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pmlst.pl pmlst.xml pmlst/.gitignore pmlst/Dockerfile pmlst/README.md pmlst/data.json pmlst/pmlst.py pmlst/pmlst_db/.gitignore pmlst/pmlst_db/INSTALL.py pmlst/pmlst_db/config pmlst/pmlst_db/incac.clpx pmlst/pmlst_db/incac.fsa pmlst/pmlst_db/incac.txt.clean pmlst/pmlst_db/incf.clpx pmlst/pmlst_db/incf.fsa pmlst/pmlst_db/incf.txt.clean pmlst/pmlst_db/inchi1.clpx pmlst/pmlst_db/inchi1.fsa pmlst/pmlst_db/inchi1.txt.clean pmlst/pmlst_db/inchi2.clpx pmlst/pmlst_db/inchi2.fsa pmlst/pmlst_db/inchi2.txt.clean pmlst/pmlst_db/inci1.clpx pmlst/pmlst_db/inci1.fsa pmlst/pmlst_db/inci1.txt.clean pmlst/pmlst_db/incn.clpx pmlst/pmlst_db/incn.fsa pmlst/pmlst_db/incn.txt.clean pmlst/pmlst_db/pbssb1-family.clpx pmlst/pmlst_db/pbssb1-family.fsa pmlst/pmlst_db/pbssb1-family.txt.clean pmlst/test.fsa pmlst/tmp_pMLST/tmp/out_inchi2.xml |
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| diff -r 000000000000 -r 6dcb66689a7d pmlst.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pmlst.pl Wed Aug 25 21:12:34 2021 +0000 |
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| @@ -0,0 +1,28 @@ +#!/usr/bin/perl -w +use strict; +use warnings; + +my $STpmlst = ""; + +my $path = $ARGV[0]; +my $seq = $ARGV[1]; +my $scheme = $ARGV[2]; + + +open PMLST, "python3 $path/pmlst/pmlst.py -i $seq -s $scheme -p $path/pmlst/pmlst_db/ |"; +while (<PMLST>) { + chomp ($_); + if ($_ =~ "sequence_type") { + #print "ST:$_ \n"; + my @table = split (/:/,$_); + $STpmlst = $table [1]; + #chomp ($STpmlst); $STpmlst = chop($STpmlst); + $STpmlst =~ s/\s+//; + $STpmlst = substr($STpmlst,1); + my @table2 = split (/'/,$STpmlst); + $STpmlst = $table2[0]; + #print "$STpmlst\n" ; + } +} + +print "Sequence Type (pMLST)\t$STpmlst\n" ; |
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| diff -r 000000000000 -r 6dcb66689a7d pmlst.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pmlst.xml Wed Aug 25 21:12:34 2021 +0000 |
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| @@ -0,0 +1,49 @@ +<tool id="pmlst" name="pmlst" version="2.0"> + <description>A plasmid multilocus sequence typing (pMLST) scheme was developed for rapid categorization of IncN plasmids</description> + + + <requirements> + <requirement type="package" version="3.2.0">python3-openid</requirement> + <requirement type="package" version="21.2.4">pip</requirement> + <requirement type="package" version="1.79">biopython</requirement> + <requirement type="package" version="1.5.6">cgecore</requirement> + <requirement type="package" version="0.8.9">tabulate</requirement> + </requirements> + + + <!--<command> python3 $__tool_directory__/pmlst/pmlst.py -i $input -s $s -p $__tool_directory__/pmlst/pmlst_db/ > $output </command>--> + + <command> perl $__tool_directory__/pmlst.pl $__tool_directory__ $input $s > $output </command> + + <inputs> + <param format="fasta" name="input" type="data" label="Select FASTA files: " /> + + <param name="s" type="select" label="Scheme database used for pMLST prediction:"> + + <option value="incac">incac</option> + <option value="incf">incf</option> + <option value="inchi1">inchi1</option> + <option value="inchi2">inchi2</option> + <option value="inci1">inci1</option> + <option value="incn">incn</option> + <option value="pbssb1-family">pbssb1-family</option> + + </param> + + + </inputs> + + <outputs> + <data format="tabular" name="output" /> + </outputs> + + <help> + + </help> + <citations> + <citation type="doi">10.1007/978-1-4939-9877-7_20</citation> + </citations> +</tool> + + + |
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| diff -r 000000000000 -r 6dcb66689a7d pmlst/.gitignore --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pmlst/.gitignore Wed Aug 25 21:12:34 2021 +0000 |
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| @@ -0,0 +1,4 @@ +.DS_Store +blast-2.2.26 +Output +*.gz \ No newline at end of file |
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| diff -r 000000000000 -r 6dcb66689a7d pmlst/Dockerfile --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pmlst/Dockerfile Wed Aug 25 21:12:34 2021 +0000 |
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| @@ -0,0 +1,43 @@ +FROM debian:stretch + +ENV DEBIAN_FRONTEND noninteractive + +### RUN set -ex; \ + +RUN apt-get update -qq; \ + apt-get install -y -qq git \ + apt-utils \ + wget \ + python3-pip \ + ncbi-blast+ \ + libz-dev \ + ; \ + rm -rf /var/cache/apt/* /var/lib/apt/lists/*; + +ENV DEBIAN_FRONTEND Teletype + +# Install python dependencies +RUN pip3 install -U biopython==1.73 tabulate cgecore==1.3.2; + +# Install kma +RUN git clone --branch 1.0.1 --depth 1 https://bitbucket.org/genomicepidemiology/kma.git; \ + cd kma && make; \ + mv kma* /bin/ + +COPY pmlst.py /usr/src/pmlst.py + +RUN chmod 755 /usr/src/pmlst.py; + +ENV PATH $PATH:/usr/src +# Setup .bashrc file for convenience during debugging +RUN echo "alias ls='ls -h --color=tty'\n"\ +"alias ll='ls -lrt'\n"\ +"alias l='less'\n"\ +"alias du='du -hP --max-depth=1'\n"\ +"alias cwd='readlink -f .'\n"\ +"PATH=$PATH\n">> ~/.bashrc + +WORKDIR /workdir + +# Execute program when running the container +ENTRYPOINT ["/usr/src/pmlst.py"] |
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| diff -r 000000000000 -r 6dcb66689a7d pmlst/README.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pmlst/README.md Wed Aug 25 21:12:34 2021 +0000 |
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| @@ -0,0 +1,146 @@ +pMLST +=================== + +Plasmid Multi-Locus Sequence Typing + + +Documentation +============= + +The pMLST service contains one python script *pmlst.py* which is the script of the latest +version of the pMLST service. The method enables investigators to determine the ST based on WGS data. + +## Content of the repository +1. pmlst.py - the program +2. README.md +3. Dockerfile - dockerfile for building the pmlst docker container +4. test.fsa - test fasta file + + +## Installation + +Setting up pMLST program +```bash +# Go to wanted location for pmlst +cd /path/to/some/dir +# Clone and enter the pmlst directory +git clone https://bitbucket.org/genomicepidemiology/pmlst.git +cd pmlst +``` + +Build Docker container +```bash +# Build container +docker build -t pmlst . +``` + +#Download and install pMLST database +```bash +# Go to the directory where you want to store the pmlst database +cd /path/to/some/dir +# Clone database from git repository (develop branch) +git clone https://bitbucket.org/genomicepidemiology/pmlst_db.git +cd pmlst_db +pMLST_DB=$(pwd) +# Install pMLST database with executable kma_index program +python3 INSTALL.py kma_index +``` + +If kma_index has not bin install please install kma_index from the kma repository: +https://bitbucket.org/genomicepidemiology/kma + +## Dependencies +In order to run the program without using docker, Python 3.5 (or newer) should be installed along with the following versions of the modules (or newer). + +#### Modules +- cgecore 1.5.5 +- tabulate 0.7.7 + +Modules can be installed using the following command. Here, the installation of the module cgecore is used as an example: +```bash +pip3 install cgecore +``` +#### KMA and BLAST +Additionally KMA and BLAST version 2.8.1 or newer should be installed. +The newest versions of KMA and BLAST can be installed from here: +```url +https://bitbucket.org/genomicepidemiology/kma +``` + +```url +ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ +``` + +## Usage + +The program can be invoked with the -h option to get help and more information of the service. +Run Docker container + + +```bash +# Run pmlst container +docker run --rm -it \ + -v $pMLST_DB:/database \ + -v $(pwd):/workdir \ + pmlst -i [INPUTFILE] -o . -s [SCHEME] [-x] [-mp] [-p] [-t] +``` + +When running the docker file you have to mount 2 directory: + 1. pmlst_db (pMLST database) downloaded from bitbucket + 2. An output/input folder from where the input file can be reached and an output files can be saved. +Here we mount the current working directory (using $pwd) and use this as the output directory, +the input file should be reachable from this directory as well. + +` -i INPUTFILE input file (fasta or fastq) relative to pwd ` + +` -s SCHEME pMLST scheme to be used, details are in config file ` + +` -o OUTDIR outpur directory relative to pwd ` + +` -x extended output. Will create an extented output ` + +` -mp METHOD_PATH Path to executable of the method to be used (kma or blast)` + +` -p DATABASE Path to database directory ` + +` -t TMP_DIR Temporary directory for storage of results from external software. ` + + +## Web-server + +A webserver implementing the methods is available at the [CGE website](http://www.genomicepidemiology.org/) and can be found here: +https://cge.cbs.dtu.dk/services/pMLST/ + +Citation +======= + +When using the method please cite: + +PlasmidFinder and pMLST: in silico detection and typing of plasmids. +Carattoli A, Zankari E, Garcia-Fernandez A, Volby Larsen M, Lund O, Villa L, Aarestrup FM, Hasman H. +Antimicrob. Agents Chemother. 2014. April 28th. +[Epub ahead of print] + +References +======= + +1. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL. BLAST+: architecture and applications. BMC Bioinformatics 2009; 10:421. +2. Clausen PTLC, Aarestrup FM, Lund O. Rapid and precise alignment of raw reads against redundant databases with KMA. BMC Bioinformatics 2018; 19:307. + +License +======= + +Copyright (c) 2014, Ole Lund, Technical University of Denmark +All rights reserved. + +Licensed under the Apache License, Version 2.0 (the "License"); +you may not use this file except in compliance with the License. +You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + +Unless required by applicable law or agreed to in writing, software +distributed under the License is distributed on an "AS IS" BASIS, +WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +See the License for the specific language governing permissions and +limitations under the License. |
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| diff -r 000000000000 -r 6dcb66689a7d pmlst/data.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pmlst/data.json Wed Aug 25 21:12:34 2021 +0000 |
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| @@ -0,0 +1,1 @@ +{"pmlst": {"user_input": {"filename": ["test.fsa"], "scheme": "inchi2", "profile": "IncHI2 DLST", "file_format": "fasta"}, "run_info": {"date": "25.08.2021", "time": "08:48:07"}, "results": {"sequence_type": "Unknown", "allele_profile": {"smr0018": {"identity": "", "coverage": "", "allele": "", "allele_name": "No hit found", "align_len": "", "gaps": "", "sbj_len": ""}, "smr0199": {"identity": "", "coverage": "", "allele": "", "allele_name": "No hit found", "align_len": "", "gaps": "", "sbj_len": ""}}, "nearest_sts": "", "clonal_complex": "", "notes": "No MLST loci was found in the input data, make sure that the correct pMLST scheme was chosen."}}} \ No newline at end of file |
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| diff -r 000000000000 -r 6dcb66689a7d pmlst/pmlst.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pmlst/pmlst.py Wed Aug 25 21:12:34 2021 +0000 |
