(sub, args.out, "fasta")\n+\n+ sys.stderr.write("OK\\n")\n+ # delete tempfile\n+ os.unlink(primer_fasta)\n+ os.unlink(output_result.name)\n' |
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| diff -r 000000000000 -r 1f4836da4a14 primer_search.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/primer_search.xml Tue Jun 14 08:52:22 2022 +0000 |
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| @@ -0,0 +1,78 @@ +<tool id="primer_search_wrapper" name="Primer Search" version="0.1"> + <description></description> + <requirements> + <requirement type="package" version="1.28">gassst</requirement> + <requirement type="package" version="1.78">biopython</requirement> + </requirements> + <stdio> + <exit_code range="1:" level="fatal" /> + </stdio> + <version_command>$__tool_directory__/primer_search.py -v</version_command> + <command> + $__tool_directory__/primer_search.py -o $output + #if str($error) + -e $error + #end if + #if str($min) + -m $min + #end if + #if str($max) + -M $max + #end if + #if $keep + -k + #end if + #if $remove + -r + #end if + $forward $reverse $database 2> $logfile + </command> + <inputs> + <param name="database" type="data" format="fasta" label="Database to search on fasta" help="FASTA format" /> + <param name="forward" type="text" value="" optional="false" size="50" + label="Forward primer sequence" + help="DNA sequence, letters corresponding to multiple nucleotide allowed" /> + <param name="reverse" type="text" value="" optional="false" size="50" + label="Reverse primer sequence" + help="DNA sequence, letters corresponding to multiple nucleotide allowed" /> + <param name="error" type="integer" value="1" optional="true" + label="Maximun error allowed on match" help="Number of mismatch allowed for each primer" /> + <param name="min" type="integer" value="100" optional="true" + label="Min len amplicon size" help="Only amplicon with this minimun length were reported" /> + <param name="max" type="integer" value="1500" optional="true" + label="Max len amplicon size" help="Only amplicon with this maximun length were reported" /> + <param name="keep" type="boolean" checked="false" + label="If set, Keep description instead of report PCR position" /> + <param name="remove" type="boolean" checked="false" + label="If set, remove primer sequance from reported amplicons" /> + </inputs> + <outputs> + <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log" /> + <data name="output" format="fasta" label="${tool.name} on ${on_string}: fasta" /> + </outputs> + <tests> + <test expect_num_outputs="2"> + <param name="database" value="input.fasta" /> + <param name="forward" value="ACCTGGTGTACGCCTCGCTGAC" /> + <param name="reverse" value="GACATAGATGCCCTGCCCCTTGAT" /> + <param name="error" value="2" /> + <output name="output" file="pcr.fasta" ftype="fasta" /> + </test> + </tests> + <help> +**What it does** + +Search primer on database and return amplicons on fasta format. + +**License and