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| b'@@ -0,0 +1,691 @@\n+#!/usr/bin/env python3\n+\n+import os, sys, re, time, pprint, io, shutil\n+import argparse, subprocess\n+\n+from cgecore.alignment import extended_cigar\n+from cgecore.blaster.blaster import Blaster\n+from cgecore.cgefinder import CGEFinder\n+import json, gzip\n+from tabulate import tabulate\n+\n+\n+def get_read_filename(infiles):\n+ \'\'\' Infiles must be a list with 1 or 2 input files.\n+ Removes path from given string and removes extensions:\n+ .fq .fastq .gz and .trim\n+ extract the common sample name i 2 files are given.\n+ \'\'\'\n+ # Remove common fastq extensions\n+ seq_path = infiles[0]\n+ seq_file = os.path.basename(seq_path)\n+ seq_file = seq_file.replace(".fq", "")\n+ seq_file = seq_file.replace(".fastq", "")\n+ seq_file = seq_file.replace(".gz", "")\n+ seq_file = seq_file.replace(".trim", "")\n+ if len(infiles) == 1:\n+ return seq_file.rstrip()\n+\n+ # If two files are given get the common sample name\n+ sample_name = ""\n+ seq_file_2 = os.path.basename(infiles[1])\n+ for i in range(len(seq_file)):\n+ if seq_file_2[i] == seq_file[i]:\n+ sample_name += seq_file[i]\n+ else: \n+ break\n+ if sample_name == "":\n+ sys.error("Input error: sample names of input files, {} and {}, \\\n+ does not share a common sample name. If these files \\\n+ are paired end reads from the same sample, please rename \\\n+ them with a common sample name (e.g. \'s22_R1.fq\', \'s22_R2.fq\') \\\n+ or input them seperately.".format(infiles[0], infiles[1]))\n+\n+ return sample_name.rstrip("-").rstrip("_")\n+\n+def is_gzipped(file_path):\n+ \'\'\' Returns True if file is gzipped and False otherwise.\n+ The result is inferred from the first two bits in the file read\n+ from the input path.\n+ On unix systems this should be: 1f 8b\n+ Theoretically there could be exceptions to this test but it is\n+ unlikely and impossible if the input files are otherwise expected\n+ to be encoded in utf-8.\n+ \'\'\'\n+ with open(file_path, mode=\'rb\') as fh:\n+ bit_start = fh.read(2)\n+ if(bit_start == b\'\\x1f\\x8b\'):\n+ return True\n+ else:\n+ return False\n+\n+def get_file_format(input_files):\n+ """\n+ Takes all input files and checks their first character to assess\n+ the file format. Returns one of the following strings; fasta, fastq, \n+ other or mixed. fasta and fastq indicates that all input files are \n+ of the same format, either fasta or fastq. other indiates that all\n+ files are not fasta nor fastq files. mixed indicates that the inputfiles\n+ are a mix of different file formats.\n+ """\n+\n+ # Open all input files and get the first character\n+ file_format = []\n+ invalid_files = []\n+ for infile in input_files:\n+ if is_gzipped(infile):#[-3:] == ".gz":\n+ f = gzip.open(infile, "rb")\n+ fst_char = f.read(1);\n+ else:\n+ f = open(infile, "rb")\n+ fst_char = f.read(1);\n+ f.close()\n+ # Assess the first character\n+ if fst_char == b"@":\n+ file_format.append("fastq")\n+ elif fst_char == b">":\n+ file_format.append("fasta")\n+ else:\n+ invalid_files.append("other")\n+ if len(set(file_format)) != 1:\n+ return "mixed"\n+ return ",".join(set(file_format))\n+\n+def import_profile(database, scheme, loci_list):\n+ """Import all possible allele profiles with corresponding st\'s\n+ for the scheme into a dict. The profiles are stored in a dict \n+ of dicts, to easily look up what st types are accosiated with \n+ a specific allele number of each loci. \n+ """\n+ # Open allele profile file from databaseloci\n+ profile_file = open("{0}/{1}.txt.clean".format(database, scheme), "r")\n+ profile_header = profile_file.readline().strip().split("\\t")[1:len(loci_list)+1]\n+ \n+ # Create dict for looking up st-type'..b't(clpx))\n+\n+ # Write tsv table header\n+ table_header = ["Locus", "Identity", "Coverage", "Alignment Length", "Allele Length", "Gaps", "Allele"]\n+ table_file.write("\\t".join(table_header) + "\\n")\n+ rows = []\n+ for locus, allele_info in allele_matches.items():\n+\n+ identity = str(allele_info["identity"])\n+ coverage = str(allele_info["coverage"])\n+ allele = allele_info["allele"]\n+ allele_name = allele_info["allele_name"]\n+ align_len = str(allele_info["align_len"])\n+ sbj_len = str(allele_info["sbj_len"])\n+ gaps = str(allele_info["gaps"])\n+\n+ # Write alleles names with indications of imperfect hits\n+ if allele_name != "No hit found":\n+ allele_name_w_mark = locus + "_" + allele\n+ else:\n+ allele_name_w_mark = allele_name \n+ \n+ # Write allele results to tsv table\n+ row = [locus, identity, coverage, align_len, sbj_len, gaps, allele_name_w_mark]\n+ rows.append(row)\n+ if "alternative_hit" in allele_info:\n+ for allele_name, dic in allele_info["alternative_hit"].items():\n+ row = [locus, identity, coverage, str(dic["align_len"]), str(dic["sbj_len"]), "0", allele_name + "!"]\n+ rows.append(row) \n+ #\n+\n+ if allele_name == "No hit found":\n+ continue\n+\n+ # Write query fasta output\n+ hit_name = allele_info["hit_name"]\n+ query_seq = query_aligns[scheme][hit_name]\n+ sbjct_seq = sbjct_aligns[scheme][hit_name] \n+ homol_seq = homol_aligns[scheme][hit_name]\n+\n+ if allele_info["match_priority"] == 1:\n+ match = "PERFECT MATCH"\n+ else:\n+ match = "WARNING"\n+ header = ">{}:{} ID:{}% COV:{}% Best_match:{}\\n".format(locus, match, allele_info["identity"], \n+ allele_info["coverage"], allele_info["allele_name"])\n+ query_file.write(header)\n+ for i in range(0,len(query_seq),60):\n+ query_file.write(query_seq[i:i+60] + "\\n")\n+\n+ # Write template fasta output\n+ header = ">{}\\n".format(allele_info["allele_name"])\n+ sbjct_file.write(header)\n+ for i in range(0,len(sbjct_seq),60):\n+ sbjct_file.write(sbjct_seq[i:i+60] + "\\n")\n+\n+ if "alternative_hit" in allele_info:\n+ for allele_name in allele_info["alternative_hit"]:\n+ header = ">{}:{} ID:{}% COV:{}% Best_match:{}\\n".format(locus, "PERFECT MATCH", 100, \n+ 100, allele_name)\n+ hit_name = allele_info["alternative_hit"][allele_name]["hit_name"]\n+ query_seq = query_aligns[scheme][hit_name]\n+ sbjct_seq = sbjct_aligns[scheme][hit_name] \n+ homol_seq = homol_aligns[scheme][hit_name]\n+ query_file.write(header)\n+ for i in range(0,len(query_seq),60):\n+ query_file.write(query_seq[i:i+60] + "\\n")\n+\n+ # Write template fasta output\n+ header = ">{}\\n".format(allele_name)\n+ sbjct_file.write(header)\n+ for i in range(0,len(sbjct_seq),60):\n+ sbjct_file.write(sbjct_seq[i:i+60] + "\\n")\n+\n+ # Write Allele profile results tables in results file and table file\n+ rows.sort(key=lambda x: x[0])\n+ result_file.write(text_table(table_header, rows))\n+ for row in rows:\n+ table_file.write("\\t".join(row) + "\\n")\n+ # Write any notes\n+ if note != "":\n+ result_file.write("\\nNotes: {}\\n\\n".format(note))\n+\n+ # Write allignment output\n+ result_file.write("\\n\\nExtended Output:\\n\\n")\n+ make_aln(scheme, result_file, allele_matches, query_aligns, homol_aligns, sbjct_aligns)\n+\n+ # Close all files\n+ query_file.close()\n+ sbjct_file.close()\n+ table_file.close()\n+ result_file.close()\n+\n+if args.quiet:\n+ f.close()\n' |
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| diff -r 000000000000 -r 6dcb66689a7d pmlst/pmlst_db/.gitignore --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pmlst/pmlst_db/.gitignore Wed Aug 25 21:12:34 2021 +0000 |
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| @@ -0,0 +1,2 @@ +inc*.b +inc*.name |
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| diff -r 000000000000 -r 6dcb66689a7d pmlst/pmlst_db/INSTALL.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pmlst/pmlst_db/INSTALL.py Wed Aug 25 21:12:34 2021 +0000 |
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| @@ -0,0 +1,61 @@ +#!/usr/bin/python3 +import shutil, os, sys + +# This scripts installs the pMLST database for using KMA +# KMA should be installed before running this script +# The scripts assumes that it is placed together with the pMLST scheme fasta files +# First clone the repository: git clone https://bitbucket.org/genomicepidemiology/pmlst_db.git + +# Check if executable kma_index program is installed, if not promt the user for path + +interactive = True +if len(sys.argv) >= 2: + kma_index = sys.argv[1] + if "non_interactive" in sys.argv: + interactive = False +else: + kma_index = "kma_index" + +while shutil.which(kma_index) is None: + if not interactive: + sys.exit("KMA index program, {}, does not exist or is not executable".format(kma_index)) + ans = input("Please input path to executable kma_index program or enter 'q'/'quit' to exit:") + if ans == "q" or ans == "quit": + print("Exiting!\n\n \ + Please install executable KMA programs in order to install this database.\n\n \ + KMA can be obtained from bitbucked:\n\n\ + git clone https://bitbucket.org/genomicepidemiology/kma.git\n\n\ + KMA programs must afterwards be compiled:\n\n\ + gcc -O3 -o kma KMA.c -lm -lpthread\n\ + gcc -O3 -o kma_index KMA_index.c -lm") + sys.exit() + + kma_index = ans + + if shutil.which(kma_index) is None: + print("Path, {}, is not an executable path. Please provide absolute path\n".format(ans)) + + +# Index databases + + +# Use config_file to go through database files +dirname = os.path.dirname(sys.argv[0]) + +config_file = open(os.path.join(dirname, "config"), "r") +for line in config_file: + if line.startswith("#"): + continue + else: + line = line.rstrip().split("\t") + scheme = line[0] + f = os.path.join(dirname, scheme) + ".fsa" + if not os.path.isfile(f): + sys.exit("Database file '{}' does not exists".format(f)) + # for each dir index the fasta files + os.system("{} -i {} -o {}".format(kma_index, f, os.path.join(dirname, scheme))) + +config_file.close() + +print("Done") + |
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| diff -r 000000000000 -r 6dcb66689a7d pmlst/pmlst_db/config --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pmlst/pmlst_db/config Wed Aug 25 21:12:34 2021 +0000 |
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| @@ -0,0 +1,11 @@ +# Database configuration file - Describes the content of the database +# Each db consist of 3 files with the following extensions: fsa, clpx, txt.clean +# Other important files are: noGenes.txt +#db_prefix name allele_lst +incac IncA/C PMLST repA,parA,parB,A053 +incf IncF RST FII,FIC,FIIK,FIIS,FIIY,FIA,FIB +inchi1 IncHI1 MLST HCM1_043,HCM1_064,HCM1_099,HCM1_116,HCM1_178ac,HCM1_259 +inchi2 IncHI2 DLST smr0018,smr0199 +inci1 IncI1 MLST repI1,ardA,trbA,sogS,pilL +incn IncN MLST repN,traJ,korA +pbssb1-family pBSSB1-family higB,mqsA,soj |
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| diff -r 000000000000 -r 6dcb66689a7d pmlst/pmlst_db/incac.fsa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pmlst/pmlst_db/incac.fsa Wed Aug 25 21:12:34 2021 +0000 |
| b |
| b'@@ -0,0 +1,436 @@\n+>repA_1\n+AAGAGAACCAAAGACAAAGACCTGGAGAAACTCGACGTAATCAAAGACTCACCGCAAATG\n+AGCCTGTTTGAGATCATTGAATCTCCGGCCAAGAAAGACGACTACTCCAACACCATCGAG\n+ATCTACGATGCGCTGCCGAAGTACATTTGGGACCAAAAGCGTGAGCATGAAGATTTATCC\n+AACGCTGTAGTGACACGACAATGCACCATCAGAGGCCAGCATTTCACGGTGAAGGTGAAG\n+CCAGCCATCATCGAGAAGGATGACGGAAGAACCGTGCTGATCTACGCGGGACAGCGAGAG\n+GAAATCCTTGAGGATGCTCTACGCAAGCTCGCAGTGAACGGGAAAGGCCATATCATCGAG\n+GGCAAGGCTGGAGTCATGTTCACTCTGTACGAACTCCAGAAAGAGCTCTCGAAGATGGGT\n+CACGGTTACAACCTGAACGAAATCAAGGAAGCAATCCAGGTTTGTCGTGGCGCAACACTC\n+GAATGTATCAGTGATGACGGCGAAGCCTTCATCAGCTCCAGCTTCTTCCCGATGGTGGGA\n+CTTACCACCAGAGGTGAGTTTCGCAAGAAAGGCGGGAACGCCAGGTGCTATGTGCAGTTC\n+AACCCGCTGGTAAACGAATCGATCATGAATCTGTCGTTTCGTCAGTACAACTACAAAATC\n+GGAATGCAAATCCGCTCCCCTCTTGCACGGTACATCTACAAGCGAATGAGCCACTACTGG\n+ACTCAAGCATCGCCAGATTCGCCGTACACGCCATCGCTTATCAGCTTCCTGACACAGAGC\n+CCTCGTGAATTGAGCCCACGGATGCCGGAGAACGTCAGAGCTATGAAGCTCGCTCTGGAG\n+GCCCTCATCAAACAAGAGGTCATAAGCGACTACGACGCGAACCAGATCAAGGATGGCCGC\n+AGAGTCATCGACGTGCGGTACGTCATAAGGCCTCATGAGAACTTCGTGAAGCAGGTGATG\n+GCGTCCAACAAGCGTAAGCAGC\n+>repA_2\n+AAGAGAACCAAAGACAAAGACCTGGAGAAACTCGACGTAATCAAAGACTCACCGCAAATG\n+AGCCTGTTTGAGATCATTGAATCTCCGGCCAAGAAAGACGACTACTCCAACACCATCGAG\n+ATCTACGATGCGCTGCCGAAGTACATTTGGGACCAAAAGCGTGAGCATGAAGATTTATCC\n+AACGCTGTAGTGACACGACAATGCACCATCAGAGGCCAGCATTTCACGGTGAAGGTGAAG\n+CCAGCCATCATCGAGAAGGATGACGGAAGAACCGTGCTGATCTACGCGGGACAGCGAGAG\n+GAAATCCTTGAGGATGCTCTACGCAAGCTCGCAGTGAACGGGAAAGGCCATATCATCGAG\n+GGCAAGGCTGGAGTCATGTTCACTCTGTACGAACTCCAGAAAGAGCTCTCGAAGATGGGT\n+CACGGGTACAACCTGAACGAAATCAAGGAAGCAATCCAGGTTTGTCGTGGCGCAACACTC\n+GAATGTATCAGTGATGACGGTGAAGCCTTCATCAGCTCCAGCTTCTTCCCGATGGTGGGA\n+CTGACCACCAGAGGTGAGTTTCGCAAGAAAGGCGGGAACGCCAGGTGCTATGTGCAGTTC\n+AACCCGCTGGTAAACGAATCGATCATGAATCTGTCGTTTCGTCAGTACAACTACAAAATC\n+GGAATGCAAATCCGCTCCCCTCTTGCACGGTACATCTACAAGCGAATGAGCCACTACTGG\n+ACTCAAGCATCACCAGATTCGCCGTACACGCCATCGCTTATCAGCTTCCTGACCCAGAGC\n+CCTCGTGAATTGAGCCCACGGATGCCGGAGAACGTCAGAGCCATGAAGCTCGCTCTGGAG\n+GCCCTCATCAAACAAGAGGTCATAAGCGACTACGACGCGAACCAGATCAAGGATGGCCGC\n+AGAGTCATCGACGTGCGGTACGTCATAAGGCCTCATGAGAACTTCGTGAAGCAGGTGATG\n+GCGTCCAACAAGCGTAAGCAGC\n+>repA_3\n+AAGAGAACCAAAGACAAAGACCTGGAGAAACTCGACGTAATCAAAGACTCACCGCAAATG\n+AGCCTGTTTGAGATCATTGAATCTCCGGCCAAGAAAGACGACTACTCCAACACCATCGAG\n+ATCTACGATGCGCTGCCGAAGTACATTTGGGACCAAAAGCGTGAGCATGAAGATTTATCC\n+AACGCTGTAGTGACACGACAATGCACCATCAGAGGCCAGCATTTCACGGTGAAGGTGAAG\n+CCAGCCATCATCGAGAAGGATGACGGAAGAACCGTGCTGATCTACGCGGGACAGCGAGAG\n+GAAATCCTTGAGGATGCTCTACGCAAGCTCGCAGTGAACGGGAAAGGCCATATCATCGAG\n+GGCAAGGCTGGAGTCATGTTCACTCTGTACGAACTCCAGAAAGAGCTCTCGAAGATGGGT\n+CACGGGTACAACCTGAACGAAATCAAGGAAGCAATCCAGGTTTGTCGTGGCGCAACACTC\n+GAATGTATCAGTGATGACGGTGAAGCCTTCATCAGCTCCAGCTTCTTCCCGATGGTGGGA\n+CTGACCACCAGAGGTGAGTTTCGCAAGAAAGGCGGGAACGCCAGGTGCTATGTGCAGTTC\n+AACCCGCTGGTAAACGAATCGATCATGAATCTGTCGTTTCGTCAGTACAACTACAAAATC\n+GGAATGCAAATCCGCTCCCCTCTTGCACGGTACATCTACAAGCGAATGAGCCACTACTGG\n+ACTCAAGCATCACCAGATTCGCCGTACACGCCATCGCTTATCAGCTTCCTGACCCAGAGC\n+CCTCGTGAATTGAGCCCACGGATGCCGGAGAACGTCAGAGCCATGAAGCTCGCTCTGGAG\n+GCCCTCATCAAACAAGAGGTCATAAGCGACTACGACGCGAACCAGATCAAGGATGGCCGC\n+AGAGTCATCGACGTGCGGTACGTCATAAGACCTCATGAGAACTTCGTGAAGCAGGTGATG\n+GCGTCCAACAAGCGTAAGCAGC\n+>repA_4\n+AAGAGAACCAAAGACAAAGACCTGGAGAAACTCGACGTAATCAAAGACTCACCGCAAATG\n+AGCCTGTTTGAGATCATTGAATCTCCGGCCAAGAAAGACGACTACTCCAACACCATCGAG\n+ATCTACGATGCGCTGCCTAAGTACATTTGGGACCAAAAGCGTGAGCATGAAGATTTGTCC\n+AACGCTGTAGTGACGCGACAATGCTCCATCAGAGGCCAGCAGTTCACGGTGAAGGTGAAG\n+CCAGCCATCATCGAGAAGGATGACGGAAGAACTGTGCTGATCTACGCGGGACAGCGAGAG\n+GAAATCCTTGAGGATGCTCTACGAAAGCTCGCAGTGAACGGGAAAGGCCATATCATCGAG\n+GGCAAGGCTGGAGTCATGTTCACTCTGTACGAACTCCAGAAAGAGCTCTCGAAGATGGGT\n+CACGGGTACAACCTGAACGAAATCAAGGAAGCAATCCAGGTTTGTCGTGGCGCAACACTC\n+GAATGTATCAGTGATGACGGTGAAGCCTTCATCAGCTCCAGCTTCTTCCCGATGGTGGGA\n+CTGACCACCAGAGGTGAGTTTCGCAAGAAAGGCGGGAACGCCAGGTGCTATGTGCAGTTC\n+AACCCGCTGGTAAACGAATCGATCATGAATCTGTCGTTTCGTCAGTACAACTACAAAATC\n+GGAATGCAAATCCGCTCCCCTCTTGCACGGTACATCTACAAGCGAATGAGCCACTACTGG\n+ACTCAAGCATCACCAGATTCGCCGTACACGCCATCGCTTATCAGCTTCCTGACCCAGAGC\n+CCTCGTGAATTGAGCCCACGGATGCCGGAGAACGTCAGAGCCATGAAGCTCGCTCTGGAG\n+GCCCTCATCAAACAAGAGGTCATAAGCG'..b'GTTGATCGAAAACATCCAGCGGGATGATTTGACTCCGGTAGAGATTGCCGAGGCGT\n+TAAACCTGTTTATTGAAGAAGGTTGGAAACAAAAGGATATTGCTGATCGTCTTGGTAAGA\n+ATATCACTTTCGTATCTACGCATCTGTCGTTGCTCAAGCTACCTGACTGTGTGCGTGAGT\n+TGTACGATAATGAAGTATGTTCTGATACAGAAACCTTGAACAATCTCCGTCTTCTGTTTG\n+AGCTTAACGAAGAAAGATGTCGCGCCGTCTGCGCTGTAGCTATGTCTGACGGGATTACCC\n+GTAAACAAAGCCGTGAGATGTTGAATGATGCCAAACGCATCAAAGAAGAAATGGAAAAAG\n+GTCCTCTGACGGGCCCCGACCAGAATGATAAACCTGGCGCTGGTAACACCGACGAGCAAG\n+CCATTAACTCTGGGAGTGGCACATCGGTACATATCGGAAATGGCGGCCAGAGCCCTGCCA\n+ACATGGAACTGGAAGGGGGGGCAAATCTCGGTGGTCAGGGCGATGATGACCAAGACCATT\n+TTCTTGACGAAGAGGGTAAGGGAAAAGCTCCTGTCCAGCAGCCAGTTAACAATGGTAAGA\n+GCAAAAATGAAGAAGGCGGCGATGCTCTTCCTCCTCTGCCGAAGGATAAGGAATGGAAGA\n+ACGTCAGGGCTGATAGTTTGATTTTTGCTGTCAACGTTAATCTGGATGGCGAGACCAAAC\n+GTGGAGTCATCATGACTGACCGTGTTGCTCTGGTTCCGGCTACAGTCTGGGTTAAAACGC\n+TCGATGGCGAAGGCAAGGAAAAGCACGTTCATGTGCCTGTGTCAG\n+>parB_8\n+TGTCCGAACTTGCTAAAGCCGCCAAAGGCAAGAAAGGCAAAGAGGTTCTTACCGTCCCTG\n+TTGACGACGTTGTTTCCAAGGTACAGGTGCGTAAGCGCTTCCGTAACATTGAAGATCTGG\n+CGGCCACCTTGCTGACCGAAGGGCAGCAGTCTCCGATCATCGTGTTTCCGAAGAACGAAG\n+AAGGCAAGTTCGTTATCCAGAAAGGGGAGCGGCGTTGGAGGGCTTGTAAACACGCTGGTA\n+TTGAGACTATCGACCTGGTGGTTAATGATAAGGTCCAGAACAACCTGGACGAGACTGCTG\n+GTGAGTTGATCGAAAACATCCAGCGGGATGATTTGACTCCGGTAGAGATTGCCGAGGCGT\n+TAAACCTGTTTGTTGAAGAAGGTTGGAAACAAAAGGATATTGCTGATCGTCTTGGTAAGA\n+ATATCACTTTCGTATCTACGCATCTGTCGTTGCTCAAGCTACCTGACTGTGTGCGCGAGT\n+TGTACGATAATGAAGTATGTTCTGATACAGAAACCTTGAACAATCTCCGTCTTCTGTTTG\n+AGCTTAACGAAGAAAGATGTCGCGCCGTCTGCGCTGTAGCTATGTCTGACGGGATTACCC\n+GTAAACAAAGCCGTGAGATGTTGAATGATGCCAAACGCATCAAAGAAGAAATGGAAAAAG\n+GTCCTCTGACGGGCTCCGACCAGAATGATAAACCTGGCGCTGGTAACACCGACGAGCAAG\n+CCATTAACTCTGGGAGTGGCACATCGGTACATATCGGAAATGGCGACCAGAGCCCTGCCA\n+ACATGGAACTGGAAGGGGGGGCAAATCTCGGTGGTCAGGGCGATGATGACCAAGACCATT\n+TTCTTGACGAAGAGGGTAAGGGCAAAACTCCTGTCCGGCAGCCAGTTAACAATGGTAAGA\n+GCAAAGATGAAGAAGGTGGCGATGCTCTTCCTCCTCTGCCGAAGGATAAGGAATGGAAGA\n+ACGTCAGGGCTGATAGTTTGATTTTTGCTGTCAACGTTAATCTGGATGGCGAGACCAAAC\n+GTGGAGTCATCATGACCGACCGTGTTGCTCTGGTTCCGGCTACAGTCTGGGTTAAAACGC\n+TCGATGGCGAAGGCAAGGAAAAGCACGTTCATGTGCCTGTGTCAG\n+>parB_9\n+TGTCCGAACTTGCTAAAGCCGCCAAAGGCAAGAAAGGCAAAGAGGTTCTTACCGTCCCTG\n+TTGACGACGTTGTTTCCAAGGTACAGGTGCGTAAGCGCTTCCGTAACATTGAAGATCTGG\n+CGGCCACCTTGCTGACCGAAGGGCAGCAGTCTCCGATCATCGTGTTTCCGAAGAACGAAG\n+AAGGCAAGTTCGTTATCCAAAAGGGGGAGCGGCGTTGGAGGGCTTGTAAACACGCTGGTA\n+TTGAGACTATCGACCTGGTGGTTAATGATAAGGTCCAGAACAACCTGGACGAGACTGCTG\n+GTGAGTTGATCGAAAACATCCAGCGGGATGATTTGACTCCGGTAGAGATTGCCGAGGCGT\n+TAAACCTGTTTATTGAAGAAGGTTGGAAACAAAAGGATATTGCTGATCGTCTTGGTAAGA\n+ATATCACTTTCGTATCTACGCATCTGTCGTTGCTCAAGCTACCTGACTGTGTGCGTGAGT\n+TGTACGATAATGAAGTATGTTCTGATACAGAAACCTTGAACAATCTCCGTCTTCTGTTTG\n+AGCTTAACGAAGAAAGATGTCGCGCCGTCTGCGCTGTAGCTATGTCTGACGGGATTACCC\n+GTAAACAAAGCCGTGAGATGTTGAATGATGCCAAACGCATCAAAGAAGAAATGGAAAAAG\n+GTCCTCTGACGGGCCCCGACCAGAATGATAAACCTGGCGCTGGTAACACCGACGAGCAAG\n+CCATTAACTCTGGGAGTGGCACATCGGTACATATCGGAAATGGCGGCCAGAGCCCTGACA\n+TCATGGAACTGGAAGGGGGGGCAAATCTCGGTGGTCAGGGCGATGATGACCAAGACCATT\n+TTCTTGACGAAGAGGGTAAGGGAAAAGCTCCTGTCCAGCAGCCAGTTAACAATGGTAAGG\n+GCAAAAATGAAGAAGGCGGCGATGCTCTTCCTCCTCTGCCGAAGGATAAGGAATGGAAGA\n+ACGTCAGGGCTGATAGTTTGATTTTTGCTGTCAACGTTAATCTGGATGGCGAGACCAAAC\n+GTGGAGTCATCATGACTGACCGTGTTGCTCTGGTTCCGGCTACAGTCTGGGTTAAAACGC\n+TCGATGGCGAAGGCAAGGAAAAGCACGTTCATGTGCCTGTGTCAG\n+>A053_1\n+AGATCTCACAGGACATGAAAAGAAAATTTGCTTTGGTGAATGCCCTGTCTAAAACGGAGA\n+AGCCAAGTCTCCAAGACCTTCACAAGGCAACAAATATTCCTGAATCAACGATCAAGAGAC\n+AGTTGTCTGCCCTGCGTGATGAGTTCGGAATGAATATCTTGTTCGTCAGGGAGTCTACCG\n+GCGAACGAGGTGCCACCGGCTACTACATGCTGACAGACTGGGGGATCTTAGACAGGTCTT\n+CGTTCTTGAA\n+>A053_2\n+AGATCTCACAGGACATGAAAAGAAAATTTGCTTTGGTGAATGCCCTGTCTAAAACGGAGA\n+AGCCAAGTCTCCAGGACCTTCACAAGGCAACAAATATTCCTGAATCAACGATCAAGAGAC\n+AGTTGTCTGCCCTGCGTGATGAGTTCGGAATGAATATCTTGTTCGTCAGGGAGTCTACCG\n+GCGAACGAGGTGCCACCGGCTACTACATGCTGACAGACTGGGGGATCTTAGACAGGTCTT\n+CGTTCTTGAA\n+>A053_3\n+AGATCTCACAGGACATGAAAAGAAAATTTGCTTTGGTGAATGCCCTGTCTAAAACGGAGA\n+AGCCAAGTCTCCAGGACCTTCACAAGGCAACAGAAATTCCTGAATCAACGATCAAGAGAC\n+AGTTGTCTGCTCTGCGTGATGAGTTCGGAATGAATATATTGTTCGTCAGGGAGTCTACCG\n+GCGAACGGGGGGCCACCGGCTACTATATGCTGACAGACTGGGGGATCTTAGACAGGTCTT\n+CGTTCTTGAA\n' |
| b |
| diff -r 000000000000 -r 6dcb66689a7d pmlst/pmlst_db/incac.txt.clean --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pmlst/pmlst_db/incac.txt.clean Wed Aug 25 21:12:34 2021 +0000 |
| b |
| @@ -0,0 +1,15 @@ +ST repA parA parB A053 +1 1 1 1 1 +2 2 1 1 1 +3 2 2 2 1 +4 2 2 3 1 +5 2 2 4 1 +6 2 2 5 1 +7 2 3 2 1 +8 2 4 2 1 +9 3 2 2 1 +10 4 5 6 2 +11 5 6 7 3 +12 6 7 8 3 +13 7 8 9 3 + |
| b |
| diff -r 000000000000 -r 6dcb66689a7d pmlst/pmlst_db/incf.fsa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pmlst/pmlst_db/incf.fsa Wed Aug 25 21:12:34 2021 +0000 |
| b |
| b'@@ -0,0 +1,1468 @@\n+>FII_1\n+CAAAAACCCCGATAATCTTCACCAGGTTTGGCGACTAAGAGAAGATTACCGGGGCTAACA\n+AGAAACTGCATAGAAGCTGTTGCTCTATGCGGGGAGTATAGTTATATGACCGGAAAAGTT\n+CAAGACTTCTTTCTGTGCTCACTCCTTCTGTGCAACA\n+>FII_2\n+CAAAAACCCCGATAATCTTCTTCAACTTTGGCGAGTACGAAAAGATTACCGGGGCCCACT\n+TAAACCGTATAGCCAACAATTCAGCTATGCGGGGAGTATAGTTATATGCCCGGAAAAGTT\n+CAAGACTTCTTTCTGTGCTCGCTCCTTCTGCGCATTG\n+>FII_3\n+CGAAAACCCCGATAATCTTTCTATGTTTGGCGACGAAGAAGATTACCGGGGCCATCTAAA\n+AACCGCATAGAAGCTGTTGCTCTATGCGGGGAGTATAGTTATATGCCCGGAAAAGTTCAA\n+GACTTCTTTCTGTGCTCACTCCTTCTGTGCAACA\n+>FII_4\n+TGAAAACCCCGATAATCTTCAGCAAGTTTGGCGACTGAGAAGAAGATTAACGGGGCTAAC\n+AAGAAACCGCATAGAAGCTGTTGCTCTATGCGGGGAGTATAGTTATATGCCCGGAAAAGT\n+TCAAGACTTCTTTCTGTGCTCACTCCTTCTGTGCAACA\n+>FII_5\n+TGAAAACCCCGATAATCTTCAGCAAGTTTGGCGACTAAGAGAAGATTAACGGGGCTAACA\n+AGAAACCGCATAGAAGCTGTTGCTCTATGCGGGGAGTATAGTTATATGCCCGGAAAAGTT\n+CAAGACTTCTTTCTGTGCTCACTCCTTCTGTGCAACA\n+>FII_6\n+TGAAAACCCCGATAATCTTCAGTAAGTTTGGCGACTGAGAAGATTACCGGGGCTAACAAG\n+AAACTGCATAGAAGCTGTTGCTCTATGCGGGGAGTATAGTTATATGCCCGGAAAAGTTCA\n+AGACTTCTTTCTGTGCTCACTCCTTCTGTGCAACA\n+>FII_7\n+TGAAAACCCCGATAATCTTCTTTAACTTTGGCGAGTGAGAAAGATTATCGGGGCTAACAA\n+GAAACTGCATAGAAGCGGTTGCTCTATGCGGGGAGTATAGTTATATGCCCGGAAAAGTTC\n+AAGACTTCTTTCTGTGCTCACTCCTTCTGTGCAACA\n+>FII_8\n+TGAAAACCCCGATAATCTTCTTCAAGTTTGGCGACTAGAAAGATTACCGGGGCCATCTAA\n+AAACCGTATAGCCAACAATTCAGCTATGCGGGGAGTATAGTTATATGCCCGGAAAAGTTC\n+AAGACTTCTTTCTGTGCTCACTCCTTCTGCGCATTG\n+>FII_9\n+TGAAAACCCCGATAATCTTCTTCAAGTTTGGCGACATGAAAGATTACCGGGGCCATCTAA\n+AAACCGTATAGCCAACAATTCAGCTATGCGGGGAGTATAGTTATATGCCCGGAAAAGTTC\n+AAGGCTTCTTTCTGTGCTCACTCCTTCTGCGCATTG\n+>FII_10\n+TGAAAACCCCGATAATCTTCTTCAAGTTTGGCGACATGAAAGATTACCGGGGCCATCTAA\n+AAACCGTATAGCCAACAATTCAGCTATGCGGGGAGTATAGTTATATGCCCGGAAAAGTTC\n+AAGACTTCTTTCTGTGCTCACTCCTTCTGCGCATTG\n+>FII_11\n+CGAAAACCCCGATAATCTTCTTCAAGTTTGGCGACATGAAAGATTACCGGGGCCATCTAA\n+AAACCGTATAGCCAACAATTCAGCTATGCGGGGAGTATAGTTATATGCCCGGAAAAGTTC\n+AAGACTTCTTTCTGTGCTCACTCCTTCTGCGCATTG\n+>FII_12\n+TGAAAACCCCGATAATCTTCTTCAAGTTTGGCGACTAGAAAGATTACCGGGGCTAACAAG\n+AAACCGTATAGCCAACAATTCAGCTATGCGGGGAGTATAGTTATATGCCCGGAAAAGTTC\n+AAGACTTCTTTCTGTGCTCACTCCTTCTGCGCATTG\n+>FII_13\n+CAAAAACCCCGATAATCTTCTTTAACTTTGGCGAGTACAGAAAGATTACCGGGGCCATCT\n+AAAAACCGTATAGCCAACAATTCAGCTATGCGGGGAGTATAGCTATATGCCCGGAAAAGT\n+TCAAGACTTCTTTCTGTGCTCACTCCTTCTGCGCATTG\n+>FII_14\n+CGAAAACCCCGATAATCTTCTCTAACTTTGGCGAGTGCAGAAAGATTACCGGGGCCATCT\n+AAAAACCGTATAGCCAACAATTCAGCTATGCGGGGAGTATAGTTATATGCCCGGAAAAGT\n+TCAAGACTTCTTTCTGTGCTCGCTCCTTCTGCGCATTG\n+>FII_15\n+TGAAAACCCCGATAATCTTCTCTAACTTTGGCGAGTACAGAAAGATTACCGGGGCCATCT\n+AAATACCGTATAGCCAACAATTCAGCTATGCGGGGAGTATAGTTATATGCCTGGAAAAGT\n+TCAAGACTTCTTTCTGTGCACACTCCTTCTGCGCATTG\n+>FII_16\n+TGAAAACCCCGATAATCTTCTTTAACTTTGGCGAGTGAGAAAGATTACCGGGGCCATCTA\n+AAAACCGTATAGCCAACAATTCAGCTATGCGGGGAGTATAGTTATATGCCCGGAAAAGTT\n+CAAGACTTCTTTCTGTGCTCACTCCTTCTGCGCATTG\n+>FII_17\n+TGAAAACCCCGATAATCTTCTTTAACTTTGGCGAGTCAGAAAGATTACCGGGGCCATCTA\n+AAAACCGTATAGCCAACAATTCAGCTATGCGGGGAGTATAGTTATATGCCCGGAAAAGTT\n+CAAGACTTCTTTCTGTGCTCACTCCTTCTGCGCATTG\n+>FII_18\n+CGAAAACCCCGATAATCTTCTTCAAGTTTGGCGACTAGAAAGATTACCGGGGCCCCATAA\n+AACCGCATAGCCAACAATTCAGCTATGCGGGGAGTATAGTTATATGCCCGGAAAAGTTCA\n+AGACTTCTTTCTGTGCTCACTCCTTCTGTGCATTG\n+>FII_19\n+TGAAAACCCCGATAATCTTCTTCAAGTTTGGCGACTAGAAAGATTACCGGGGCCTCATAA\n+AACCGTATAGCCAACAATTCAGCTATGCGGGGAGTATAGTTATATGCCTGGAAAAGTTCA\n+AGACTTCTTTCTGTGCTCACTCCTTCTGCGCATTG\n+>FII_20\n+CAAAAACCCCGATAATCTTCGAGAAGTTTGGCGACTAAGAGAAGATTACCGGGGCCCCAT\n+AAAACCGCATAGCCAACAATTCAGCTATGCGGGGAGTATAGTTATATGCCCGGAAAAGTT\n+CAAGACTTCTTTCTGTGCTCACTCCTTCTGCGCATTG\n+>FII_21\n+CAAAAACCCCGATAATCTTCTCAAAGTTTGGCGACTAGAAAGATTACCGGGGCCCACTTA\n+AACCGTATAGCCAACAATTCAGCTATGCGGGGAGTATAGTTATATGCCCGGAAAAGTTCA\n+AGACTTCTTTCTGTGCTCACTCCTTCTGCGCATTG\n+>FII_22\n+TAAAAACCCCGATAATCTTCACCAGGTTTGGCGACTAAGAGAAGATTACCGGGGCCCACT\n+TAAACCGTATAGCCAACAATTCAGCTATGCGGGGAGTATAGTTATATGCCCGGAAAAGTT\n+CAAGACTTCTTTCTGTGCTCACTCCTTCTGCGCATTG\n+>FII_23\n+CAAAAACCCCGATAATCTTCAGAAAGTTTGGCGACTGAGAAGATTACCGGGGCCCACTTA\n+AACCGTATAGCCAACAATTCAGCTATGCGGGGAGTATAGTTATATGCTCGGAAAAGTTCA\n+AGACTTCTTTCTGTGCTCGCTCCTTCTGCGCATTG\n+>FII_24\n+CAAAAACCCCGATAATCTTCGTCAAGTTTGGCGACTGC'..b'TGCCTTTTGTCGAGTTTGCAAAAC\n+TGTGTGGTATACC\n+>FIB_69\n+ATTCAGACATCAAAAAACTGTTCGGCGAGGTGGATAAGTCGTCCGGTGAGCTGGTGACAC\n+TGACACCAAACAATAACAACAGCGTACAACCTGTGGCGCTGATGCGTCTGGGCGTCTTTG\n+TACCGACCCTTAAGTCACTGAAGAACAGTAAAAAAAATACACTGTCACGCACCGATGCCA\n+CGGAAGAACTGACGCGTCTTTCTCTGGCCCGTGCAGAAGGATTCGATAAGGTTGAGATCA\n+CCGGCCCCCGGCTGGATATGGATAACGATTTCAAGACCTGGGTGGGGATCATTCATTCCT\n+TTGCCCGCCATAACGTGATTGGTGACAAAGTTGAACTGCCTTTTGTTGAGTTTGCAAAAC\n+TGTGTGGTATACC\n+>FIB_70\n+ATCTGGACTTAAAAAAGTTGTTTGAAGAGGTGGATAAATCCTCCGGTGAAGTCGTAAATC\n+TCACTCCTAATGCCAGTAATACAGTGCAGCCAGTGGCACTGATGCGGCTCGGAGTGTTTG\n+TCCCTACTCTCAAATCACTGAAAAACAGTAAAAAGAACACGCTTTCGCGTACTGATGCGA\n+CGGAAGAACTGACGCGTCTATCTCTCGCCAGAGCCGAAGGGTTTGATAAGGTGGAGATCA\n+CCGGTCCCCGCCTGGATATGGATAATGACTTCAAGACCTGGGTAGGGGTGATCCATTCCT\n+TTGCACGCCATAAGGTTATCGGCGATAAGGTTGAACTGCCGTTTGTTGAGTTCGCCAAAC\n+TCTGTGGGATCCC\n+>FIB_71\n+TTCAGACATCAAAAAACTGTTCGGCGAGGTGGATAAGTCGTCCGGTGAGCTGGTGACACT\n+GACACCAAACAATAACAACACCGTACAACCTGTGGCGCTGATGCGTCTGGGCGTCTTTGT\n+ACCGACCCTTAAGTCACTGAAGAACAGTAAAAAAAATACTCTGTCACGCACCGATGCCAC\n+GGAAGAACTGACGCGTCTTTCCCTGGCCCGTGCAGAAGGATTCGATAAGGTTGAGATCAC\n+CGGCCCCCGGCTGGATATGGATAACGATTTCAAGACCTGGGTGGGGATTATTCATTCCTT\n+TGCCCGCCATAACGTGATTGGTGACAAAGTTGAACTGCCTTTTGTCGAGTTTGCAAAACT\n+GTGTGGTATACC\n+>FIB_72\n+ATTCAGACATCAAAAAACTGTTCGGCGAGGTGGATAAGTCGTCCGGTGAGCTGGTGACAC\n+TGACACCAAACAATAACAACACCGTACAACCTGTGGCGCTGATGCGTCTGGGCGTCTTTG\n+TACCGACCCTTAAGTCACTGAAGAACAGTAAAAAAAATACACTGTCACGCACCGATGCCA\n+CGGAAGAACTGACGCGTCTTTCTCTGGCCCGTGCAGAAGGATTCGATAAGGTTGAGATCA\n+CCGGCCCCCGCCTGGATATGGATAACGATTTCAAGACCTGGGTGGGGATCATTCATTCCT\n+TTGCCCGCCATAACGTGACTGGTGACAAAGTTGAACTGCCTTTTGTCGAGTTTGCAAAAC\n+TGTGTGGTATACC\n+>FIB_73\n+ATTCAGACATCAAAAAACTGTTCGGCGAGGTGGATAAGTCGTCCGGTGAACTGGTGACAC\n+TGACACCAAACAATAACAACACCGTACAACCTGTGGCGCTGATGCGTCTGGGCGTTTTTG\n+TACCGACCCTTAAATCACTGAAGAACAGTAAAAAAAATACACTGTCACGTACTGATGCCA\n+CGGAAGAGCTGACACGTCTTTCCCTGGCCCGTGCTGAGGGATTCGATAAGGTTGAGATCA\n+CTGGCCCCCGCCTGGATATGGATAACGATTTCAAGACCTGGGTAGGGATCATTCATTCCT\n+TTGCCCGCCATAACGTGATTGGTGACAAAGTTGAACTGCCTTTTGTTGAGTTTGCAAAAC\n+TGTGTGGTATACC\n+>FIB_74\n+ATTCAGACATCAAAAAACTGTTCGGCGAGGTGGATAAGTCGTCCGGTGAGCTGGTGACAC\n+TGACACCAAACAATAACAACACCGTACAACCTGTGGCGCTGATGCGTCTGGGCGTCTTTG\n+TACCTACCCTTAAGTCACTGAAGAACAGTAAAAAAAATACACTGTCACGCACCGATGCCA\n+CGGAAGAACTGACGCGTCTTTCTCTGGCCCGTGCAGAAGGATTCGATAAGGTTGAGATCA\n+CCGGCCCCTGGCTGGATATGGATAACGATTTCAAGACCTGGGTGGGGATCATTCATTCCT\n+TTGCCCGCCATAACGTGATTGGTGACAAAGTTGAACTGCCTTTTGTCGAGTTTGCAAAAC\n+TGTGTGGTATACC\n+>FIB_75\n+ATTCAGACATCAAAAAACTGTTCGGCGAGGTGGATAAGTCGTCCGGTGAGCTGGTGACAC\n+TGACACCAAACAATAACAACACCGTACAGCCTGTGGCGCTGATGCGTCTGGGCGTATTTG\n+TACCGACCCTTAAATCACTGAAGAATAGTAAAAAAAATACACTGTCACGCACCGATGCCA\n+CGGAAGAACTGACGCGTCTTTCCCTGGCCCGTGCAGAAGGATTCGATAAGGTTGAGATCA\n+CCGGCCCCCGGCTGGATATGGATAACGATTTCAAGACCTGGGTGGGGATCATTCATTCCT\n+TTGCCCGCCATAACGTGATTGGTGACAAAGTTGAACTGCCTTTTGTCGAGTTTGCAAAAC\n+TGTGTGGTATACC\n+>FIB_76\n+ATTCAGACATCAAAAAACTGTTCGGCGAGGTGGATAAGTCCTCCGGTGAGCTGGTGACAC\n+TGACACCAAACAATAACAACACCGTACAACCTGTGGCGCTGATGCGTCTGGGCGTTTTTG\n+TACCGACCCTTAAATCACTGAAGAACAGTAAAAAAAATACACTGTCACGTACTGATGCCA\n+CGGAAGAGCTGACACGTCTTTCCCTGGCCCGTGCTGAGGGATTCGATAAGGTTGAGATCA\n+CCGGCCCCCGCCTGGATATGGATAACGATTTCAAGACCTGGGTGGGGATCATTCATTCCT\n+TTGCCCGCCATAACGTGATTGGTGACAAAGTTGAACTGCCTTTTGTTGAGTTTGCAAAAC\n+TGTGTGGTATACC\n+>FIB_77\n+ATTCAGACATCAAAAAACTGTTCGGCGAGGTGGATAAGTCGTCCGGTGAGCTGGTGACAC\n+TGACACCAAACAATAACAACACCGTACAACCTGTGGCGCTGATGCGTCTTGGCGTCTTTG\n+TACCGACCCTTAAGTCACTGAAGAACAGTAAAAAAAATACACTGTCACGCACTGATGCCA\n+CGGAAGAACTGACGCGTCTTTCCCTGGCCCGTGCAGAAGGATTCGATAAGGTTGAGATCA\n+CCGGTCCCCGGCTGGATATGGATAACGATTTCAAGACCTGGGTGGGGATCATTCATTCCT\n+TTGCCCGCCATAACGTGACTGGTGACAAAGTTGAACTGCCTTTTGTCGAGTTTGCAAAAC\n+TGTGTGGTATACC\n+>FIB_78\n+ATTCAGACATCAAAAAACTGTTCGGCGAGGTGGATAAGTCGTCCGGTGAGCTGGTGACAC\n+TGACACCAAACAATAACAACACCGTACAACCTGTGGCGCTGATGCGTCTGGGCGTCTTTG\n+TACCGACCCTTAAGTCACTGAAGAACAGTAAAAAAAATACTCTGTCACGCACCGATGCCA\n+CGGAAGAACTGACGCGTCTTTCCCTGGCCCGTGCAGAAGGATTCGATAAGGTTGAGATCA\n+CCGGCCCCCGGCTGGATATGGATAATGATTTCAAGACCTGGGTGGGGATCATTCATTCCT\n+TTGCCCGCCATAACGTGATTGGTGACAAAGTTGAACTGCCTTTTGTCGAGTTTGCAAAAC\n+TGTGTGGTATACC\n' |
| b |
| diff -r 000000000000 -r 6dcb66689a7d pmlst/pmlst_db/incf.txt.clean --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pmlst/pmlst_db/incf.txt.clean Wed Aug 25 21:12:34 2021 +0000 |
| b |
| @@ -0,0 +1,1 @@ +ST FII FIC FIIK FIIS FIIY FIA FIB |
| b |
| diff -r 000000000000 -r 6dcb66689a7d pmlst/pmlst_db/inchi1.fsa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pmlst/pmlst_db/inchi1.fsa Wed Aug 25 21:12:34 2021 +0000 |
| b |
| b'@@ -0,0 +1,189 @@\n+>HCM1_043_1\n+GGCTGCTGAAGGCGCGTTGCAGAATGGCCAGCCCGTCCGCTATCTGGAAACCAAAGAAAG\n+CTCTCCGTATCTCATCGTACACCCTGACGCCTCACTGCCGTCGGTGACGCAAAACGTCTG\n+GATGCACGCTGATCATGATGGCTGGGAAGAGCATTTCAACGGAGAGACCGATGCCCTGAC\n+TCCAGAGATGAGCGAGCAGTTCCGCCAGCAGGTTTATGCACTGCTGACGCCGGAATCCCA\n+TACCACCTCTTCAGAAATGAGACTGACTTTGCAGGACTGGCAACTGGGTGAAGCCGAGAT\n+CCCAGAAGAAGACTGTCAGCCCTACCAGGTGAAGGTGTTAGCAGAAAATAA\n+>HCM1_043_2\n+GGCAGTTGATGAAGCTTTGCTGGATGGCCAGCCTGTCCGCTATCTGGAAACAAAAGAAAG\n+CTCCCCATATCTCATCGTACACCCTGACGACTCACTACCGTCTCTGACGCATAACGTTTG\n+GATGCACGCTGATCCTGATGGCTGGGAAGAACATTTCGATGGCGAGGACAATCCCCTGAT\n+GGAGGAGTTGAGCCAGCAGTTCCGCCAGCAGGTGTATGCGCTTCTGACGCCGGAATCGCA\n+GGCAACGCCTTCAGAGATTATCCGGACGTTACAGGACTGGCAACTGGGTGAAACCCAGCT\n+GCCAGAAGAAGACTGTCAGTCCTATCAGGTGAAGGTGTTGTTAGAAGAGAA\n+>HCM1_043_3\n+GGCTGCTGAAGGCGCGTTGCAGAATGGCCAGCCCGTCCGCTATCTGGAAACCAAAGAAAG\n+CTCTCCGTATCTCATCGTACACCCTGACGCCTCACTGCCGTCGGTGACGCAAAACGTCTG\n+GATGCACGCTGATCCTGATGGCTGGGAAGAGCATTTCAACGGAGAGACCGATGCCCTGAC\n+TCCAGAGATGAGCGAGCAGTTCCGCCAGCAGGTTTATGCACTGCTGACGCCGGAATCCCA\n+TACCACCTCTTCAGAAATGAGACTGACTTTGCAGGACTGGCAACTGGGTGAAGCCGAGAT\n+CCCAGAAGAAGACTGTCAGCCCTACCAGGTGAAGGTGTTAGCAGAAAATAA\n+>HCM1_064_1\n+GGTGGGAACTAAAGAGAAGCGATACAGAAATTTTGAGGTTGACGCTTCTGATGAGTTGTC\n+GAGCATGGAGCTGGCCCGTTCAGAAGGATACGATGACATTCGGATCACTGGTCTTAAGCT\n+TTCGATGTCAACCGATTTTAAGTGTTGGCTCGGTTGCATAATGGCGTTCAGCAAATATGG\n+TTTCGCTTCCGATAAAATCACATTGTCATTCAATGAGTTTGCAAAAATGTGTGGTATCAG\n+TTCTACAAACATAAACAAGCGAACTCGCTCACGATTTCAGGAGGCGCTAGCAAACCTAGC\n+TTCCGTTGTGATTTCTTTCCGTGATTCAAAAACTGAACGTTTTACTGTCACGCACCTTGT\n+GCAGAAAGCAGTGATTGATCCTAAGAAGGACACCGTAGAGTTGGTGGGCGATCCCTCAAT\n+GTGGGAGCTTTACCGGTATGATCATAAAACCTTACTTAGTTTGCAGGTGCTTTCGGTTCT\n+CGCTAAAAAAGAGGCAGCACAAAGCCTGTACATATATTTTGAGGCGA\n+>HCM1_064_2\n+GGTGGGAACTAAAGAGAAGCGATACAGAAATTTTGAGGTTGACGCTTCTGATGAGTTGTC\n+GAGCATGGAGCTGGCCCGTTCAGAAGGATACGATGACATTCGGATCACTGGTCTTAAGCT\n+TTCGATGTCAACCGATTTTAAGTGTTGGCTCGGTTGCATAATGGCGTTCAGCAAATATGG\n+TTTCGCTTCCGATAAAATCACATTGTCATTCAATGAGTTTGCAAAAATGTGTGGTATCAG\n+TTCTACAAACATAAACAAGCGAACTCGCTCACGATTTCAGGAGGCGCTAGCAAACCTAGC\n+TTCCGTTGTGATTTCTTTCCGTGATTCAAAAACTGAACGTTTTACTGTCACGCACCTTGT\n+GCAGAAAGCAGTGATTGATCCTAAGAAGGACACCGTAGAGTTGGTGGGCGATCCCTCAAT\n+GTGGGAGCTTTACCGGTATGATCATAAAACCTTACTTAGCTTGCAGGTGCTTTCGGTTCT\n+CGCTAAAAAAGAGGCAGCACAAAGCCTGTACATATATTTTGAGGCGA\n+>HCM1_064_3\n+GGTGGGAACTAAAGAGAAGCGATACAGAAATTTTGAGGTTGACGCTTCTGATGAGTTGTC\n+GAGCATGGAGCTGGCCCGTTCAGAAGGATACGATGACATTCGGATCACTGGTCTTAAGCT\n+TTCGATGTCAACCGATTTTAAGTGTTGGCTCGGTTGCATAATGGCGTTCAGCAAATATGG\n+TTTCGCTTCCGATAAAATCACATTGTCATTCAATGAGTTTGCAAAAATGTGTGGTATCAG\n+TTCTACAAACATAAACAAGCGAACTCGCTCACGATTTCAGGAGGCGCTAGCAAACCTAGC\n+TTCCGTTGTGATTTCTTTCCGTGATTCAAAAACTGAACGTTTTACTGTCACGCACCTTGT\n+GCAGAAAGCAGTGATTGATCCTAAGAAGGACACCGTAGAGTTGGTGGGCGATCCCTCAAT\n+GTGGGAGCTTTACCGGTATGATCATAAAACCTTACTTAGCTTGCAGGTGCTTTCGGTTCT\n+CGCTAAAAAAGAGGCAGCACAAAGTCTGTACATATATTTTGAGGCGA\n+>HCM1_064_4\n+GGTGGGAACTAAAGAGAAGCGATTCAGAAATTTTGAGGTTGATGCTTCTGATGAGTTGTC\n+GAGCATGGAACTGGCCCGGTCAGAAGGATACGATGACATCCGGATCACTGGCCTTAAGCT\n+TTCGATGTCCACGGACTTCAAGTGTTGGCTTGGGTGCATTATGGCGTTCAGTAAATATGG\n+ATTCGCCTCCGAGAAAATAACATTGTCGTTCAATGAGTTTGCAAAAATGTGTGGTATCAG\n+TTCTACAAATATCAACAAGCGAACCCGTTCACGATTTCAGGAAGCGCTGGCAAACCTCGC\n+GTCCGTTGTTATTTCTTTCCGTGATTCTAAAACTGAACGCTTCACTGTCACACACCTTGT\n+GCAGAAAGCTATGATTGACCCTAAGAAGGACACAGTAGAGCTCGTGGGTGATCCCTCGAT\n+GTGGGAGCTTTACCGGTATGATCATAAAACCCTATTAAGCTTACAGGTACTGTCGGTTCT\n+CGCCAAAAAAGAAGCTGCACAGAGCCTGTACATCTATTTTGAGGCAA\n+>HCM1_099_1\n+TGCAGGCAGTTATAGACCATACGCAGGCTATCCGCGCTCAGAGTAATAACTCGGAAGCAG\n+TTAACGACATCATTCGCAGACGTGATGAGATTCAGGGAAATTCACAGCTCAGCGAGTCTG\n+CACTGAAATCCGTCGAAAATAAACCAGAAGTTATGCGCAGTCAGTCTTCGAATATCGAAA\n+AGATGTTTGGTTCATCAGGAATCACCGCCGCTGACTTCGAGCGTAAAATAGACAGCAGTC\n+GGGAAGAGGTGCTCTCGACAGAAAACGGTATCACTATCTTTGCGTCATTTAGCTTGCCTG\n+ATTACGTCCTGGAAGATCTACTCCGTACCGCGTCAGAACATAAGGCGAGAGTGGTTTTTA\n+ATGGTCTGAAGAAAGGCACTACACGCCTCCCTGAAACTCAGGCAGCTATCA\n+>HCM1_099_2\n+TGCAGGCAGTTATAGACCATACGCAGGCTATCCGCGCTCAGAGTAATAACTCGGAAGCTG\n+TTAACGACATCATTCGCAGACGTGATGAGATTCAGGGAAATTCACAGCTCAGCGAGTCTG\n+CACTGAAATCCGTCGAAAATAAACCAGAAGTTATGCGCAGTCAGT'..b'ATCCTTG\n+CACCTGTAACT\n+>HCM1_116_3\n+GTGATTATAGCGATGAGAAATTCGTCAAGCTAATTGAAGGGTTTATATGTCATGAAGCTG\n+GACACGGTCGCTATACAGAACATGAAGTATACCGTGAAGCTTTTGTTGGGGAACTGATTA\n+ATGCAGATGGCTTCATCAGTATAGATGATAAGCTGAACGCTGAATTTCAAACCCTTAAAC\n+AAAAGAAAATCGCATATGCCCGGGCTTACCGTCTACATGGACTTATTAATCTCTTTGATG\n+ATGTCCAGATGGAAGAGAAAACGGGTATTGACTATCAGGAGGCAAAAAAGCGCCTCGCGG\n+TAAGTTATGCCTTGATGGTTGAAGCTGGGCGAATGACGGTTGATGTTTCTTCAAGCCCTC\n+AAAACCCTGTTCAGTTTATTGAAATGTTCCTGCTTAATACATTGCGGGTTAACGTTCTCC\n+AGCAAGAAGGGCATAAAGAAACGCTTGATCCATTTTTCGATTATGCAAAGAAAATCCTTG\n+AGCCTGTAATT\n+>HCM1_116_4\n+GTGATTATAGCGATGAGAAATTCGTCAAGCTAATTGAAGGGTTTATATGTCATGAAGCTG\n+GACACGGTCGCTATACAGAACATGAAGTATACCGTGAAGCTTTTGTTGGGGAACTGATTA\n+ATGCAGATGGCTTCATCAGTATAGATGATAAGCTGAACGCTGAATTTCAAACCCTTAAAC\n+AAAAGAAAATCGCATATGCCAGGGCTTACCGTCTACATGGACTTATTAATCTCTTTGATG\n+ATGTCCAGATGGAAGAGAAAACGGGTATTAACTATCAGGAGGCAAAAAAGCGCCTCGCGG\n+TAAGTTATGCCTTGATGGTTGAAGCTGGGCGAATGACGGTTGATGTTTCTTCAAGCCCTC\n+AAAACCCTGTTCAGTTTATTGAAATGTTCCTGCTTAATACATTGCGGGTTAACGTTCTCC\n+AGCAAGAAGGGCATAAAGAAACGCTTGATCCATTTTTCGATTATGCAAAGAAAATCCTTG\n+AGCCTGTAATT\n+>HCM1_178ac_1\n+GTCCAGGTTTTCGTTTCACCATTAACATCAGTGTATTTATATTTCGCAGGGCGCGGTTCG\n+CGAACTTTTTTAGGTGCTCCGGACTTTGCAGAGAAAGAACTCAGTAACTCTTCAGGGTCA\n+ATTCCATCTTCAAGCATTAATTGACGCAGGGATTCAATCTTCTCCAGACGCGCTTTCAGC\n+TCAGCTTCTTTTGAAGATTCTTCCTGACGTCGTTCTTCAACAACAACGCTTAATTTTTCC\n+AGCAGTTCTTCAAGGATCTCTAACGGCAGTTCACGGCCCTGCGCACGAAGAGTACGAATG\n+TTGTTTAATGATTTGAGTGCTTCGGACATATGACCTCACTAAGAGTAATAAATAAAATCA\n+ATAGAATACTTTGCGATATTACACTCTTTTATTATTT\n+>HCM1_178ac_2\n+GTCCAGGTTTTCGTTTTACCATTAACATCAGTGTATTTATATTTCGCAGGGCGCGGTTCG\n+CGAACTTTTTTAGGTGCTCCGGACTTTGCAGAGAAAGAACTCAGTAACTCTTCAGGGTCA\n+ATTCCATCTTCAAGCATTAATTGACGCAGGGATTCAATCTTCTCCAGACGCGCTTTCAGC\n+TCAGCTTCTTTTGAAGATTCTTCCTGACGTCGTTCTTCAACAACAACGCTTAATTTTTCC\n+AGCAGTTCTTCAAGGATCTCTAACGGCAGTTCACGGCCCTGCGCACGAAGAGTACGAATG\n+TTGTTTAATGATTTGAGTGCTTCGGACATATGACCTCACTAAGAGTAATAAATAAAATCA\n+ATAGAATACTTTGCGATATTACACTCTTTTATTATTT\n+>HCM1_178ac_3\n+GTCCAGGTTTTCGTTTCACCATTTTCATCGGTAAACGAATATTTCGCCGGACGCGGATCG\n+CGAGCTTTTTTTGGTGCGCTGGATTTAGCAGAGAAAGAGCTCAGAAGTTCTTCAGGATCG\n+ATTCCGTCTTCAAGCATTAATTTACGCAGGGAATCGAGTTTTTCCTGACGTGCTTCCTGC\n+TCAGCTTTTTTGGAAGATTCTTCCTGACGGCGTTCGTCTACGACAACGCTTAATTTTTCC\n+AGCAGTTCTTCAAGAACCTCTAATGGCAGTTCACGGCCCTGCGCACGAAGAGTACGAATG\n+TTGTTTAATGCTTTTAGTGCTTCGGACATATGGCCTCACTTAGAGATTTTGAAATTAAAA\n+GGATACGGAATGATAGTACACTGTTTTAATATTTTAC\n+>HCM1_259_1\n+CTCCCGTTTTTTCGGGATTGATGCGGAGTTGGTCTTTACGCTTTTTGATAATGAGGGCGG\n+AAAAGTCGGGACGTTCAGCCGTAATAAAAATGGCACTTATGATATTGGGCCTATGCAGAT\n+CAATTCGTCCAACCTGCCAGAAATACGCGACCATTTTCCGTCTGTTACGTGGCGGGTGCT\n+GGCCTATGACGCCTGTGCCAGTTTCTGGGTGGGCACCTGGTGGCTTTACCGGAAGATTGT\n+TGACCGGAAGGGTAACGTATTTGAAGGGATTGCCGATTACAACAGCAAAACCCCTAAGGT\n+CCGGGCGACGTATATCTTCAACTTCATGATCAAATACAATCGCCGGATTCAGCGCCGAAA\n+TGGAATGGACGAATTATATCAGTGGAC\n+>HCM1_259_2\n+CTCCCGTTTTTTCGGGATTGATGCGGAGTTGGTCTTTACGCTTTTTGATAATGAGGGCGG\n+AAAAGTCGGGACGTTCAGCCGTAATAAAAATGGCACTTATGATATTGGGCCTATGCAGAT\n+CAATTCGTCCAACCTGCCGGAAATACGCGACCATTTTCCGTCTGTTACGTGGCGGGTGCT\n+GGCCTATGACGCCTGTGCCAGTTTCTGGGTGGGCACCTGGTGGCTTTACCGGAAGATTGT\n+TGACCGGAAGGGTAACGTATTTGAAGGGATTGCCGATTACAACAGCAAAACCCCTAAGGT\n+CCGGGCGACGTATATCTTCAACTTCATGATCAAATACAATCGCCGGATTCAGCGCCGAAA\n+TGGAATGGACGAATTATATCAGTGGAC\n+>HCM1_259_3\n+CTCCCGTTTTTTCGGGATTGATGCGGAGTTGGTCTTTACGCTTTTTGATAATGAGGGCGG\n+AAAAGTGGGGACGTTCAGCCGTAATAAAAATGGCACTTATGATATTGGGCCTATGCAGAT\n+CAATTCGTCCAACCTGCCGGAAATACGCGACCATTTTCCGTCTGTTACGTGGCGGGTGCT\n+GGCCTATGACGCCTGTGCCAGTTTCTGGGTGGGCACCTGGTGGCTTTACCGGAAGATTGT\n+TGACCGGAAGGGTAACGTATTTGAAGGGATTGCCGATTACAACAGCAAAACCCCTAAGGT\n+CCGGGCGACGTATATCTTCAACTTCATGATCAAATACAATCGCCGGATTCAGCGCCGAAA\n+TGGAATGGACGAATTATATCAGTGGAC\n+>HCM1_259_4\n+CTCCCGCTTTTTCGGGATTGATGCAGAATTGGTCTTTACGCTTTTTGATAATGAAGGCGG\n+AAAAGTGGGAACGTTCAGCCGGAATAAAAATGGCACTTATGATATTGGACCTATGCAGAT\n+CAATTCGTCCAATCTGCCGGAAATACGTGGCCACTTTCCGTCTGTTACCTGGCGGGTATT\n+GGCCTATGACGCCTGTGCCAGTTTCTGGGTAGGTACCTGGTGGCTTTACCGGAAAATTGT\n+AGACCGAAATGGTAATGTATTTGAAGGGATTGCCGATTACAACAGCAAAACCCCTAAGGT\n+CCGGGCGAGGTATATCTTTAACTTCATGGTCAAATACAATCGCCGGATTCAGGGCCGGAA\n+TGGCATGGACGAGTTATATCAGTGGAC\n' |
| b |
| diff -r 000000000000 -r 6dcb66689a7d pmlst/pmlst_db/inchi1.txt.clean --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pmlst/pmlst_db/inchi1.txt.clean Wed Aug 25 21:12:34 2021 +0000 |
| b |
| @@ -0,0 +1,18 @@ +ST HCM1_043 HCM1_064 HCM1_099 HCM1_116 HCM1_178ac HCM1_259 +1 1 1 1 1 1 1 +2 1 2 1 1 1 1 +3 1 1 1 1 1 3 +4 1 2 3 1 1 1 +5 3 2 1 2 1 2 +6 3 2 2 2 2 3 +7 3 2 2 2 1 3 +8 3 2 2 0 1 3 +9 1 3 1 1 1 1 +10 1 2 1 1 1 2 +11 2 4 4 3 3 4 +12 2 4 4 3 0 4 +13 2 4 4 4 0 4 +14 0 2 1 1 1 2 +15 1 1 2 2 1 1 +16 1 1 1 1 0 2 + |
| b |
| diff -r 000000000000 -r 6dcb66689a7d pmlst/pmlst_db/inchi2.fsa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pmlst/pmlst_db/inchi2.fsa Wed Aug 25 21:12:34 2021 +0000 |
| b |
| @@ -0,0 +1,127 @@ +>smr0018_1 +TCGTCCAATAACCATAACCACCGAGGATATTTTTTCTTTTCTCAATATAAACGGGTTCAG +AAAATACTAAATGTTGATATTTAGGAAGAGATAAGATTTCATATTTTCCTTGTCCAACTA +AGAGGTAATTCTTCTCTTTAGGATTGATGGTTACTGGATTACCAACACTTTGAGGTATGT +TAAGTTTTTTTATATTTAGGTCAGAATAGTCAGGAACGGACACTTGATCATTAGACGTAT +TTCCGGGAAGAGTAAACCCTTTACCCTGATCCGGTCCAAAGATGGCAATTATATCTTTGT +TGTTTCTTGTGATCGAAACGATAGCCTGAA +>smr0018_2 +TCGTCCAATAACCATAACCACCGAGGATATCTTTTCTTTTCTCAATATAAACCGGTTCAG +AAAATTCTAAATGTTGATATTTCGGAAGAGATAAGATTTTATATTTTACTTGTCCAACTA +AGAGGTAATTCTTCTCTTTAGGATTGATGGTTACTGAATTACCAACACTTTGAGGTATGT +TAAGTTTTTTTATATTTAGATCAGAATCGTCAGGAACGGACACTTGATCATTAGATGTCT +TTCCGGGAAGAGTAAACCCTTTATCCTGATCCGGTCCAAAGATGGCAATTACATCTTTGT +TGTTTCTTGTGATCGAAACGATAGCCTGAA +>smr0018_3 +TCGTCCAATAACGATAACCACCGAGGATATCTTTTCTTTTCTCAATATAAACCGGTTCAG +AAAATTCTAAATGTTGATATTTCGGAAGAGATAAGATTTTATATTTTACTTGTCCAACTA +AGAGGTAATTCTTCTCTTTAGGATTGATGGTTACTGAATTACCAACACTTTGAGGTATGT +TAAGTTTTTTTATATTTAGATCAGAATCGTCAGGAACGGACACTTGATCATTAGATGTCT +TTCCGGGAAGAGTAAACCCTTTACCCTGATCCGGTCCAAAGATGGCAATTACATCTTTGT +TGTTTCTTGTGATCGAAACGATAGCCTGAA +>smr0018_4 +TCGTCCAATAACCATAACCACCGAGGATATCTTTTCTTTTCTCAATATAAACCGGTTCAG +AAAATTCTAAATGTTGATATTTCGGAAGAGATAAGATTTTATATTTTACTTGTCCAACTA +AGAGGTAATTCTTCTCTTTAGGATTGATGGTTACTGAATTACCAACACTTTGAGGTATGT +TAAGTTTTTTTATATTTAGATCAGAATCGTCAGGAACGGACACTTGATCATTAGATGTCT +TTCCGGGAAGAGTAAACCCTTTACCCTGATCCGGTCCAAAGATGGCAATTACATCTTTGT +TGTTTCTTGTGATCGAAACGATAGCCTGAA +>smr0018_5 +TCGTCCAATAACCATAACCACCGAGGATATTTTTTCTTTTCTCAATATAAACGGGTTCAG +AAAATACTAAATGTTGATATTTAGGAAGAGATAAGATTTCATATTTTCCTTGTCCAACTA +AGAGGTAATTCTTCTCTTTAGGATTGATGGTTACTGGATTACCAACACTTTGAGGTATGT +TAAGTTTTTTTATATTTAGGGCAGAATAGTCAGGAACGGACACTTGATCATTAGACGTAT +TTCCGGGAAGAGTAAACCCTTTACCCTGATCCGGTCCAAAGATGGCAATTATATCTTTGT +TGTTTCTTGTGATCGAAACGATAGCCTGAA +>smr0018_6 +TCGTCCAATAACCATAACCACCGAGGATATCTTTTCTTTTCTCAATATAAACCGGTTCAG +AAAATTCTAAATGTTGATATTTCGGAAGAGATAATATTTTATATTTTACTTGTCCAACTA +AGAGGTAATTCTTCTCTTTAGGATTGATGGTTACTGAATTACCAACACTTTGAGGTATGT +TAAGTTTTTTTATATTTAGATCAGAATCGTCAGGAACGGACACTTGATCATTAGATGTCT +TTCCGGGAAGAGTAAACCCTTTACCCTGATCCGGTCCAAAGATGGCAATTACATCTTTGT +TGTTTCTTGTGATCGAAACGATAGCCTGAA +>smr0018_7 +TCGTCCAATAACCATAACCACCGAGGATATCTTTTCTTTTCTCAATATAAACCGGTTCAG +AAAATTCTAAATGTTGATATTTCGGAAGAGATAAGATTTTATATTTTACTTGTCCAACTA +AGAGGTAATTCTTCTCTTTAGGATTGATGGTTACTGAATTACCAACACTTTGAGGTATGT +TAAGTTTTTTTATATTTAGATCAGAATCGTTAGGAACGGACACTTGATCATTAGATGTCT +TTCCGGGAAGAGTAAACCCTTTACCCTGATCCGGTCCAAAGATGGCAATTACATCTTTGT +TGTTTCTTGTGATCGAAACGATAGCCTGAA +>smr0018_8 +TCGTCCAATAACCATAACCACCGAGGATATCTTTTCTTTTCTCAATATAAACCGGTTCAG +AAAATTCTAAATGTTGATATTTCGGAAGAGATAAGATTTTATATTTTACTTGTCCAACTA +AGAGGTAATTCTTCTCTTTAGGATTGATGGTTACTGAATTACCAACACTTTGAGGTATGT +TAAGTATTTTTATATTTAGATCAGAATCGTCAGGAACGGACACTTGATCATTAGATGTCT +TTCCGGGAAGAGTAAACCCTTTACCCTGATCCGGTCCAAAGATGGCAATTACATCTTTGT +TGTTTCTTGTGATCGAAACGATAGCCTGAA +>smr0018_9 +TCGTCCAATAACCATAACTACCGAGGATATCTTTTCTTTTCTCAATATAAACCGGTTCAG +AAAATTCTAAATGTTGATATTTCGGAAGAGATAAGATTTTATATTTTACTTGTCCAACTA +AGAGGTAATTCTTCTCTTTAGGATTGATGGTTACTGAATTACCAACACTTTGAGGTATGT +TAAGTTTTTTTATATTTAGATCAGAATCGTCAGGAACGGACACTTGATCATTAGATGTCT +TTCCGGGAAGAGTAAACCCTTTATCCTGATCCGGTCCAAAGATGGCAATTACATCTTTGT +TGTTTCTTGTGATCGAAACGATAGCCTGAA +>smr0018_10 +TCGTCCAATAACCATAACCACCGAGGATATCTTTTCTTTTCTCAATATAAACCGGTTCAG +AAAATTCTAAATGTTGATATTTCGGAAGAGATAAGATTTTATATTTTACTTGTCCAACTA +AGAGGTAATTCTTCTCTTTAGGATTGATGGTTACTGAATTACCAACACTTTGAGGTATGT +TAAGTTTTTTATATTTAGATCAGAATCGTCAGGAACGGACACTTGATCATTAGATGTCTT +TCCGGGAAGAGTAAACCCTTTACCCTGATCCGGTCCAAAGATGGCAATTACATCTTTGTT +GTTTCTTGTGATCGAAACGATAGCCTGAAG +>smr0018_11 +TCGTCCAATAACGATAACCACCGAGGATATCTTTTCTTTTCTCAATATAAACCGGTTCAG +AAAATTCTAAATGTTGATATTTCGGAAGAGATAAGATTTTATATTTTACTTGTCCAACTA +AGAGGTAATTCTTCTCTTTAGGATTGATGGTTACTGAATTACCAACACTTTGAGGTATGT +TAAGTTTTTTTATATTTAGATCAGAATCGTCAGGAACGGACACTTGATCATTAGATGTCT +TTCCGGGAAGAGTAAACCCTTTATCCTGATCCGGTCCAAAGATGGCAATTACATCTTTGT +TGTTTCTTGTGATCGAAACGATAGCCTGAA +>smr0018_12 +TCGTCCAATAACCATAACCACCGAGGATATCTTTTCTTTTCTCAATATAAACCGGTTCAG +AAAATTCTAAATGTTGATATTTCGGAAGAGATAAGATTTTATATTTTACTTGTCCAACTA +AGATGTAATTCTTCTCTTTAGGATTGATGGTTACTGAATTACCAACACTTTGAGGTATGT +TAAGTTTTTTTATATTTAGATCAGAATCGTCAGGAACGGACACTTGATCATTAGATGTCT +TTCCGGGAAGAGTAAACCCTTTATCCTGATCCGGTCCAAAGATGGCAATTACATCTTTGT +TGTTTCTTGTGATCGAAACGATAGCCTGAA +>smr0018_13 +TCGTCCAATAACCATAACCACCGAGGATATTTTTTCTTTTCTCAATATAAACGGGTTCAG +AAAATACTAAATGTTGATATTTAGGAAGATATAAGATTTCATATTTTCCTTGTCCAACTA +AGAGGTAATTCTTCTCTTTAGGATTGATGGTTACTGGATTACCAACACTTTGAGGTATGT +TAAGTTTTTTTATATTTAGGTCAGAATAGTCAGGAACGGACACTTGATCATTAGACGTAT +TTCCGGGAAGAGTAAACCCTTTACCCTGATCCGGTCCAAAGATGGCAATTATATCTTTGT +TGTTTCTTGTGATCGAAACGATAGCCTGAA +>smr0199_1 +ACCTATTCCCGTTCCTGATGAGATTTACACTCAGTGCATTACGGATGCCGCCCGCTACTT +CGGAATTGATGCTGAACTGGTTTTTACGTTGTTTGACAATGAAGGCGGTAAGGTTGGTAC +TTTCAGCAGGAATACTAACGGCACTTATGATATTGGCCCAATGCAGATCAACTCATCCAA +TCTACCTGAAATAAAAAAGCATTTCCCGACGGTAACGTGGCGGGTTCTGGCTTACGATGC +TTGCGCAAGTTTCTGGGTTGGAACATGGTGGCTCTATAGAAAAATTGTTGATCGCAAGGG +CAATGTGTTTGAAGGGATTGCAGATTACAACAGCAAAACCCCAAAGGTACGTGCAAAGTA +CATATTTAACTTCATGGTAAAGTACAATCGCCGGATCCAGCAGCGTAACGGGATGGGTGA +GCTTTATCAATGGACCCAGCAACCTCCTCGATACAATGGC +>smr0199_2 +ACCTATTCCCGTTCCTGATGAGATTTACACTCAGTGCATTACGGATGCCGCCCGCTTCTT +CGGAATTGATGCCGAACTGGTTTTTACGTTGTTTGACAATGAAGGCGGTAAGGTTGGTAC +TTTCAGCAGGAATACTAACGGCACTTATGATATTGGCCCGATGCAGATCAACTCATCCAA +TCTGCCTGAAATAAAAAAGCATTTCCCGACTGTAACGTGGCGGGTTCTGGCTTACGATGC +TTGCGCTAGTTTCTGGGTTGGAACATGGTGGCTCTACAGAAAAATTGTTGATCGCAAGGG +CAATGTGTTTGAAGGGATTGCAGATTACAACAGCAAAACCCCAAAGGTACGTGCAAAGTA +CATATTTAACTTCATGGTAAAGTACAATCGCCGGATCCAGCAGCGTAACGGGATGGGTGA +GCTTTATCAATGGACCCAACAACCTCCTCGATACAATGGC +>smr0199_3 +ACCTATTCCCGTTCCTGATGAGATTTACACTCAGTGCATTACGGATGCCGCCCGCTACTT +CGGAATTGATGCTGAACTGGTTTTTACGTTGTTTGACAATGAAGGCGGTAAGGTTGGTAC +TTTCAGCAGGAATACAAACGGCACTTATGATATTGGCCCAATGCAGATCAACTCATCCAA +TCTGCCTGAAATAAAAAAGCATTTTCCGACGGTAACGTGGCGGGTTCTGGCTTACGATGC +TTGCGCAAGTTTCTGGGTTGGAACATGGTGGCTCTATAGAAAAATTGTTGATCGCAAGGG +CAATGTGTTTGAAGGGATTGCAGATTACAACAGCAAAACCCCAAAGGTACGTGCAAAGTA +CATATTTAACTTCATGGTAAAGTACAATCGCCGAATCCAGCAGCGTAACGGGATGGGTGA +GCTTTATCAATGGACCCAGCAACCTCCTCGATACAATGGC +>smr0199_4 +ACCTATTCCCGTTCCTGATGAAATTTACACTCAGTGCATAACGGATGCCGCCCGCTACTT +CGGAATTGATGCTGAACTGGTTTTTACGTTGTTTGACAATGAAGGCGGTAAGGTTGGTAC +TTTCAGCAGGAATACTAACGGCACTTATGATATTGGCCCAATGCAGATCAACTCATCCAA +TCTGCCTGAAATAAAAAAGCATTTCCCGACGGTAACGTGGCGTGTTCTGGCTTACGATGC +TTGCGCAAGTTTCTGGGTTGGAACATGGTGGCTCTATAGAAAAATTGTTGATCGCAAGGG +CAATGTGTTTGAAGGGATTGCAGATTACAACAGCAAAACCCCAAAGGTACGTGCAAAGTA +CATATTTAACTTCATGGTAAAGTACAATCGTCGGATCCAGCAGCGTAACGGGATGGGTGA +GCTTTATCAATGGACCCAGCAACCTCCTCGATACAATGGC |
| b |
| diff -r 000000000000 -r 6dcb66689a7d pmlst/pmlst_db/inchi2.txt.clean --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pmlst/pmlst_db/inchi2.txt.clean Wed Aug 25 21:12:34 2021 +0000 |
| b |
| @@ -0,0 +1,18 @@ +ST smr0018 smr0199 +1 1 1 +2 2 2 +3 3 2 +4 4 2 +5 2 3 +6 6 2 +7 4 3 +8 7 2 +9 8 2 +10 9 2 +11 10 2 +12 11 2 +13 12 2 +14 1 2 +15 13 1 +16 1 4 + |
| b |