citation** + +This Galaxy tool is Copyright © 2018 `B. Valot` and is released under the `GPL3 license`. + +This tool uses Gassst, which is licensed separately. +Please cite: Rizk G. and Dominique Lavenier D. (2010) GASSST: global alignment short sequence search tool. *Bioinformatics* 26(20), 2534-2540. +http://www.irisa.fr/symbiose/projects/gassst/ + </help> + <citations> + <citation type="doi">10.1093/bioinformatics/btq485</citation> + </citations> +</tool> |
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| diff -r 000000000000 -r 1f4836da4a14 qpcr_search.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qpcr_search.py Tue Jun 14 08:52:22 2022 +0000 |
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| b'@@ -0,0 +1,361 @@\n+#!/usr/bin/env python3\n+# -*- coding: utf-8 -*-\n+\n+"""Search primers/probe on database and return result"""\n+\n+import argparse\n+import os\n+import subprocess\n+import sys\n+import tempfile\n+\n+from Bio import SeqIO\n+\n+gasst_exe = "Gassst"\n+nucleo = {\n+ "R": ("A", "G"),\n+ "Y": ("C", "T"),\n+ "S": ("G", "C"),\n+ "W": ("A", "T"),\n+ "K": ("G", "T"),\n+ "M": ("A", "C"),\n+ "B": ("C", "G", "T"),\n+ "D": ("A", "G", "T"),\n+ "H": ("A", "C", "T"),\n+ "V": ("A", "C", "G"),\n+ "N": ("A", "T", "C", "G"),\n+}\n+\n+desc = "Search primer/probe on database and return position and errors."\n+command = argparse.ArgumentParser(\n+ prog="primer_search.py",\n+ description=desc,\n+ usage="%(prog)s [options] forward probe reverse database",\n+)\n+command.add_argument(\n+ "-o",\n+ "--out",\n+ nargs="?",\n+ type=argparse.FileType("w"),\n+ default=sys.stdout,\n+ help="Return amplicon position on file, default=stdout",\n+)\n+command.add_argument(\n+ "-d",\n+ "--debug",\n+ nargs="?",\n+ type=argparse.FileType("w"),\n+ default=None,\n+ help="Conserve a copy of primer search, default No",\n+)\n+command.add_argument(\n+ "-e",\n+ "--error",\n+ nargs="?",\n+ type=int,\n+ default=1,\n+ help="Maximun error allowed on match, default=1",\n+)\n+command.add_argument(\n+ "-m",\n+ "--min",\n+ nargs="?",\n+ type=int,\n+ default=50,\n+ help="Min len amplicon size, default=50",\n+)\n+command.add_argument(\n+ "-M",\n+ "--max",\n+ nargs="?",\n+ type=int,\n+ default=200,\n+ help="Max len amplicon size, default=200",\n+)\n+command.add_argument(\n+ "-t", "--taxo", action="store_true", help="Parse description to report species only"\n+)\n+command.add_argument("forward", type=str, help="Forward primer sequence")\n+command.add_argument("probe", type=str, help="Probe sequence")\n+command.add_argument("reverse", type=str, help="Reverse primer sequence")\n+command.add_argument(\n+ "database", type=argparse.FileType("r"), help="Database to search on fasta"\n+)\n+command.add_argument("-v", "--version", action="version", version="%(prog)s 0.3.0")\n+\n+\n+class GassstResult:\n+ """A simple Gassst class containing result\n+ rev : True indicate if reverse primers, else forward\n+ """\n+\n+ def __init__(self, line):\n+ h = line.strip().split()\n+ if len(h) != 9:\n+ raise Exception("Line seems not correspond to gassst result\\n" + line)\n+ self.primer = h[0]\n+ # self.rev = h[0] != "Forward"\n+ self.match = h[1]\n+ self.strand = int(h[2])\n+ self.start = int(h[3])\n+ self.error = int(h[5])\n+ self.stop = self.start + len(h[7])\n+\n+ def __repr__(self):\n+ return (\n+ self.match\n+ + " : "\n+ + str(self.start)\n+ + " in strand:"\n+ + str(self.strand)\n+ + " in primer: "\n+ + self.primer\n+ + " with error: "\n+ + str(self.error)\n+ )\n+\n+ def __eq__(self, other):\n+ return (\n+ isinstance(other, GassstResult)\n+ and self.primer == other.primer\n+ and self.match == other.match\n+ and self.strand == other.strand\n+ and self.start == other.start\n+ )\n+\n+ def __ne__(self, other):\n+ return not self == other\n+\n+ def __lt__(self, other):\n+ if self != other:\n+ raise Exception("Only compare equal GassstResult")\n+ return self.error < other.error\n+\n+\n+class Amplicon:\n+ """A simple Amplicon class containing forward and reverse gassst result\n+ Add probe including\n+ """\n+\n+ def __init__(self, forw, reve):\n+ if forw.strand == reve.strand:\n+ raise Exception(\n+ "Amplicon could be in inverse strand for reverse/forward primer\\n"\n+ + forw\n+ + reve\n+ )\n+ self.forw = forw\n+ self.prob = None\n+ self.reve = reve\n+ self.strand = forw.strand\n+\n+ def'..b'n primer_fasta.name\n+\n+\n+def performed_gassst(command):\n+ proc = subprocess.Popen(command, stderr=subprocess.PIPE, stdout=sys.stderr)\n+ error = ""\n+ for line in iter(proc.stderr.readline, b""):\n+ error += line.decode()\n+ if error != "":\n+ sys.stdout.write("Error during processing Gassst\\n")\n+ raise Exception(error)\n+\n+\n+def read_result(f_res, f_debug):\n+ result = {}\n+ for line in iter(f_res.readline, ""):\n+ if line[0] == "F" or line[0] == "R" or line[0] == "P":\n+ if f_debug is not None:\n+ f_debug.write(line)\n+ res = GassstResult(line)\n+ other_res = result.setdefault(res.match, {}).setdefault(res.primer, [])\n+ notfound = True\n+ for i, res2 in enumerate(other_res):\n+ if res == res2:\n+ notfound = False\n+ if res < res2:\n+ other_res[i] = res\n+ # print res\n+ break\n+ if notfound:\n+ other_res.append(res)\n+ return result\n+\n+\n+def get_amplicons(result):\n+ """Function to get amplicon on a sequence from forward / reverse result"""\n+ for forw in result["Forward"]:\n+ for reve in result["Reverse"]:\n+ if forw.strand != reve.strand:\n+ amp = Amplicon(forw, reve)\n+ if amp.get_start() < amp.get_stop(): # must be side by side\n+ for probe in result["Probe"]:\n+ if amp.contain_probe(probe):\n+ yield amp\n+ break\n+ del amp\n+ else:\n+ del amp\n+\n+\n+if __name__ == "__main__":\n+ """Performed job on execution script"""\n+ args = command.parse_args()\n+ primer_fasta = write_primer_fasta(args.forward, args.probe, args.reverse)\n+ output_result = tempfile.NamedTemporaryFile(delete=False, mode="w+")\n+ identity = int(\n+ 100 - args.error / float(max(len(args.forward), len(args.reverse))) * 100\n+ )\n+\n+ command = [\n+ gasst_exe,\n+ "-p",\n+ str(identity),\n+ "-g",\n+ "0",\n+ "-w",\n+ "6",\n+ "-h",\n+ "0",\n+ "-i",\n+ primer_fasta,\n+ "-d",\n+ args.database.name,\n+ "-o",\n+ output_result.name,\n+ ]\n+ performed_gassst(command)\n+ result = read_result(output_result, args.debug)\n+\n+ # load amplicons\n+ sys.stderr.write("Search amplicons : ")\n+ amplicons = {}\n+ for seq in result.keys():\n+ if len(result[seq]) == 3:\n+ # print "Search amplicon on seq: " + seq\n+ for amplicon in get_amplicons(result[seq]):\n+ if len(amplicon) > args.min and len(amplicon) < args.max:\n+ amplicons.setdefault(seq, []).append(amplicon)\n+ else:\n+ del amplicon\n+ # print "Find amplicons : " + str(len(amplicons[seq]))\n+ sys.stderr.write(str(sum(map(len, amplicons.values()))) + "\\n\\n")\n+\n+ # print amplicons\n+\n+ sys.stderr.write("Write result : ")\n+ sep = "\\t"\n+ args.out.write(\n+ "Id\\tAmpli number\\tDescription\\tStart\\tStop\\tError forward\\tError probe\\tError reverse\\n"\n+ )\n+ for record in SeqIO.parse(args.database, "fasta"):\n+ if record.id not in amplicons:\n+ continue\n+ for i, amplicon in enumerate(amplicons.get(record.id)):\n+ desc = record.description.lstrip(record.id)\n+ if args.taxo:\n+ desc = record.description.split(";")[-1].strip()\n+ args.out.write(\n+ record.id\n+ + sep\n+ + str(i + 1)\n+ + sep\n+ + desc\n+ + sep\n+ + sep.join(amplicon.get_tab_data())\n+ + "\\n"\n+ )\n+ sys.stderr.write("OK\\n")\n+ # delete tempfile\n+ os.unlink(primer_fasta)\n+ os.unlink(output_result.name)\n' |
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| diff -r 000000000000 -r 1f4836da4a14 qpcr_search.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qpcr_search.xml Tue Jun 14 08:52:22 2022 +0000 |
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| @@ -0,0 +1,79 @@ +<tool id="qpcr_search_wrapper" name="qPCR Search" version="0.1"> + <description></description> + <requirements> + <requirement type="package" version="1.28">gassst</requirement> + <requirement type="package" version="1.78">biopython</requirement> + </requirements> + <stdio> + <exit_code range="1:" level="fatal" /> + </stdio> + <version_command>$__tool_directory__/qpcr_search.py -v</version_command> + <command> + $__tool_directory__/qpcr_search.py -o $output + #if str($error) + -e $error + #end if + #if str($min) + -m $min + #end if + #if str($max) + -M $max + #end if + #if $taxo + -t + #end if + $forward $probe $reverse $database 2> $logfile + </command> + + <inputs> + <param name="database" type="data" format="fasta" label="Database to search on fasta" help="FASTA format" /> + <param name="forward" type="text" value="" optional="false" size="50" + label="Forward primer sequence" + help="DNA sequence, letters corresponding to multiple nucleotide allowed" /> + <param name="probe" type="text" value="" optional="false" size="50" + label="Probe sequence" + help="DNA