| diff -r 000000000000 -r 6dcb66689a7d pmlst/pmlst_db/inci1.clpx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pmlst/pmlst_db/inci1.clpx Wed Aug 25 21:12:34 2021 +0000 |
| b |
| @@ -0,0 +1,31 @@ +ST CLONAL_COMPLEX +2 CC-2 +3 CC-3 +5 CC-5 +7 CC-7 +8 CC-31 +9 CC-9 +10 CC-5 +12 CC-12 +15 CC-7 +17 CC-2 +21 CC-5 +23 CC-2 +26 CC-26 +27 CC-26 +28 CC-3 +29 CC-26 +30 CC-7 +31 CC-31 +36 CC-5 +38 CC-3 +42 CC-3 +49 CC-9 +50 CC-12 +58 CC-58 +59 CC-58 +61 CC-61 +62 CC-61 +64 CC-3 +66 CC-12 +68 CC-31 \ No newline at end of file |
| b |
| diff -r 000000000000 -r 6dcb66689a7d pmlst/pmlst_db/inci1.fsa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pmlst/pmlst_db/inci1.fsa Wed Aug 25 21:12:34 2021 +0000 |
| b |
| b'@@ -0,0 +1,1193 @@\n+>repI1_1\n+GAGAGATGGCATGTACGGGCAGTAAGTCAGAAGACTGAAGATGTTCCGGAAGCCATAAAA\n+GGAAAACCCCCACTATCTTTCTT\n+>repI1_2\n+GAGAGATGGCATGTACGGACAGTAAGTCAGAAGACTGAAGATGTTCCGGAAGCCATAAAA\n+GGAAAACCCCCACTATCTTTCTT\n+>repI1_3\n+GAGAGATGGCATGTACGGGCAGTAAGTCAGAAGACTGAAGATGCTCCGGAAGCCATAAAA\n+GGAAAACCCCCACTATCTTTCTT\n+>repI1_4\n+GAGAGATGGCATTTACGGGCAGTAAGTCAGAAGACCGAAGATGTTCCGGAAGCCATAAAA\n+GGAAAACCCCCACAATCTTTCG\n+>repI1_5\n+GAGAGATGGCATGTACGGACAGTAAGTCAGAAGACTGAAGATGTTCCGGAAGCCATAAAA\n+GGAAAACCCCCACAATCTTTCG\n+>repI1_6\n+GAGAGATGGCACGTACGGGCAGTAAGTCAGAAGACTGAAGATGTTCCGGAAGCCATAAAA\n+GGAAAACCCCCACAATCTTTCG\n+>repI1_7\n+GAGAGATGGCATGTACGGGCAGTAAGTCAGAAGACAGAAGATGTTCCGGAAGCCATAAAA\n+GGAAAACCCCCACTATCTTTCTT\n+>repI1_8\n+GAGAGATGGCATGTACGGACAGTAAGTCAGAAGACTGAAGATGTTCCGGAAGCCATAAAA\n+GGAAAACCCCCACTATCTTTCTTTCTT\n+>repI1_9\n+GATAGATGGCATGTACGGGCAGTAAGTCAGAAGACTGAAGATGTTCCGGAAGCCATAAAA\n+GGAAAACCCCCACTATCTTTCTT\n+>repI1_10\n+GAGAGATGGCATGTACGGGCAGTAAGTCAGAAGACTGAAGATGTTCCGGAAGCCATAAAA\n+GGAAAACCCCCACAATCTTTCG\n+>repI1_11\n+GAGGGATGGCATGTACGGGCAGTAAGTCAGAAGACTGAAGATGTTCCGGAAGCCATAAAA\n+GGAAAACCCCCACTATCTTTCTT\n+>repI1_12\n+GAGAGATGGCAGGTACGGAGAGTAAGTCAGAAGACTGAAGATGTGCCGGAAGCCATAAAA\n+GGAAAACCCCCATAATCTTCTC\n+>repI1_13\n+GAGAGATGGCATGTACGGGCGGTAAGTCAGAAGACTGAAGATGCTCCGGAAGCCATAAAA\n+GGAAAACCCCCACTATCTTTCTT\n+>repI1_14\n+GAAAGATGGCATTTACGGGCAGTAAGTCAGAAGACCGAAGATGTTCCGGAAGCCATAAAA\n+GGAAAACCCCCACAATCTTTCG\n+>ardA_1\n+AATACAACTGTGGAAGCATCGCTGGCCGCTGGTTTGACCTGGCCACGTTTGATGATGAAC\n+GCGACTTTTTCGCCGCCTGCCGCTCTCTTCACCAGGATGAAGCCGATCCTGAACTGATGT\n+TTCAGGATTATGAGGGATTCCCGGGGAATATGGCCTCAGAATGCCATATCAACTGGGCCT\n+ATGTTGAAGGCTTCCGCCAGGCGCGGGATGAAGGCTGCGAAGAGGCTTATCGTCTCTGGG\n+TGGATGATACCGGTGAGACGGATTTTGACACCTTCCGCGATGCCTGGTGGGGCGAGGCTG\n+ACAGTGAGGAGGCTTTTGCGGTTGAGTTCGCCAGTGATACCGG\n+>ardA_2\n+AATACAACTGTGGAAGCATCGCCGGACGCTGGTTTGACCTGACCACGTTTGATGATGAGC\n+GCGACTTTTTCGCCGCCTGCCGTGCTCTTCACCAGGATGAAGCCGATCCTGAACTGATGT\n+TTCAGGATTATGAGGGATTCCCGGGGAATATGGCCTCTGAATGCCATATCAACTGGGCCT\n+GGGTTGAAGGCTTCCGCCAGGCACGGGATGAAGGCTGCGAAGAGGCTTATCGTCTCTGGG\n+TGGAGGATACCGGTGAGACGGATTTTGACACCTTCCGCGATGCCTGGTGGGGCGAGGCTG\n+ACAGTGAGGAGGCTTTTGCGGTTGAGTTCGCCAGTGATACCGG\n+>ardA_3\n+AATACAACTGTGGAAGCATCGCCGGACGCTGGTTTGACCTGACCACGTTTGATGATGAGC\n+GCGACTTTTTCGCCGCCTGCCGTGCTCTTCACCAGGATGAAGCCGATCCTGAACTGATGT\n+TTCAGGATTATGAGGGATTCCCGGGGAATATGGCCTCTGAATGCCATATCAACTGGGCCT\n+GGGTTGAAGGCTTCCGCCGGGCACGGGATGAAGGCTGCGAAGAGGCTTATCGTCTCTGGG\n+TGGATGATACCGGTGAGACGGATTTTGACACCTTCCGCGATGCCTGGTGGGGCGAGGCTG\n+ACAGTGAGGAGGCTTTTGCGGTTGAGTTCGTCAGTGATACCGG\n+>ardA_4\n+AATACAACTGTGGAAGCATCGCCGGACGCTGGTTTGACCTGACCACGTTTGATGATGAGC\n+GCGACTTTTTCGCCGCCTGCCGTGCTCTTCACCAGGATGAAGCCGATCCTGAACTGATGT\n+TTCAGGATTATGAGGGATTCCCGGGGAATATGGCCTCTGAATGCCATATCAACTGGGCCT\n+GGGTTGAAGGCTTCCGCCTGGCACGGGATGAAGGCTGCGAAGAGGCTTATCGTCTCTGGG\n+TGGAGGATACCGGTGAGACGGATTTTGACACCTTCCGCGATGCCTGGTGGGGCGAGGCTG\n+ACAGTGAGGAGGCTTTTGCGGTTGAGTTCGCCAGTGATACCGG\n+>ardA_5\n+AATACAACTGTGGAAGCATCGCCGGACGCTGGTTTGACCTGACCACGTTTGATGATGAGC\n+GCGACTTTTTCGCCGCCTGCCGTGCTCTTCACCAGGATGAAGCCGATCCTGAACTGATGT\n+TTCAGGATTATGAGGGATTCCCGGGGAATATGGCCTCTGAATGTCATATCAACTGGGCCT\n+GGGTTGAAGGCTTCCGCCGGGCACGGGATGAAGGCTGCGAAGAGGCTTATCGTCTCTGGG\n+TGGATGATACCGGTGAGACGGATTTTGACACCTTCCGCGATGCCTGGTGGGGCGAGGCTG\n+ACAGTGAGGAGGCTTTTGCGGTTGAGTTCGCCAGTGATACCGG\n+>ardA_6\n+AATATAACTGCGGAAGCATCGCCGGCCGCTGGTTTGACCTGACCACGTTTGATGATGAAC\n+GCGATTTTTTCGCCGCCTGCCGTGCCCTTCACCAGGATGAAACCGATCCGGAACTGATGT\n+TTCAGGATTATGAGGGTTTCCCGGGGAATATGGCCTCTGAATGTCATATCAACTGGGCCT\n+GGGTTGAAGGCTTCCGCCGGGCACGGGATGAAGGCTGCGAAGAGGCTTATCGTCTCTGGG\n+TGGATGATACCGGTGAGACGGATTTTGACAGCTTCCGCGATGCCTGGTGGGGCGAGGCTG\n+ACAGTGAGGAGGCTTTTGCGGTTGAGTTCGTCAGTGATACCGG\n+>ardA_7\n+AATACAACTGTGGAAGCATCGCTGGCCGCTGGTTTGACCTGGCCACGTTTGATGATGAAC\n+GCGACTTTTTCGCCGCCTGCCGCTCTCTTCACCAGGATGAAGCCGATCCTGAACTGATGT\n+TTCAGGATTATGAGGGATTCCCGGGGAATATGGCCTCAGAATGCCATATCAACTGGGCCT\n+GGGTTGAAGGCTTCCGCCAGGCGCGGGATGAAGGCTGCGAAGAGGCTTATCGTCTCTGGG\n+TGGATGATACCGGTGAGACGGATTTTGACACCTTCCGCGATGCCTGGTGGGGCGAGGCTG\n+ACAGTGAGGAGGCTTTTGCGGTTGAGTTCGCCAGTGATACCGG\n+>ardA_8\n+AATACAACTGTGGAAGCATCGCCGGACGCTGGTTTGACCTGACCACGTTTGATGATGAGC\n'..b'CGGTCATGAGCGGGATAGACTT\n+GACTGTGGAGCCGGTTGGAGTCGGGGTGGCGGCGGGCGTTGACGAAGATACGCTGTTTCC\n+CCTGAATGGATTTCGTGGCTTGTTTTGGCTATTTGCTGTCGTTGGAGATTCAGGGTAAAT\n+GGATGTGGTTACCA\n+>pilL_21\n+TTTTGTTTCTTCTGCCCACTTGATAATGTTCTCTCTTAATGTGGTGCCTGCCGGCGCACG\n+CCACTCTTTACCCTGAGATACCGGTTTAACAGGCGTTCCGGTCATGAGCGGGATAGACTT\n+GACTGTGGAGCCGGTTGGAGTCGGGGTGGCGGCGGGCGTTAACGAAGATACGCTGTTTCC\n+CCTGAATGGATTTCGTGGTTTGTTCTGGCTATTTGCTGTTGTTGGAGATTCAGGGGAAGT\n+GGATGTGGTTACCA\n+>pilL_22\n+TTTTGTTTCTTCTGCCCACTTAATAATGTTTTCCCTTAATGTAGTGCCTGCCGGCGCACG\n+CCACTCTTTACCCTGAGATACCGGTTTGACAGGTGTCCCGGTCATTAGTGGGATAGACTT\n+GACTGTAGAGCCGGTCGGAGTCGGGATTGCTGCGGGCGTAGACGGAGATACGCTGTTTCC\n+CCTGAATGGGTTTCGTGGTTTGTTCTGGCTATTTGCTGTCGTTGAAGACTCCGGGGAAGT\n+GGATGTGGTTACCA\n+>pilL_23\n+TTTTGTTTCTTCTGCCCACTTAATAATGTTTTCTCTTAATGTGGTGCCTGCCGGCGCACG\n+CCACTCTTTACCCTGAGATACCGGTTTGACAGGCGTCCCGGTCATGAGCGGGATAGACTT\n+GACTGTGGAGCCGGTTGGAGTCGGGGTGGCGGCGGGGGTTGACGAAGATACGCTGTTTCC\n+TCTGAATGGATTTCGTGGTTTGTTCTGGCTATTTGCTGTTGTTGGAGATTCAGGGGAAGT\n+GGATGTGGTTACCA\n+>pilL_24\n+TTTTGTTTCTTCTGCCCACTTGATAATGTTCTCTCTTAATGTGGTGCCTGCCAGCGCACG\n+CCACTCTTTACCCTGAGATACCGGTTTAACAGGCGTTCCGGTCATGAGCGGGATAGACTT\n+GACTGTGGAGCCGGTTGGAGTCGGGGTGGCGGCGGGCGTTGACGAAGATACGCTGTTTCC\n+CCTGAATGGATTTCGTGGCTTGTTTTGGCTATTTGCTGTCGTTGGAGATTCAGGGTAAGT\n+GGATGTGGTTACCA\n+>pilL_25\n+TTTTGTTTCTTCTGCCCACTTAATAATGTTTTCCCTTAATGTAGTGCCTGCCGGCGCACG\n+CCACTCTTTACCCTGAGATACCGGTTTGACAGGTGTCCCGGTCATGAGTGGGATAGACTT\n+GACTGTAGAGCCGGTCGGAGTCGGGATTGATGCGGGCGTAGACGGAGATACGCTGTTTCC\n+CCTGAATGGGTTTCGTGGTTTGTTCTGGCTATTTGCTGTCGTTGAAGACTCCGGGGAAGT\n+GGATGTGGTTACCA\n+>pilL_26\n+TTTTGTTTCTTCTGCCCACTTAATAATGTTCTCTCTTAATGTGGTGCCTGCCGGCGCACG\n+CCACTCTTTACCCTGAGATACCGGTTTGACAGGCGTCCCGGTCATGAGCTGGATAGACTT\n+GACTGTGGAGCCGGTTGGAGTTGGGGTGGCGGCGGGGGTTGACGAAGATACGCTGTTTCC\n+TCTGAATGGATTTCGTGGTTTGTTCTGGCTATTTGCTGTTGTTGGAGATTCAGGGGAAGT\n+GGATGTGGTTACCA\n+>pilL_27\n+TTTGTTTCTTCTGCCCACTTAGATAATGTTTTCCCTTAATGTAGGTGCCTGCCGGCGCAC\n+GCCACTCTTTACCCTGAGATACCGGTTTGACAGGTGTCCCGGTCATGAGTGGGATAGACT\n+TGACTGTAGAGCCGGTCGGAGTCGGGATTGCTGCGGGCGTAGACGGAGATACGCTGTTTC\n+CCCTGAATGGGTTTCGTGGTTTGTTCTGGCTATTTGCTGTCGTTGAAGACTCCGGGGAAG\n+TGGATGTGGTTACC\n+>pilL_28\n+TTTTGTTTCTTCTGCCCACTTGATAATGTTCTCTCTTAATGTGGTGCCTGCCGGCGCACG\n+CCACTCTTTACCCTGAGATACCGGTTTAACAGGCGTTCCGGTCATGAGAGGGATAGACTT\n+GACTGTGGAGCCGGTTGGAGTCGGGGTGGCGGCGGGGGTTGACGAAGATACGCTGTTTCC\n+TCTGAATGGATTTCGTGGTTTGTTCTGGCTATTTGCTGTTGTTGGAGATTCAGGGGAAGT\n+GGATGTGGTTACCA\n+>pilL_29\n+TTTTGTTTCTTCTGCCCACTTGATAATGTTCTCTCTTAATGTGGTGCCTGCCGGCGCACG\n+CCACTCTTTACCCTGAGATACCGGTTTAACAGGCGTTCCGGTCATGAGCGGGATAGACTT\n+GACTGTGGAGCCGGTTGGAGTCAGGGTGGTGGCGGGCGTTGACGAAGATACGCTGTTTCC\n+CCTGAATGGATTTCGTGGTTTGTTCTGGCTATTTGCTGTCGTTGGAGATTCAGGGGTAGT\n+GGATGTGGTTACCA\n+>pilL_30\n+TTTTGTTTCTTCTGCCCACTTGATAATGTTCTCTCTTAATGTGGTGCCTGCCGGCGCACG\n+CCACTCTTTACCCTGAGATACCGGTTTAACAGGCATTCCGGTCATGAGCGGGATAGACTT\n+GACTGTGGAGCCGGTTGGAGTCGGGGTGGCGGCGGGCGTTGACGAAGATACGCTGTTTCC\n+CCTGAATGGATTTCGTGGCTTGTTTTGGCTATTTGCTGTCGTTGGAGATTCAGGGTAAGT\n+GGATGTGGTTACCA\n+>pilL_31\n+TTTTGTTTCTTCTGCCCACTTAATAATGTTTTCCCTTAATGTAGTGCCTGCCGGCGCACG\n+CCACTCTTTACCCTGAGATACCGGTTTGACAGGTGTCCCGGTCATGAGTGGGATAGAATT\n+GACTGTGGAGCCGGTCGGAGTCGGGATTGCAGCGGGCGTAGACGGAGATACGCTGTTTCC\n+CCTGAATGGGTTTCGTGGTTTGTTCTGGCTATTTGCTGTCGTTGAAGACTCCGGGGAAGT\n+GGATGTGGTTACCA\n+>pilL_32\n+TTTTGTTTCTTCTGCCCACTTGATAATGTTCTCTCTTAATGTGGTGCCTGCCGGCGCACG\n+CCACTCTTTACCCTGAGATACCGGTTTAACAGGCGTTCCGGTCATGAGCGGGATAGACTT\n+GACTGTGGAGTCGGTTGGAGTCGGGGTGGCGGCGGGCGTTGACGAAGATACGCTGTTTCC\n+CCTGAATGGATTTCGTGGTTTGTTCTGGCTATTTGCTGTCGTTGGAGATTCAGGGGAAGT\n+GGATGTGGTTACCA\n+>pilL_33\n+TTTTGTTTCTTCTGCCCACTTAATAATGTTTTCCCTTAATGTAGTGCCTGCCGGCGCACG\n+CCATTCTTTACCCTGAGATACCGGTTTGACAGGTGTCCCGGTCATGAGTGGGATAGACTT\n+GACTGTAGAGCCGGTCGGAGTCGGGATTGCTGCGGGCGTAGACGGAGATACGCTGTTTCC\n+CCTGAATGGGTTTCGTGGTTTGTTCTGGCTATTTGCTGTCGTTGAAGACTCCGGGGAAGT\n+GGATGTGGTTACCA\n+>pilL_34\n+TTTTGTTTCTTCTGCCCACTTGATAATGTTCTCTCTTAATGTGGTGCCTGCCGGCGCACG\n+CCACTCTTTACCCTGAGATACCGGTTTAACAGGCGTCCCGGTCATGAGCGGGATAGACTT\n+GACTGTGGAGCCGGTTGGAGTCGGGGTGGTGGCGGGCGTTGACGAAGATACGCTGTTTCC\n+CCTGAATGGATTTCGTGGTTTGTTTTGGCTATTTGCTGTCGTTGGAGATTTAGGGGTAGT\n+GGATGTGGTTACCA\n' |
| b |
| diff -r 000000000000 -r 6dcb66689a7d pmlst/pmlst_db/inci1.txt.clean --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pmlst/pmlst_db/inci1.txt.clean Wed Aug 25 21:12:34 2021 +0000 |
| b |
| @@ -0,0 +1,331 @@ +ST repI1 ardA trbA sogS pilL +1 1 1 1 1 1 +2 1 2 3 2 1 +3 2 1 4 1 2 +4 1 3 3 4 1 +5 1 2 2 3 3 +6 1 2 5 4 2 +7 2 1 5 4 2 +8 3 2 6 3 3 +9 3 2 3 3 3 +10 1 4 2 3 3 +11 1 2 3 6 2 +12 1 4 3 4 1 +13 1 1 5 1 1 +14 1 2 9 7 5 +15 2 1 5 1 2 +16 1 5 10 8 6 +17 1 2 3 6 1 +18 1 4 3 2 1 +19 1 3 3 4 3 +20 1 1 3 9 1 +21 1 2 11 3 3 +22 1 6 3 4 1 +23 1 2 3 1 1 +24 1 4 4 1 1 +25 1 4 5 4 1 +26 1 4 13 2 1 +27 1 2 13 2 1 +28 2 4 4 1 2 +29 1 1 13 2 1 +30 2 7 5 4 2 +31 3 4 6 3 3 +32 3 4 14 3 3 +33 1 2 7 1 1 +34 1 2 8 5 4 +35 3 5 10 3 3 +36 1 4 2 9 3 +37 1 8 12 3 7 +38 1 1 4 1 2 +39 1 5 4 1 3 +40 1 6 3 8 3 +41 1 9 13 3 6 +42 2 6 4 1 2 +43 1 1 15 11 1 +44 1 5 3 2 3 +45 1 1 3 2 1 +46 1 2 2 9 2 +47 1 4 2 2 2 +48 1 4 16 9 2 +49 3 10 3 3 3 +50 1 4 12 4 1 +51 1 1 15 9 3 +52 1 4 15 11 2 +53 2 1 15 11 2 +54 1 4 5 11 2 +55 4 5 15 11 3 +56 2 1 15 11 3 +57 3 2 6 13 8 +58 1 2 17 1 7 +59 1 2 4 1 7 +60 1 2 8 6 3 +61 2 1 11 3 2 +62 2 1 11 7 2 +63 1 4 5 4 7 +64 2 1 4 1 4 +65 1 4 18 10 3 +66 1 4 11 4 1 +67 1 4 6 10 3 +68 1 4 6 3 3 +69 1 4 19 4 1 +70 1 9 5 6 9 +71 4 11 8 14 10 +72 1 4 15 4 2 +73 1 2 15 3 3 +74 1 5 15 4 2 +75 1 2 15 11 3 +76 1 8 15 1 3 +77 1 5 13 11 3 +78 4 5 13 11 3 +79 1 5 15 11 6 +80 1 4 5 4 2 +81 4 2 15 11 1 +82 2 6 15 11 3 +83 2 1 15 1 2 +84 1 12 16 3 6 +85 2 4 15 11 2 +86 1 4 3 4 2 +87 8 1 4 1 2 +88 1 16 20 16 3 +89 1 3 15 15 6 +90 4 5 15 4 2 +91 2 4 3 4 2 +92 1 1 15 1 1 +93 1 14 4 8 2 +94 1 14 15 11 2 +95 1 17 13 2 1 +96 1 5 15 11 2 +97 1 2 16 9 1 +98 1 3 16 9 10 +99 2 1 4 1 1 +100 1 4 13 2 2 +101 2 1 4 2 2 +102 1 1 16 6 10 +103 1 18 13 2 1 +104 2 3 8 6 12 +105 3 19 15 3 13 +106 4 10 3 1 7 +107 1 9 5 4 14 +108 2 13 5 1 2 +109 5 3 15 11 10 +110 2 1 15 11 15 +111 1 3 15 11 2 +112 1 5 10 6 10 +113 1 2 5 10 10 +114 1 2 8 10 3 +115 1 4 5 10 10 +116 1 2 6 2 1 +117 4 19 10 17 16 +118 4 2 21 8 17 +119 1 21 17 6 18 +120 1 2 13 1 1 +121 1 4 22 2 1 +122 1 1 5 9 1 +123 1 22 18 2 1 +124 1 14 13 2 1 +125 1 14 5 2 1 +126 3 4 18 10 3 +127 1 2 9 2 7 +128 1 4 3 1 1 +129 1 2 3 18 1 +130 1 2 8 10 19 +131 1 9 23 4 3 +132 1 2 23 4 3 +133 4 4 5 6 7 +134 1 2 8 6 10 +135 2 23 4 1 2 +136 1 2 24 9 1 +137 4 7 15 11 3 +138 1 1 15 11 2 +139 1 4 4 11 3 +140 2 4 15 1 2 +141 4 5 15 4 3 +142 2 1 14 1 2 +143 1 1 14 11 2 +144 1 5 14 11 2 +145 3 2 10 3 3 +146 1 4 3 10 1 +147 1 14 3 2 1 +148 1 4 3 4 3 +149 1 2 17 2 1 +150 1 5 3 1 1 +151 1 2 3 20 1 +152 1 4 25 19 2 +153 6 24 17 7 10 +154 1 3 8 10 10 +155 1 2 16 9 2 +156 1 2 5 4 1 +157 2 18 4 1 2 +158 3 19 15 3 8 +159 1 2 9 1 7 +160 1 2 8 1 6 +161 1 5 10 4 6 +162 1 13 5 1 1 +163 1 19 6 1 2 +164 1 4 13 2 3 +165 1 4 5 4 3 +166 1 3 8 1 6 +167 1 5 10 8 1 +168 4 4 15 11 3 +169 1 2 16 21 6 +170 3 25 6 3 3 +171 1 3 27 6 10 +172 2 26 5 1 2 +173 1 27 20 16 3 +174 3 2 6 22 3 +175 3 28 6 3 3 +176 1 8 12 3 20 +177 3 2 15 23 13 +178 1 4 3 18 1 +179 1 2 17 1 3 +180 1 1 8 3 10 +181 1 2 8 3 10 +182 1 4 13 11 2 +183 1 2 8 10 10 +184 4 5 10 8 22 +185 3 2 29 3 13 +186 1 3 6 25 3 +187 2 1 5 26 2 +188 3 4 15 3 3 +189 4 2 3 6 7 +190 1 4 5 1 1 +191 1 30 15 11 6 +192 1 31 8 6 12 +193 1 32 17 1 7 +194 2 34 4 1 2 +195 2 33 4 1 2 +196 1 3 8 3 6 +197 1 2 17 1 2 +198 1 4 4 1 2 +199 1 4 16 10 2 +200 1 2 17 3 2 +201 1 9 3 4 3 +202 1 3 5 4 3 +203 7 4 13 2 1 +204 1 2 30 1 5 +205 1 36 6 7 23 +206 1 1 5 2 1 +207 1 2 16 1 1 +208 1 2 3 10 3 +209 1 2 21 9 3 +210 1 1 9 2 7 +211 1 19 2 9 3 +212 1 4 8 6 12 +213 1 2 2 9 3 +214 2 37 4 1 2 +215 1 6 13 2 1 +216 1 38 16 3 2 +217 1 4 15 11 3 +218 2 40 4 1 2 +219 2 4 3 18 2 +220 2 1 4 27 2 +221 2 39 4 1 2 +222 1 3 5 4 1 +223 10 41 31 7 3 +224 1 4 17 1 24 +225 1 2 3 1 3 +226 1 2 5 2 1 +227 1 9 4 5 3 +228 1 2 21 10 10 +229 1 9 32 23 3 +230 1 2 5 4 3 +231 1 9 5 4 3 +232 4 29 28 24 21 +233 1 4 3 29 1 +234 1 43 3 1 1 +235 1 2 17 5 26 +236 1 25 6 3 27 +237 1 2 21 4 1 +238 1 25 6 3 3 +239 4 5 15 9 3 +240 1 2 17 9 1 +241 1 4 17 4 1 +242 1 2 16 3 6 +243 1 2 3 4 28 +244 1 2 2 10 10 +245 11 44 34 3 2 +246 2 2 5 6 12 +247 3 45 35 30 29 +248 1 2 36 6 6 +249 1 2 37 3 2 +250 1 2 38 2 3 +251 1 2 27 1 30 +252 1 46 27 1 3 +253 1 47 2 4 1 +254 1 47 2 9 1 +255 1 4 5 4 4 +256 1 2 27 2 10 +257 1 4 17 1 2 +258 4 14 15 4 4 +259 2 4 5 10 2 +260 1 4 2 3 4 +261 1 2 26 12 1 +262 1 4 9 12 1 +263 1 19 6 3 1 +264 1 2 9 1 1 +265 1 11 3 1 1 +266 1 2 3 9 2 +267 1 2 3 9 3 +268 2 3 3 10 2 +269 1 7 5 1 1 +270 1 6 5 4 3 +271 1 1 5 4 1 +272 3 14 6 3 8 +273 3 4 6 3 8 +274 1 3 8 6 10 +275 4 2 10 3 3 +276 1 37 13 2 1 +277 1 4 16 1 4 +278 1 3 16 6 3 +279 3 2 16 3 8 +280 3 29 16 3 8 +281 3 4 17 3 3 +282 1 2 39 10 1 +283 1 2 40 2 1 +284 1 4 41 9 6 +285 1 2 42 10 10 +286 3 2 43 23 13 +287 4 5 15 31 3 +288 13 1 3 30 5 +289 14 2 40 6 5 +290 1 3 3 6 31 +291 1 4 3 4 32 +292 10 15 26 7 3 +293 3 4 13 3 25 +294 2 14 5 4 2 +295 2 48 4 1 2 +296 2 49 4 1 2 +297 2 2 15 4 17 +298 1 18 3 4 1 +299 1 2 5 4 10 +300 1 4 44 4 1 +301 1 2 45 3 3 +302 1 3 3 6 10 +303 1 1 1 3 1 +304 1 5 3 2 1 +305 2 2 3 4 2 +306 1 2 2 2 1 +307 1 4 5 9 3 +308 1 2 4 2 1 +309 2 1 12 1 2 +310 1 8 33 3 7 +311 1 7 2 10 3 +312 2 50 4 1 2 +313 1 51 3 1 1 +314 1 2 17 4 1 +315 1 2 11 1 1 +316 1 38 16 2 33 +317 2 19 4 1 2 +318 2 52 4 1 2 +319 1 4 27 4 6 +320 3 2 15 3 34 +321 1 4 46 4 2 +322 3 19 15 3 34 +323 3 4 13 32 3 +324 1 38 4 11 4 +325 1 2 27 1 2 +326 1 2 47 3 3 +327 1 2 16 10 10 +328 2 2 5 4 2 +329 2 1 17 1 2 + |
| b |
| diff -r 000000000000 -r 6dcb66689a7d pmlst/pmlst_db/incn.fsa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pmlst/pmlst_db/incn.fsa Wed Aug 25 21:12:34 2021 +0000 |
| b |
| b'@@ -0,0 +1,252 @@\n+>repN_1\n+TGCTTACTACCTCTCGCTAAAAGCAAAGCGCGTTCTCTGGTTATGTCTTATGCAGACGTA\n+TTTCACAGCTTCAGTAAGCGAAGATGATGATGAGATGGCTGTACTCGGTGACTCTACTTT\n+CAAAGTAAAGGTGGCTGACTATCAGCAAATTTTTCAGGTAAGCCGTAACCAGGCTATCAA\n+GGATGTTAAAGAAGGCGTGTTTGAGTTAAGCCGTTCTGCGGTAATCTTTTACCCGAAAGA\n+AGGGAGTTTTGACTGCGTCGCGCGCCCCTGGCTAACAGAGGCTGGCAGCCGATCAGCTCG\n+TGGTATCTGGGAAATCGAATTTAACCATAAACTCCTGCGGTACATTTACGGCCTGACGAA\n+CCAGTTCACCACCTACTCGCTCCGCGATTGTGGCAGTCTTCGAAATCCACGGACGATCCG\n+CCTTTATGAAAGTCTTGCTCAATTCAAATCTTCAGGCTTATGGG\n+>repN_2\n+TGCTTACTACCTCTCGCTAAAAGCAAAGCGCGTTCTCTGGTTATGTCTTATGCAGACGTA\n+TTTCACAGCTTCAGTAAGCGAAGATGATGATGAGATGGCTGTACTCGGTGACTCTACTTT\n+CAAAGTAAAGGTGGCTGACTATGAGCAAATTTTTCAGGTAAGCCGTAACCAGGCTATCAA\n+GGATGTTAAAGAAGGCGTGTTTGAGTTAAGCCGTTCTGCGGTAATCTTTTACCCGAAAGA\n+AGGGAGTTTTGACTGCGTCGCGCGCCCCTGGCTAACAGAGGCTGGCAGCCGATCAGCTCG\n+TGGTATCTGGGAAATCGAATTTAACCATAAACTCCTGCGGTACATTTACGGCCTGACGAA\n+CCAGTTCACCACCTACTCGCTCCGCGATTGTGGCAGTCTTCGAAATCCACGGACGATCCG\n+CCTTTATGAAAGTCTTGCTCAATTCAAATCTTCAGGCTTATGGG\n+>repN_3\n+TGCTTACTACCTCTCGCTAAAAGCAAAGCGCGTTCTCTGGTTATGTCTTATGCAGACGTA\n+TTTCACAGCTTCAGTAAGCGAAGATGATGATGAGATGGCTGTACTCGGTGACTCTACTTT\n+CAAAGTAAAGGTGGCTGACTATGAGCAAATTTTTCAGGTAAGCCGTAACCAGGCTATCAA\n+GGATGTTAAAGAAGGCGTGTTTGAGTTAAGCCGTTCTGCGGTAATCTTTTACCCGAAAGA\n+AGGAAGTTTTGACTGCGTCGCGCGCCCCTGGCTAACAGAGGCTGGCAGCCGATCAGCTCG\n+TGGTATCTGGGAAATCGAATTTAACCATAAACTCCTGCGGTACATTTACGGCCTGACGAA\n+CCAGTTCACCACCTACTCGCTCCGCGATTGTGGCAGTCTTCGAAATCCACGGACGATCCG\n+CCTTTATGAAAGTCTTGCTCAATTCAAATCTTCAGGCTTATGGG\n+>repN_4\n+TGCTTACTACCTCTCGCTAAAAGCAAAGCGCGTTATCTGGTTATGTCTTATGCAGACGTA\n+TTTCACAGCTTCAGTAAGCGAAGATGATGATGAGATGGCTGTACTCGGTGACTCTACTTT\n+CAAAGTAAAGGTGGCTGACTATGAGCAAATTTTTCAGGTAAGCCGTAACCAGGCTATCAA\n+GGATGTTAAAGAAGGCGTGTTTGAGTTAAGCCGTTCTGTGGTAATCTTTTACCCGAAAGA\n+AGGGAGTTTTGACTGCGTCGCGCGCCCCTGGCTAACAGAGGCTGGCAGCCGATCAGCTCG\n+TGGTATCTGGGAAATCGAATTTAACCATAAACTCCTGCGGTACATTTACGGCCTGACGAA\n+CCAGTTCACCACCTACTCGCTCCGCGATTGTGGCAGTCTTCGAAATCCACGGACGATCCG\n+CCTTTATGAAAGTCTTGCTCAATTCAAATCTTCAGGCTTATGGG\n+>repN_5\n+TGCTTACTACCTCTCGCTAAAAGCAAAGCGCGTTCTCTGGTTATGCCTTATGCAGACGTA\n+TTTCACAGCTTCAGTAAGCGAAGATGATGATGAGATGGCTGTACTCGGTGACTCTACTTT\n+CAAAGTAAAGGTGGCTGACTATCAGCAAATTTTTCAGGTAAGCCGTAACCAGGCTATCAA\n+GGATGTTAAAGAAGGCGTGTTTGAGTTAAGCCGTTCTGCGGTAATCTTTTACCCGAAAGA\n+AGGGCGTTTTGACTGCGTCGCGCGCCCCTGGCTAACAGAGGCTGGCAGCCGATCAGCTCG\n+TGGTATCTGGGAAATCGAATTTAACCATAAACTCCTGCCGTACATTTACGGCCTGACGAA\n+CCAGTTCACCACCTACTCGCTCCGCGATTGTGGCAGTCTTCGAAATCCCCGGACGATCCG\n+CCTTTATGAAAGTCTTGCTCAATTCAAATCTTCAGGCTTATGGG\n+>repN_6\n+TGCTTACTACCTCTCGCTAAAAGCAAAGCGCGTTCTCTGGTTATGTCTTATGCAGACGTA\n+TTTCACAGCTTCAGTAAGCGAAGATGATGATGAGATGGCTGTACTCGGTGACTCTACTTT\n+CAAAGTAAAGGTGGCTGACTATCAGCAAATTTTTCAGGTAAGCCGTAACCAGGCTATCAA\n+GGATGTTAAAGAAGGCGTGTTTGAGTTAAGCCGTTCTGCGGTAATCTTTTACCCGAAAGA\n+AGGGCGTTTTGACTGCGTCGCGCGCCCCTGGCTAACAGAGGCTGGCAGCCGATCAGCTCG\n+TGGTATCTGGGAAATCGAATTTAACCATAAACTCCTGCGGTACATTTACGGCCTGACGAA\n+CCAGTTCACCACCTACTCGCTCCGCGATTGTGGCAGTCTTCGAAATCCCCGGACGATCCG\n+CCTTTATGAAAGTCTTGCTCAATTCAAATCTTCAGGCTTATGGG\n+>repN_7\n+TGCTTACTACCTCTCGCTAAAAGCAAAGCGCGTTCTCTGGTTATGTCTTATGCAGACGTA\n+TTTCACAGCTTCAGTAAGCGAAGATGATGATGAGATGGCTGTACTCGGTGACTCTACTTT\n+CAAAGTAAAGGTGGCTGACTATCAGCAAATTTTTCAGGTAAGCCGTAACCAGGCTATCAA\n+GGATGTTAAAGAAGGCGTGTTTGAGTTAAGCCGTTCTGCGGTAATCTTTTACCCGAAAGA\n+GGGGCGTTTTGACTGCGTCGCGCGCCCCTGGCTAACAGAGGCTGGCAGCCGATCAGCTCG\n+TGGTATCTGGGAAATCGAATTTAACCATAAACTCCTGCGGTACATTTACGGCCTGACGAA\n+CCAGTTCACCACCTACTCGCTCCGCGATTGTGGCAGTCTTCGAAATCCCCGGACGATCCG\n+CCTTTATGAAAGTCTTGCTCAATTCAAATCTTCAGGCTTATGGG\n+>traJ_1\n+GTATAGGCTGTGAAGTTTTTTCGAAACTTCACTAAAAATAAGACGGCCATAGCCGAACCA\n+TTCTTCAGTAGCCATATCAGGGCTTTCCTGAACAATAGAGTTCACTAAGCGCTCGTAATC\n+ATATGAACGGCGAATTTCATTGAAAAACACCCAGCCTTCAGTGCGTTTATCATAGGCGTT\n+TAAAATAACATCGCCGGGACGATAGAAATTCTTTAAGAACCCCCCATTTGGATCTAAAGC\n+AATATTTTTGCCGCCTCTAATGATGCTCTTAAATAACAGTTCATTGAAAATTGTGGTTTT\n+ACCAGTACCGGTTGTACCGGCAATCGAAAAATGCAAGTTCTCAGCGTATGTAGGTATGGG\n+GATATTAGCCACGGTTAACTGGTTGACACCTCTTTCGCGTGTTTTATCAGCGAGTGTTCT\n+GGCGCGAACAAGCTCTGTACCACGATAAATCTTTTTGAATCTTTCGCCTTTAAACACGCG\n+TGATTTATCATAAATGATAAAAGCGATCAGACCGCCAACACCAATAAACCAG'..b'CTTCACTAAAAATAAGACGGCCATAGCCGAACCA\n+TTCTTCAGTAGCCATATCAGGGCTTTCCTGAACAATAGAGTTCACTAAGCGCTCGTAATC\n+ATATGAACGGCGAATTTCATTGAAAAACACCCAGCCTTCAGTGCGTTTATCATAGGCGTT\n+TAAAATAACATCGCCGGGACGATAGAAATTCTTTAAGAAGCCCCCATATGGATCTAAAGC\n+AATATTTTTGCCGCCTCTAATGATGCTCTTAAATAACAGTTCATTGAAAATTGTGGTTTT\n+ACCAGTACCGGTTGTACCGGCAATCGAAAAATGCAAGTTCTCAGCGTATGTAGGTATGGG\n+GATATTAGCCACGGTTAACTGGTTGACACCTCTTTCGCGTGTTTTATCAGCGAGTGTTCT\n+GGCGCGAACAAGCTCTGTACCACGATAAATCTTTTTGAATCTTTCGCCTTTAAACACGCG\n+TGATTTATCATAAATGATAAAAGCGATCAGACCGCCAACACCAATAAACCAGCCAGCAAT\n+TAAAGCTGACCATAAAGG\n+>traJ_12\n+GTATAGGCTGTGAAGTTTTTTCGAAACTTCACTAAAAATAAGACGGCCATAGCCGAACCA\n+TTCTTCAGTAGCCATATCAGGGCTTTCCTGAACAATAGAGTTCACTAAGCGCTCGTAATC\n+ATATGAACGGCGAATTTCATTGAAAAACACCCAGCCTTCAGTGCGTTTATCATAGGCGTT\n+TAAAATAACATCGCCGGGACGATAGAAATTCTTTAAGAACCCCCCATTTGGATCTAAAGC\n+AATATTTTTGCCGCCTCTAATGATGCTCTTAAATAACAGTTCATTGAAAATTGTGGTTTT\n+ACCAGTACCGGTTGTACCGGCAATCGAAAAATGCAAGTTCTCAGCGTATGTAGGTATGGG\n+GATATTAGCCACGGTTAACTGGTTGACACCTCTTTCGAGTGTTTTATCAGCGAGTGTTCT\n+GGCGCTAACAAGCTCTGTACCACGATAAATCTTTTTGAATCTTTCGCCTTTAAACACGCG\n+TGATTTATCATAAATGATAAAAGCGATCAGACCGCCAACACCAATAAACCAGCCAGCAAT\n+TAAAGCTGACCATAAAGG\n+>traJ_13\n+GTATAGGCTGTGAAGTTTTTTCGAAACTTCACTAAAAATAAGACGGCCATAGCCGAACCA\n+TTCTTCAGTAGCCATATCAGGGCTTTCCTGAACAATAGAGTTCACTAAGCGCTCGTAATC\n+ATATGAACGGCGAATTTCATTGAAAAACACCCAGCCTTCAGTGCGTTTATCATAGGCATT\n+TAAAATAACATCGCCGGGACGATAGAAATTCTTTAAGAACCCCCCATTTGGATCTAAAGC\n+AATATTTTTGCCGCCTCTAATGATGCTCTTAAATAACAGTTCATTGAAAATTGTGGTTTT\n+ACCAGTACCGGTTGTACCGGCAATCGAAAAATGCAAGTTCTCAGCGTATGTAGGTATGGG\n+GATATTAGCCACGGTTAACTGGTTGACACCTCTTTCGCGTGTTTTATCAGCGAGTGTTCT\n+GGCGCTAACAAGCTCTGTACCACGATAAATCTTTTTGAATCTTTCGCCTTTAAACACGCG\n+TGATTTATCATAAATGATAAAAGCGATCAGACCGCCAACACCAATAAACCAGCCAGCAAT\n+TAAAGCTGACCATAAAGG\n+>traJ_14\n+GTATAGGCTGTGAAGTTTTTTCGAAACTTCACTAAAAATAAGACGGCCATAGCCGAACCA\n+TTCTTCAGTAGCCATATCAGGGCTTTCCTGAACAATAGAGTTCACTAAGCGCTCGTAATC\n+ATATGAACGGCGAATTTCATTGAAAAAAACCCAGCCTTCAGTGCGTTTATCATAGGCGTT\n+TAAAATAACATCGCCGGGACGATAGAAATTCTTTAAGAACCCCCCATTTGGATCTAAAGC\n+AATATTTTTGCCGCCTCTAATGATGCTCTTAAATAACAGTTCATTGAAAATTGTGGTTTT\n+ACCAGTACCGGTTGTACCGGCAATCGAAAAATGCAAGTTCTCAGCGTATGTAGGTATGGG\n+GATATTAGCCACGGTTAACTGGTTGACACCTCTTTCGCGTGTTTTATCAGCGAGTGTTCT\n+GGCGCGAACAAGCTCTGTACCACGATAAATCTTTTTGAATCTTTCGCCTTTAAACACACG\n+TGATTTATCATAAATGATAAAAGCGATCAGACCGCCAACACCAATAAACCAGCCAGCAAT\n+TAAAGCTGACCATAAAGG\n+>korA_1\n+CCTGGAGTTATTTGAAGCAGGAAAAGTGAAGGAGGTAACGATAGAACGGGTTTCATTAAA\n+GAAGTGGTATCCCGTTTTTCAGATAGACGATGAACAGCTGGGCCAGATCGCATGTTCCAT\n+TCGGGTTAACAAAGAGCATGAGCTACGAACCTGGGCTGATTTAAGGCTACTGGCAGAGTT\n+TTTGAAAGATAAGTGTGGCGTTGAAGAATGCCGGTTAAATCTG\n+>korA_2\n+CCTGGAGCTATTTGAAGCAGGAAAAGTGAAGGAGGTAACGATAGAACGGGTTTCATTAAA\n+GAAGTGGTATCCCGTTTTTCAGATAGACGATGAACAGCTGGGCCAGATCGCATGTTCCAT\n+TAGGGTTAACAAAGAGCATGAGCTACGAACCTGGGCTGATTTAAGGCTACTGGCAGAGTT\n+TTTGAAAGATAAGTGTGGCGTTGAAGAATGCCGGTTAAATCTG\n+>korA_3\n+CCTGGAGCTATTTGAAACAGGAAAAGTGAAGGAGGTAACGATAAAACGGGTTTCATTAAA\n+GACGTGGTATCCCGTTTTTCAGATAGACGATGAACAGTTGGGCCAGATCGCATGTTCCAT\n+TCGGGTTAACAAAGAGCATGAACTACGAACCTGGGCTGATTTAAGGCTACTGGCAGAGTT\n+TTTGAAAGATAAGTGTGGCGTTGAAGAATGCCGGTTAAATCTG\n+>korA_4\n+CCTGGAGCTATTTGAAGCAGGAAAAGTGAAGGAGGTAACGATAGAACGGGTTTCATTAAA\n+GAAGTGGTATCCCGTTTTTCAGATAGACGATGAACAGCTGGGCCAGATCGCATGTTCCAT\n+TCGGGTTAACAAAGAGCATGAGCTACGAACCTGGGCTGATTTAAGGCTACTGGCAGAGTT\n+TTTGAAAGATAAGTGTGGCGTTGAAGAATGCCGGTTAAATCTG\n+>korA_5\n+CCTGGAGCTATTTGAAGCAGGAAAAGTGAAGGAGGTAACGATAGAACGGGTTTCATTAAA\n+GAAGTGGTATCCCGTTTTTCAGATAGACGATGAACAGCTGGGCCAGATCGCATGTTCCAT\n+TAGGGTTAACAAAGAGCATGAGCTACGCACCTGGGCTGATTTAAGGCTACTGGCAGAGTT\n+TTTGAAAGATAAGTGTGGCGTTGAAGAATGCCGGTTAAATCTG\n+>korA_6\n+CCTGGAGCTATTTGAAGCAGGAAAAAGTGAAGGAGGTAACGATAGAACGGGTTTCATTAA\n+AGAAGTGGTATCCCGTTTTTCAGATAGACGTATGAACAGCTGGGCCAGATCGCATGTTCC\n+ATTAGGGTTAACAAAAGAGCATGAGCTACGAACCTGGGCTGATTTAAGGCTACTGGCAGA\n+GTTTTTGAAAAGATAAGTGTGGCGTTGAAGAATGCCGGTTAAATCTG\n+>korA_7\n+CCTGGAGCTATTTGAAGCAGGAAAAGTGAAGGAGGTAACGATAAAACGGGTTTCATTAAA\n+GACGTGGTATCCCGTTTTTCAGATAGACGATGAACAGCTGGGCCAGATCGCATGTTCCAT\n+TCGGGTTAACAAAGAGCATGAGCTACGAACCTGGGCTGATTTAAGGCTACTGGCAGAGTT\n+TTTGAAAGATAAGTGTGGCGTTGAAGAATGCCGGTTAAATCTG\n' |