sequence, letters corresponding to multiple nucleotide allowed" /> + <param name="reverse" type="text" value="" optional="false" size="50" + label="Reverse primer sequence" + help="DNA sequence, letters corresponding to multiple nucleotide allowed" /> + <param name="error" type="integer" value="1" optional="true" + label="Maximun error allowed on match" help="Number of mismatch allowed for each primer" /> + <param name="min" type="integer" value="50" optional="true" + label="Min len amplicon size" help="Only amplicon with this minimun length were reported" /> + <param name="max" type="integer" value="200" optional="true" + label="Max len amplicon size" help="Only amplicon with this maximun length were reported" /> + <param name="taxo" type="boolean" checked="false" + label="If set, parse description to report species only" /> + </inputs> + + <outputs> + <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log" /> + <data name="output" format="txt" label="${tool.name} on ${on_string}: search" /> + </outputs> + <tests> + <test expect_num_outputs="2"> + <param name="database" value="input.fasta" /> + <param name="forward" value="TTCAACTTCGGCGACTTCC" /> + <param name="probe" value="CGGTGCGCCCGATCGCCGGTACCCG" /> + <param name="reverse" value="TCTTCGTTGATCCCGCGC" /> + <param name="error" value="2" /> + <output name="output" file="qpcr.txt" ftype="txt" /> + </test> + </tests> + <help> +**What it does** + +Search qPCR primer/probe on database and return position and errors. + +**License and citation** + +This Galaxy tool is Copyright © 2018 `B. Valot` and is released under the `GPL3 license`. + +This tool uses Gassst, which is licensed separately. +Please cite: Rizk G. and Dominique Lavenier D. (2010) GASSST: global alignment short sequence search tool. *Bioinformatics* 26(20), 2534-2540. +http://www.irisa.fr/symbiose/projects/gassst/ + </help> + <citations> + <citation type="doi">10.1093/bioinformatics/btq485</citation> + </citations> +</tool> |
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| diff -r 000000000000 -r 1f4836da4a14 test-data/input.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input.fasta Tue Jun 14 08:52:22 2022 +0000 |
| b |
| b'@@ -0,0 +1,121324 @@\n+>NODE_1_length_344587_cov_27.773165\n+ATGGTGTCCACCAAAAACAGGTGGACACCATGCCGCTAGCTGGAAGAACCGGGGAGGTGT\n+GTTGGCCAGACGCTTACACTGTTTCGCCCATATGTCTGTCGATGCGGATCAGCACAAACC\n+GAATTGGACTTGGGTATAGATGGCCTTCGGGCCGCCTTTTTTGCCAATGGAGGCATCCCG\n+GGGGGTGGGCCGACAACGCACCCCCGGTGGGAGCTACTGTTAAGAGTCAGCGCCGAAGGT\n+ATTACGCAGAAAGGCTTGCACGGTCGACAGGATTTCCTGAGATAGCTCATCGTCCGCGAC\n+CGCACGCGAAAGCCCCAAGGCACCGACCATAGTGCTGAAAGCCACAATCGCTTCAGCGCG\n+CTTTTCACTATTGCCGCCCCCCACCAAAGCCGAAATGCCCTTGATGTTGGCCTTGAGCTT\n+ACGCGTATACAGCTCCCGCGCCTCACCCTCTACGCGACCAATATCACTTACCAGCGCGCC\n+CACTGCGCATCCTGTGCCTACGGAGTCACGGTGCTCTTGGCTCAGATACTCGCTCACGAG\n+CTTATCGAAGGTCGCCTTATAGGTGCGGTCAGGATTTTCCGAGCGCTGAAAAGCGACATC\n+CAAAGCCTCAACAACCAACTGGTCACGGGACTCGAAGTGCTTGTAGAAGCCACCATGGGT\n+AAGGCCAGCTTCTTTCATGAGGTCGGCGATGCTTAAGCCATCAATTCCCAGCTCGCAAAA\n+TCGTTCAGCCGCGATGCTGACAATGCGGTCATGAGTTGCCTGCTTGCTAGCTTGTGAGTG\n+CCCCATCTCTGATGACCTTGATCTCTGATCCGTAGCGGATGATATCACCCGCTACGGATG\n+CGCTTTTAGCTCACCATTTTTCGCCAAAGGGGCGGATTTCCGTCAGGAAGGACCAAGCAC\n+TTCTGGGCTGTTGAATGAGGTGACCCACTTCGGCGGCGATGTCTGCCGGCTGGATGAAAA\n+ACTCATCAGGTGCAGTCGGGTGCATCTTGCGCGTCCATTCCACATCGATCACAGCATCGA\n+TGACCACGTAGGCGACATGGATGCCTTTCGGCCCCAACTCTCGGGCAATCGACTCGCTCA\n+AGATGCGCTGTGCTGCCTTGGTAGGGGCGAAACCGGCAAAGTGGCTTTTTCCGCGTAGCG\n+CGGAGGTATTGCCGGTGACGATGATCGCGCCTTCGCCTTTATCGATCATTGCAGGTGAGA\n+GATGGCGGGCTAGGTGCAGTAGCGAAACGACATTCGTTTCGAAGTTGTTGGTGAGCGCCT\n+TGGGATCGATCTCTAGGAAGCTGCCAAATGTCCCACCCACCGCATTGTGAACCAGTACCG\n+CAGCGTCCCCGAGCTGGGACTTGATGCGATCCAAAGCCAGCTCAAGCTGCTCAATATCGG\n+CAACGTCAGTGGGGAATATGTAGGTGTCCGGTAGCTCTGTCGCCAGCGCTGTCAGGCGCT\n+CCTCATTGCGAGCAATCATTGCTACCCGGAAGCCGTCCTCGACGAGCCGACGAACGATTG\n+CCGCGCCGGTGCCTGGCCCAACGCCAGTGACGATTGCGAGTTTCTTGGTATTCATTTCGA\n+GGCTCCTTTGGCTTTTTGCAGAGCGGCACGCACGAAGTCGAGTCGGTCATTGCCGAAGAA\n+CATTTCGTCGCCGCAGAAGAGGGTCGGCACACCAAATACGCCGCGTCGAGCGGCTTCTTC\n+ATTGTTGGCGGCCAGTTGGTCACGAACGGCAGGTCGATCCGCTAACTGCCAGATGTCTTC\n+GTCTACGCCGAGATTTTTCAGAAAGGTAGATCGTCCTTCTGCGGTGATGAGGTCGTCAGT\n+ACCCGCCCATACGGCTTGAAATAAGGCCGGATGGACGACTTCAAACGAGCCGGTCTGCTG\n+AGCCGCAAGAGCGGCGCGGGCCAAGATCGCGCCTTCAACTTGCCCTGCGCGCATTGCTTG\n+GAAGAACGCGCCATTTGGTGCAAGCGGGACGCCGTAGACGGCTGCCCAACGCGCGGCGTC\n+GATGCCCGAGTACTTCGCTTTGGCAGGGCAAGCAGGAGAGGGTTGGTTATTCACCTTCTT\n+CATCACCTCCAAAATGTCGATGGCGAAGTAGCTGATGGGCGTATCGAACTCTGGCAGGCG\n+GGTGTTGGCCAGGTAAGCGTAAGGGCTTCGGTAATCAAAAACGGACTGGAGATTCATTGA\n+TCTCTCCCGTGGGGGAATGGATTGGTCGGAGCGCGCTCAACTGGATGTTATTCATCATCC\n+ATTCTGGATGTCAAATAACATCCAGAGTGTCGGCCAGCCGACCATGGAGTTGCTGACGCT\n+GCCCTAGGATTGAGGCCCCAAATCCGTTCCACCCAGGGACGCTAGGAGATCCGCTTTATG\n+TCCGGCTTTCAGCACAAGTACGCATTCACCAATGGCATTCGCATGCACTATGTCGACGAG\n+GGCGTGGGGCCGGTCGTTGTTCTTCTCCACGGCTGGCCGGAGTCCTGGTATTCCTGGCGG\n+CACCAGATTTCGTTCTTGGCTGAAGCGGGCTATCGGGTTATCGCGCCCGATCAGCGAGGG\n+TATGGGGATACCGAGATTCCATCGGAGGTAGGCAGCTACCACATCCTCAATTTGGTCGGG\n+GACGTGGTGGGGCTGTTGAACGCGTTGGAAATTAAGTCGGCGGCCCTTGTCGGCCATGAC\n+TGGGGATCGATGGTTGCAGCGGCAGCGGCGCTCCTGCGGCCTGACCTGTTTCATCGTGTC\n+TGTCTGCTGAGCGTTCCCTACATGCCTCGTCGGAGCCTACGACCTAGCACTCGCTTCCAG\n+CTCGCAACCCAGGGAAAGCACTTCTATCAGGACTATTTCCAGCGTGTCGGCATCGTCGAG\n+AAAGAGCTGGGTGAGGATACGCATCGAAGCATTTTGGGTGCCCTTTACGCCCGCTCGGGC\n+GAGGCGAAAAAGCACCCAGAGCACAGCCGCTCAGGCTTCATCGCCTTCGACAAAAGCACT\n+CGCTTTGTAGACAACTTGGCTGTTCCGGACCAGCTGCCGGCTTGGCTTACGGAAGAGGAC\n+CTTGATGTCTTCGTGAAGCAGTTCGAGCGTTCTGGCTTCTTCGGCGGCATCAACTGGTAC\n+AGGAACATGGACCGAAACTGGGAGCTGACGCCCTTTTGGAATGGTGCCGTGTTGATTCAG\n+CCGTTGCTGTTCATCGCAGGCGAGCTCGACGGTGTTCTCACGATGGCCGGTGAAGAGTAC\n+GAAGCGCTGGATATCAATGCTAGGCAGCTGATTGGGAAGGAGTTGATTCCTGGGGCAGGC\n+CATTGGATTCAGCAGGAGCGTCCAGACCACGTTAACCAACTACTGCTGAACTTCGTAGAG\n+CCTGACAGCCCGAGGGATATCTGCCCCTGACCGATTTTCTAACGTTCTGTCCAGGTCACC\n+AATAAAGGGCGTCTGAACAAGCGATATAACGATCGATAGCTTCGTCGGTAATTTGCATCG\n+GAATTGGTAGGTCGTATGGGTGCTAAAGCACTAGCAGTGCATTGATTGGTTCTCTACTGC\n+CAGCGACATACCAAGGAGAACATGTACATGGAGTTTCGGCATCTTCGTTGCTTCCTCGCA\n+GTTGCCGAGGAGCTGCATTTTGCGCGGGCAGCTGAGCGACTGCACATTGAGCAGTCTCCG\n+TTATCTCGTGCGATTAAGGAGCTTGAGGAAGAGTTGGGCACACAGCTTTTCGTGCGAACC\n+ACCCGGAGTACGAGACTTACGCATGCCGGACGACTATTTCTAGATCATGTGCCTCGTGTA\n+TTCACTGCTTTGCAACAGGCGCGCGACAGCGTGAGGGCCGTCGCGAATGGGTACTGTGGC\n+CAACTGCGATTGGCTCTCTCGGACGGGATCTCTC'..b'CC\n+GGCGCCGAGGACCTGATTGTCGAGGACGGAGTGGACCACGTCGTTTTCCAAACCGCTTGG\n+CGTAGCGGTAACCCTTGGCTCTACGCGATCAGGAAGGACTGACATGGCTTATTTCACAGG\n+AACAGCGAACAACCCGGCCGACTTGCTCGCCAAGGTGCGCGTCCACGCCGAGTCGCTCGG\n+CTGGGT\n+>NODE_226_length_359_cov_20.244681\n+TGGTTGTAGTCCCGCAGCCAGCCGCAAGTGACAACGAAGCGAGGAGCAGGCACAGGGGAA\n+GCACCTGGTGCCGGCCGATATTGGGTCGAGACATGGGCGATACGCTCCGATAGCTGTTGC\n+TGGAGGGCAGTGAACTGATCCTGGGCTGACAGGAATCGCGCTTCCGCCTGATTCGCGCGA\n+GTGACCTGCTGTTGGAACTGCAGGAGGTTGTCCTCAGCGATCTTGGCCAGCTCGTTGGAA\n+TGCTGCAGTTGCAGGTTGAGCAGCGCTGCGTCACCTTCAGCACGAGCGGTGGCGTACCCA\n+CGGTCGTAGCTTGCGGAGCCGTGGATCACTACAGCTACGCTGTACAGCACCGCAATCAG\n+>NODE_227_length_356_cov_22.627240\n+AGCGCTCCATCGGGATGACGACCAAGGCGCCGGACTGGGTGATAGCGGCTTGGCCACCGG\n+TGGCCTCCGCCAGTTGCCGGTGGAGATGCTGGGCCTCGTTGCACCACCCTTCGGCACATT\n+CCTCCATGCGGGTCAGCTCGGTGCGCAGGTGCTCGTTCTCTTCGGCAAGGCGCGCAGCTT\n+CGATGCAGAGCTGCTCATAGGCTTTCTCGTCCAGGCGCCGCAGCAGCGCCTGCAGGTTGA\n+TGGACTCACTCATCGTCAGCCACTCCAAAGTCCAGTTGAGGGGTTTCTGCCTGGGCGACG\n+TTGCCGTGGTGCCAAGCGAGGGATTCGAGGCCGGCGCGGATGGCGTCCAGGGTCTG\n+>NODE_228_length_350_cov_31.344322\n+ACAGCGAACAACCCGGCCGACTTGCTCGCCAAGGTGCGCGTCCACGCCGAGTCGCTCGGC\n+TGGGTCACCGACCGCGCGTCGGCATCGGAATGGATCTGTCACAACGCTGATGGGTACTGG\n+TCATTCAATGCCGGAGCCAATCAGTTTCAGATCGCGGGCAATACGGGGTTCGACAACGGG\n+CTGGCGTGGAACGCGCAGCCCGGTAACTCGGTGCAGAACAACCCGTATTCGTCGAAAGAA\n+GCAACCATAGCGCAGCTCAGCGCCGGGCCATTCACGCGCTATCACCTGTTCGCCACCGCT\n+GCCTATCTGCACCTGCACGTCGAAATCGCTGCCGGTCAGTTTCGTCCAGT\n+>NODE_229_length_339_cov_28.759542\n+CCGTGCTGTCGGGCTTACCCTTTTCCCCGGGCGACCACTTTCAGCGACTCGATGTCGAGG\n+TGGGCCTCGGCGAGCAATTTCTTCAATCGGCTGTTTTCCAGTTCAAGATCCTTCAACCGT\n+TTGGCGTCCGCCACGGTCATACCGCCAAACTTGGCCCGCCAGGTGTAGAACGAGGCATCA\n+CTGAAGCCGTGTCGGCGACACAGTTCCTTCACCGGCACACCGGCCTCCGCCTGCTTGAGG\n+AAGTCGAGAATCTGCTCTTCGATAAAACGCTTTTTCACTGCCGTCTCCTGCTCGGAAAAC\n+GGACTCTACTAAGTTCGGCGTGGTACTGAAATCGGGGAG\n+>NODE_230_length_337_cov_22.915385\n+GTAAATCGCGACCGTAGGCTGGCCTCGGCATCCGGCGCCGACCAGCTGGCCTGGTTCGAT\n+TCCGTCGAGCGCTTCAATTCCGGGCGCTCGGCCGCCAACTTCCGCGAGAACCGCAACTAC\n+CCGCGCCTCATCCTGCTGCGCTACGAGCGGATCTATCTGCAGTGGGGCGACGGTGTGTGC\n+GGCGAGAGGTACACCCTGTGAGACTGTCCCCCAGCATCACCCTGGCTCTGAACATTACCT\n+ACCTCGACCTAGCGCTGATCCAGCGGCTGTTCGCAGGCAGTCGCGACTTCCTACCGGCAC\n+CTGAGCTGTATTGCTCGCCAGTGCCGCGCGAGCGGCA\n+>NODE_231_length_335_cov_57.887597\n+TCTCCTCCATATCTTCGAACAGCTCATATTGGGCGACGATGTCACCTTGCTCGGCGGAGT\n+CGAGGAGCGAGGCAAGCTTTGAAGGCGTGAGTCCACGGGATGGGTGACCAGCGACTTCCT\n+GGTGAAGGCTGGTCAGGTGGGCGGTCTGGGCTTCTTTCAGGTCAGCATCGGCCATGCTCT\n+GCTGCCCGAAAATGCGCGCGACAGTGGCGCGTAGCGTCTGCATCACCATGCGGAAGGCTC\n+CGGTAGTTCAATGTCATCGTTGTGGTCCTGGACGTTGTCGAAGCCGCGGCTATGGCGTGG\n+CAGCGCCGTGAAGGCGATCTCGCCACCCTCCATGT\n+>NODE_233_length_321_cov_145.581967\n+CTCAATAACGTGATCGAGGCCGATCACGGAAAGCTCAAGATACTGATCAAGCCGGTGCGC\n+GGTTTCAAATCGATCCCCACGGCCTATGCCACGATCAAGGGATTCGAAGTCATGCGAGCC\n+CTGCGCAAAGGACAGGCTCGCCCCTGGTGCCTGCAGCCCGGCATCAGGGGCGAGGTGCGC\n+CTTGTGGAGAGAGCTTTTGGCATTGGGCCCTCGGCGCTGACGGAGGCCATGGGCATGCTC\n+AACCACCATTTCGCAGCAGCCGCCTGATCGGCGCAGAGCGACAGCCTACCTCTGACTGCC\n+GCCAATCTTTGCAACAGAGCC\n+>NODE_234_length_313_cov_43.343220\n+GGCATACTGGGTGCCGCGATGGACCACCCGCACCGGCCGCCACCAGGCGTTGAAGTCGGC\n+ACGCGGATGACCTTCCAAGGCAAAGGCGTGGCCCGGGATCAGCCGCGGGTCGTCGCCGCT\n+GACCGATGCCTCCCGCGCATCGCGCCGGTGCCCTCTGAGGCGGCTTTCGGTGAAAGGCCG\n+GCCGGCGCCGCTCCGCTTGTAGCGACCGGGGTAGTCGTAGCGCTCGTAGGACGAGCCCTG\n+ATGCTCGAGCGCCTCGCCAGCGAGATGATGCTCCTGGTCGTAGGTCGGGCGCTTGAAGCT\n+GTAGTCCCGCTGG\n+>NODE_235_length_306_cov_24.820961\n+AGGATCGAACGGCGGGGCATGCGGTTTCCTTCTTCTTGAAAACGTAGGTTTGTGACAAGC\n+CCGCCAAGGCAACCGGCTGTCATTTTCAGAAGACGACTGCACCAGTTGATTGGGCGTAAT\n+GGCTGTTGTGCAGCCAGCTCCTGACAGTTCAATATCAGAAGTGATCTGCACCAATCTCGA\n+CTATGCTCAATACTCGTGTGCACCAAAGCGAGGTGAGCATGGCGACGGAGGCTCTGTTGC\n+AAAGATTGGCGGCAGTCAGAGGTAGGCTGTCGCTCTGCGCCGATCAGGCGGCTGCTGCGA\n+AATGGT\n+>NODE_236_length_305_cov_44.745614\n+GGCTGGGCGCTGAACAGTACCGGGCCGCCGGCGATACGCTCCTGGACGTAGAGCCGGTCG\n+CTGCAGACCAGGGTGTGACGGTGTTCGTCGAAGCGGAAGTAGTAGACCAGGCCTTCCTCG\n+AAGGCCAGCCGGTCGTGCAGGTAGTGATCGCTGTCGCCGGCCTGCACGCAGTATTCGCGT\n+GGCAGGTGCTCGTGGTAGATGCGCTGTTCGTAGTCGAGCACCCGGTGCTCCTTGAGCAGC\n+GCCTGGAGAATCTCCGGAACACTCTTCTCCTGGAAGATCCGCCAGTTGCAGCACAGCTCC\n+AGGCG\n' |
| b |
| diff -r 000000000000 -r 1f4836da4a14 test-data/pcr.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pcr.fasta Tue Jun 14 08:52:22 2022 +0000 |
| b |
| @@ -0,0 +1,16 @@ +>NODE_33_length_85799_cov_26.696344_ampli_0 20191 : 21033 in strand:1; error F:0,R:0 +ACCTGGTGTACGCCTCGCTGACCCACGAGCGGGTCTTCGACTACCGTCCGGGCGAAGTCT +ACTGGTGCACCGCCGACATCGGCTGGGTCACCGGCCACACCTACATCGTCTATGGCCCGC +TGGCCAACGGCGCCACCACCATTCTGTTCGAGGGCGTGCCGAACTACCCCGACGTGACCC +GCGTGGCGAAAATCATCGACAAGCACAAGGTCAACATCCTCTACACCGCGCCGACCGCGA +TCCGCGCGATGATGGCCGAAGGCAAGGCGGCGGTGGCCGGTGCCGACGGTTCCAGCCTGC +GTCTGCTCGGTTCGGTGGGCGAGCCGATCAACCCGGAAGCCTGGCAGTGGTACTACGAGA +CCGTCGGCCAGTCGCGCTGCCCGATCGTCGACACCTGGTGGCAGACCGAGACCGGCGCCT +GCCTGATGACCCCGCTGCCGGGCGCCCACGCGATGAAGCCGGGCTCTGCAGCCAAGCCGT +TCTTCGGCGTGGTACCGGCACTGGTGGACAACCTCGGCAACCTGATCGAGGGCGCCGCCG +AGGGCAACCTGGTGATCCTCGACTCCTGGCCGGGCCAGGCGCGGACCCTGTTCGGCGACC +ATGACCGCTTCGTCGACACCTACTTCAAGACCTTCAAGGGCATGTACTTCACCGGCGACG +GCGCGCGCCGCGACGAGGACGGCTACTACTGGATCACCGGGCGGGTCGACGACGTGCTCA +ACGTCTCCGGCCACCGCATGGGCACCGCCGAGGTGGAAAGCGCGATGGTCGCCCACCCGA +AGGTCGCCGAGGCGGCGGTGGTCGGCATGCAGCACGACATCAAGGGGCAGGGCATCTATG +TC |
| b |
| diff -r 000000000000 -r 1f4836da4a14 test-data/qpcr.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/qpcr.txt Tue Jun 14 08:52:22 2022 +0000 |
| b |
| @@ -0,0 +1,2 @@ +Id Ampli number Description Start Stop Error forward Error probe Error reverse +NODE_2_length_251595_cov_31.920467 1 215345 215464 0 0 0 |