| b |
| diff -r 000000000000 -r 6dcb66689a7d pmlst/pmlst_db/incn.txt.clean --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pmlst/pmlst_db/incn.txt.clean Wed Aug 25 21:12:34 2021 +0000 |
| b |
| @@ -0,0 +1,25 @@ +ST repN traJ korA +1 1 1 1 +2 1 2 1 +3 1 8 1 +4 2 1 2 +5 2 3 2 +6 2 4 2 +7 3 4 2 +8 4 5 1 +9 5 6 3 +10 6 7 1 +11 6 7 4 +12 1 9 1 +13 2 4 1 +14 2 3 5 +15 7 6 3 +16 7 4 3 +17 1 3 2 +18 6 10 1 +19 3 11 2 +20 3 4 6 +21 2 12 2 +22 2 13 2 +23 6 14 7 + |
| b |
| diff -r 000000000000 -r 6dcb66689a7d pmlst/pmlst_db/pbssb1-family.fsa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pmlst/pmlst_db/pbssb1-family.fsa Wed Aug 25 21:12:34 2021 +0000 |
| b |
| b'@@ -0,0 +1,544 @@\n+>higB_1\n+ATGAATTTACTACACTTCATTGAAACCAAAGTCTTTCAGAGAGTAATCGATGGATTGCTC\n+TCACCCGACGAACTCCGGGAGTTTCAGGAAGTGTTAAGGCAAGATCCTACCGCTGGCGAT\n+ACCATATCAGGTACGGGCGGTTGCCGTAAAATTCGCTGGGCTTTACCTGGTATGGGTAAG\n+AGTGGTGGTATCAGGGTCATATACTACTATCTGACAGCAGATAACGAAGTATTCCTTCTT\n+ATCGCTTATCCCAAGAACGAGAAAGACAATCTCACTAATGCTGAAAAGAACCAGTTGAAA\n+AAAGCCGTAGAAGGTATAGAGCAAGCCTCCCAGGAGGCAAGGGGGAAGAAATGA\n+>higB_2\n+ATGAATTTACTACACTTCATTGAAACCAAAGTCTTTCAGAGAGTGATTGATGGATTGCTT\n+TCACCTGACGAACTCCGGGAGTTTCAGGAAGTGTTAAGGCAAGATCCTACCGCTGGCGAT\n+ACCATATCAGGTACGGGCGGTTGCCGTAAGATTCGCTGGGCTTTGCCTGGTATGGGTAAA\n+AGTGGTGGTATCAGGGTCATATACTACTATCTGACAGCAGATAACGAAGTATTCCTTCTT\n+ATAGCTTATCCCAAGAACGAGAAAGACAATCTCACTAATGCTGAAAAGAACCAGTTGAAG\n+AAAGCCGTAGAAGGTATAGAGCAAGCCTCCCAGGAGGCAAGGGGGAAGAAATGA\n+>higB_3\n+ATGAATTTACTACACTTCATTGAAACCAAAGTCTTTCAGAGAGTAATCGATGGATTGCTC\n+TCACCCGACGAACTCCGGGAGTTTCAGGAAGTGTTAAGGCAAGATCCTACCGCTGGCGAT\n+ACCATATCAGGTACGGGCGGTTGCCGTAAGATTCGCTGGGCTTTGCCTGGTATGGGTAAG\n+AGTGGTGGTATCAGGGTCATATACTACTATCTGACAGCAGATAACGAAGTATTCCTTCTT\n+ATCGCTTATCCTAAGAACGAGAAAGACAATCTCACTAATGCTGAAAAGAACCAGTTGAAG\n+AAAGCCGTAGAAGGTATCGAGCAAGCCTCCCAGGAGGCAAGGGGGAAGAAATGA\n+>higB_4\n+ATGAATTTACTACACTTCATTGAAACCAAAGTCTTTCAGAGAGTGATCGATGGATTGCTT\n+TCACCTGACGAACTCCGGGAGTTTCAGGAAGTGTTAAGGCAAGATCCTACCGCTGGCGAT\n+ACCATATCAGGTACGGGCGGTTGCCGTAAGATTCGCTGGGCTTTGCCTGGTATGGGTAAA\n+AGTGGTGGTATCAGGGTCATATACTACTATCTGACAGCAGATAACGAAGTATTCCTTCTT\n+ATCGCTTATCCTAAGAACGAGAAAGACAATCTCACTAATACTGAAAAGAACCAGTTGAAG\n+AAAGCCGTAGAAGGTATAGAGCAAGCCTCCCAGGAGGCAAGGGGGAAGAAATGA\n+>higB_5\n+ATGAATTTACTACACTTCATTGAAACCAAAGTCTTTCAGAGAGTAATCGATGGATTGCTT\n+TCACCCGACGAACTCCGGGAGTTTCAGGAAGTGTTAAGGCAAGATCCTACCGCTGGCGAT\n+ACCATATCAGGTACGGGCGGTTGCCGTAAGATTCGCTGGGCTTTGCCTGGTATGGGTAAA\n+AGTGGTGGTATCAGGGTCATATACTACTATCTGACAGCAGATAACGAAGTATTCCTTCTT\n+ATAGCTTATCCCAAGAACGAGAAAGACAATCTCACTAATGCTGAAAAGAACCAGTTGAAG\n+AAAGCCGTAGAAGGTATAGAGCAAGCCTCCCAGGAGGCAAGGGGGAAGAAATGA\n+>higB_6\n+ATGAATTTACTACACTTCATTGAAACCAAAGTCTTTCAGAGAGTAATCGATGGATTGCTT\n+TCACCCGACGAACTCCGGGAGTTTCAGGAAGTGTTAAGGCAAGATCCTACCGCTGGCGAT\n+ACCATATCAGGTACGGGCGGTTGCCGTAAGATTCGCTGGGCTTTGCCTGGTATGGGTAAG\n+AGTGGTGGTATCAGGGTCATATACTACTATCTGACAGCAGATAACGAAGTATTCCTTCTT\n+ATCGCTTATCCTAAGAACGAGAAAGACAATCTCACCAATGCTGAAAAGAACCAGTTGAAG\n+AAAGCCGTAGAAGGTATAGAGCAAGCCTCCCAGGAGGCAAGGGGGAAGAAATGA\n+>higB_7\n+ATGAATTTACTACACTTCATTGAAACCAAAGTCTTTCAGAGAGTAATCGATGGATTGCTT\n+TCACCCGACGAACTCCGGGAGTTTCAGGAAGTGTTAAGGCAAGATCCTACCGCTGGCGAT\n+ACCATATCAGGTACGGGCGGTTGCCGTAAGATTCGCTGGGCTTTGCCTGGTATGGGTAAG\n+AGTGGTGGTATCAGGGTCATATACTACTATCTGACAGCAGATAACGAAGTATTCCTTCTT\n+ATCGCTTATCCTAAGAACGAGAAAGACAATCTCACCAATGCTGAAAAGAACCAGTTGAAG\n+AAAGCCGTAGAAGGTTTAGAGCAAGCCTCCCAGGAGGCAAGGGGGAAGAAATGA\n+>higB_8\n+ATGAATTTACTACACTTCATTGAAACCAAAGTCTTTCAGAGAGTAATCGATGGATTGCTT\n+TCACCCGACGAACTCCGGGAGTTTCAGGAAGTGTTAAGGCAAGATCCTACCGCTGGCGAT\n+ACCATATCAGGTACGGGCGGTTGCCGTAAGATTCGCTGGGCTTTGCCTGGTATGGGTAAG\n+AGTGGTGGTATCAGGGTCATATACTACTATCTGACAGCAGATAACGAAGTATTCCTTCTT\n+ATCGCTTATCCCAAGAATGAGAAAGACAATCTCACCAATGCTGAAAAGAACCAGTTGAAG\n+AAAGCCGTAGAAGGTATAGAGCAAGCCTCCCAGGAGGCAAGGGGGAAGAAATGA\n+>higB_9\n+ATGAATTTACTACACTTCATTGAAACCAAAGTCTTTCAGAGAGTGATTGATGGATTGCTT\n+TCACCTGACGAACTCCGGGAGTTTCAGGAAGTGTTAAGGCAAGATCCTACCGCTGGCGAT\n+ACCATATCAGGTACGGGCGGTTGCCGTAAGATTCGCTGGGCTTTGCCTGGTATGGGTAAG\n+AGTGGTGGTATCAGGGTCATATACTACTATCTGACAGCAGATAACGAAGTATTCCTTCTT\n+ATCGCTTATCCTAAGAACGAGAAAGACAATCTCACCAATGCTGAAAAGAACCAGTTGAAG\n+AAAGCCGTAGAAGGTATCGAGCAAGCCTCCCAGGAGGCAAGGGGGAAGAAATGA\n+>higB_10\n+ATGAATTTACTACACTTCATTGAAACCAAAGTCTTTCAGAGAGTGATCGATGGATTGCTT\n+TCACCTGACGAACTCCGGGAGTTTCAGGAAGTGTTAAGGCAAGATCCTACCGCTGGCGAT\n+ACCATATCAGGTACGGGCGGTTGCCGTAAGATTCGCTGGGCTTTGCCTGGTATGGGTAAA\n+AGTGGTGGTATCAGGGTCATATACTACTATCTGACAGCAGATAACGAAGTATTCCTTCTT\n+ATCGCTTATCCTAAGAACGAGAAAGACAATCTCACTAATGCTGAAAAGAACCAGTTGAAG\n+AAAGCCGTAGAAGGTATAGAGCAAGCCTCCCAGGAGGCAAAGGGGAAGAAATGA\n+>higB_11\n+ATGAATTTACTACACTTCATTGAAACCAAAGTCTTTCAGAGAGTGATTGATGGATTGCTT\n+TCACCCGACGAACTCCGGGAGTTTCAGGAAGTGTTAAGGCAAGATCCTACCGCTGGCGAT\n+ACCATATCAGGTACAGGCGGTTGCCGTAAGATTCGCTGGGCTTTGCCTGGTATGGGTAAG\n+AGTGGTGGTATCAGGGTCATATACTACTATCTG'..b'CGAATCGAAAAGCACATTGCT\n+GATATGAAAGCAAAAGAGAAGGCATAA\n+>soj_19\n+ATGATTCCGTATTCTGTCTGGAACTTCAAGGGAGGTGTCGGGAAGAGCCACACTAGTCTA\n+ACTCTCTCCGGGTATCTGGCCAGTCAGGGTAAGCGTGTGGCACTGGTTGATTATGACCCA\n+CAAAACGGGGCTATGATCTGTTCAGACATTGCCAAAGCAAATGGAAGCCCTTTACCCTTT\n+GTGGTTGTTAAAAGCCTGAGTGAAATAAACCGCGACGAGATAGATGCTGTTGTGTTCGAT\n+CACTCCCCAGGTGTTAACCCTGGCGGTCAGCTTGCCCCTATCGTTATCATTCCGACTATC\n+CTCGATGCAGCAAGCCATTCAATCACTATCAAGAGTGTTCACGAACTGGACGGAACGGAC\n+AAGCTCTGTATCGTCATTCCTAATCGTGTAGAACTGCAAAACAAAGAGCATAAAGACCTG\n+CTCGAAATGCAGTTTGAAAATGTCCCCTACATGAAGAAGCGAGTCTCTTACTCTCGTGCC\n+TACGGCATGGGTGTAACTATCTATTCGGAAGGTACAGGCTTACCGAACCTGGGGATCACT\n+CGCCAGGAGTTCGACGGTGTAGCTAAATACATTCATAAACGAATCGAAAAACACATTGCT\n+GATATGAAAGCAAAAGAGAAGGCATAA\n+>soj_20\n+ATGATTCCGTATTCTGTCTGGAATTTCAAGGGAGGTGTTGGGAAGAGCCATACTAGTCTA\n+ACTCTCTCCGGGTATCTGGCCAATCAGGGTAAGCGTGTGGCACTGGTTGATTATGACCCA\n+CAAAACGGGGCTATGATCTGTTCAGACATTGCCAAAGCAAATGGAAGCCCTTTACCCTTT\n+TTGGTTGTTAAAAGCCTGAGTGAAATAAACCGCGACGAGATAGATGCTGTTGTGTTCGAT\n+CACTCCCCAGGTGTTAACCCTGGCGGTCAGCTTGCCCCTATCGTTATCATTCCGACTATC\n+CTCGATGCAGCAAGCCATTCAATCACTATCAAGAGTGTTCACGAACTGGACGGAACGGAC\n+AAGCTCTGTATCGTCATTCCTAATCGTGTAGAACTGCAAAACAAAGAGCATAAAGACCTG\n+CTCGAAATGCAGTTTGAAAATGTCCCCTACATGAAGAAGCGAGTCTCTTACTCTCGTGCC\n+TACGGCATGGGTGTAACTATCTATTCGGAAGGTACAGGCTTACCGAACCTGGGGATCACT\n+CGCCAGGAGTTCGACGGTGTAGCTAAATACATTCATAAACGAATCGAAAAACACATTGCT\n+GATATGAAAGCAAAAGAGAAGGCATAA\n+>soj_21\n+ATGATTCCGTATTCAGTATGGAACTTCAAGGGAGGTGTTGGGAAAACCCACACTAGTTTA\n+ACTCTCTCCGGGCATCTGGCCAGTCAAGGTAAACGGGTGGCACTTGTTGACTACGACCCT\n+CAGAACGGGGCTACAATCTGTTCAGATATTGCCAAAGCAAATGGAAGCCCTTTACCGTTT\n+TTGGTGGTAAAAAGCCTGAGTGAAATAAACCGCGACGAGATAGATGCTGTTGTCTTCGAC\n+CATTCTCCAGGTGTCAACCCTGGCGGTCAGCTTGCCCCTATCGTTATCGTTCCTACTATC\n+CTCGATGCAGCAAGCCATTCCATCACTATCAAGAGTGTTCACGAACTGGACGGAACGGAC\n+AAGCTATGTATCGTCATTCCTAACCGCGTAGAACTGCAAAACAGGGAACATAAAGACCTC\n+CTGGAAATGCAGTTTGAAAATGTTCCTTATATGAAGAAGCGAGTCTCTTACTCTCGTGCA\n+TACGGCATGGGTGTAACTATCTATTCAGAAGGTACGGGCTTACCGAACCTGGGGATCACT\n+CGCCAGGAGTTCGACGGGGTAGCTAAATACATTCATAAACGAATCGAAAAACACATTGCT\n+GATATGAAAGCAAAAGAGAAGGCATAA\n+>soj_22\n+ATGATTCCGTATTCAGTATGGAACTTCAAGGGAGGTGTTGGGAAAACTCACACTAGTTTA\n+ACTCTCTCCGGGCATCTGGCCAGTCAAGGTAAACGGGTGGCACTTGTTGACTACGACCCT\n+CAGAACGGGGCTACAATCTGTTCAGATATTGCCAAAGCAAATGGAAGCCCTTTACCGTTT\n+TTGGTGGTAAAAAGCCTGAGTGAAATAAACCGCGACGAGATAGATGCCGTTGTCTTTGAC\n+CATTCCCCAGGTGTTAACCCTGGTGGTCAGCTTGCCCCTATCGTTATTGTTCCTACCATC\n+CTCGATGCTGCAAGCCATTCTATCACTATCAAAAGTGTTCACGAACTGGACGGAACAGAT\n+AAGCTCTGTATCGTCATTCCAAACCGTGTCGAACTGCAAAACAGGGAACATAAAGACCTT\n+CTGGAAATGCAGTTTGAAAATGTTCCCTACATGAAGAAGCGAGTCTCTTACTCTCGTGCA\n+TACGGTATGGGTGTAACTATCTATTCAGAAGGAACAGGCTTACCGAACCTGGGGATCACT\n+CGCCAGGAGTTCGACGGGGTAGCTAAATACATTCATAAACGAATCGAAAAACACATTGCT\n+GATATGAAAGCAAAAGAGAAGGCATAA\n+>soj_23\n+ATGATTCCGTATTCTGTCTGGAATTTCAAGGGAGGTGTTGGGAAGAGTCACACGAGTTTA\n+ACTCTCTCTGGGTATCTGGCCAGTCAGGGTAAGCGGGTGGCACTGGTTGATTATGACCCA\n+CAGAACGGGGCTATGATCTGTTCTGATATCGCCAAAGCAAATGGAAGCCCTTTACCATTT\n+TTGGTTGTTAAAAGCCTGAGTGAAATAAACCGCGACGAGATAGATGCTGTTATCTTCGAC\n+CATTCCCCAGGTGTCAACCCTGGCGGTCAGCTTGCCCCTATCGTTATCATTCCGACTATC\n+CTCGATGCAGCAAGCCATTCAATCACTATCAAGAGTGTTCACGAACTGGACGGAACGGAC\n+AAGCTCTGTATCGTCATTCCTAACCGTGTAGAACTGCAAAACAGGGAACACAAAGACCTC\n+CTGGAAATGCAGTTTGAAAATGTTCCATACATGAAAAAGCGAGTCTCTTACTCTCGTGCA\n+TACGGTATGGGGGTAACTATCTATTCGGAAGGTACTGGCTTGCCGAACCTGGGGATCACT\n+CGCCAGGAGTTCGACGGTGTAGCTAAATATATTCATAAACGAATCGAAAAGCACATTGCT\n+GATATGAAAGCAAAAGAGAAGGCATAA\n+>soj_24\n+ATGATTCCGTATTCCGTCTGGAACTTTAAGGGTGGCGTTGGGAAGAGTCACACGAGTTTA\n+ACTCTCTCTGGGTATCTGGCCAGTCAGGGTAAGCGGGTGGCACTGGTTGATTATGACCCA\n+CAGAACGGGGCTATGATCTGTTCTGATATCGCCAAAGCAAATGGAAGCCCTTTACCATTT\n+TTGGTTGTTAAAAGCCTGAGTGAAATAAACCGCGACGAGATAGATGCTGTTATCTTCGAC\n+CATTCCCCAGGTGTCAACCCTGGCGGTCAGCTTGCCCCTATCGTTATCATTCCGACTATC\n+CTCGATGCTGCAAGCCATTCCATCACTATCAAGAGTGTTCACGAACTGGATGGAACAGAT\n+AAGCTCTGTATCGTCATTCCTAACCGTGTCGAACTGCAAAACAGGGAACACAAAGACCTC\n+CTGGAAATGCAGTTTGAAAATGTTCCCTACATGAAGAAGCGAGTCTCTTACTCTCGTGCA\n+TACGGTATGGGTGTAACTATCTATTCAGAAGGTACAGGCTTACCGAACCTGGGGATCACT\n+CGCCAGGAGTTCGACGGTGTAGCTAAATACATTCACAAACGAATCGAAAAACATATTGCT\n+GATATGAAAGCAAAAGAGAAGGCATAA\n' |
| b |
| diff -r 000000000000 -r 6dcb66689a7d pmlst/pmlst_db/pbssb1-family.txt.clean --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pmlst/pmlst_db/pbssb1-family.txt.clean Wed Aug 25 21:12:34 2021 +0000 |
| b |
| @@ -0,0 +1,37 @@ +ST higB mqsA soj +1 4 1 4 +2 5 2 3 +3 6 4 5 +4 11 4 9 +5 9 7 6 +6 12 9 10 +7 9 7 3 +8 13 10 11 +9 6 4 3 +10 3 3 3 +11 14 11 12 +12 2 2 13 +13 6 4 14 +14 6 4 6 +15 2 12 3 +16 1 1 1 +17 5 2 16 +18 2 2 3 +19 6 4 17 +20 6 14 5 +21 15 13 18 +22 16 15 3 +23 6 9 19 +24 2 16 20 +25 1 13 15 +26 17 7 21 +27 18 7 22 +28 19 4 3 +29 8 6 7 +30 10 8 8 +31 21 2 3 +32 22 17 24 +33 20 14 23 +34 7 5 3 +35 2 2 2 + |
| b |
| diff -r 000000000000 -r 6dcb66689a7d pmlst/test.fsa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pmlst/test.fsa Wed Aug 25 21:12:34 2021 +0000 |
| b |
| b'@@ -0,0 +1,1734 @@\n+>pSFO157\r\n+ATGACAGAGCAGAAGCGACCGGTAGTGACACTGAAGCGGAAGACAGAGGGAACAGCGCCTGTCCGCAGCC\r\n+GGAAAACCATCATCAATGTCACCACGCCACCAAAATGGAAGGTGAAAAAGCAGAAGCTGGCGGAGAAAGC\r\n+GGCTCGGGAAGCAGAGCTGGTGGCAAAAAAAGCGCAGGCCAGACAGGCGCTGTCCATTTATCTGAACCTG\r\n+CCCACACTGGATGAAGCCGTGAACACCCTGAAGCCCTGGTGGCCGGGATTATTTGACGGTGACACCCCCC\r\n+GGCTTCTGGCCTGCGGTATCCGGGACGTGTTACTGGAAGACGTGGCGCAGCGGAATATCCCGCTTTCGCA\r\n+TAAAAAACTGCGCAGGGCGCTGAAGGCCATCACCCGTTCAGAAAGCTATCTTGGCGCCATGAAAGCCGGT\r\n+GCCTGCCGGTATGACACGGAAGGGTATGTGACGGAGCATATTTCTCAGGAGGAGGAAGCGTATGCGGCAG\r\n+CGCGTCTGGATAAAATCCGCCGCCAGAACCGGATAAAGGCAGAACTTCAGTCCGTGCTTGATGAGAAATA\r\n+AAAAAAAGCCTCCCTCAGAGAGAGGAGGCAGGGAAATAAGGCTTAAAAGGAAATAACTTCCGTACCCGAA\r\n+AGGAAGTCAGTCCAGTGGATTATTTAACACCATAATACAGACGGGTTAAAGGGGAGAGCTAAAGATGAAT\r\n+GGATTCAGAAACAGTTCACGGAACGGTCAGGTCTGGCGTTACCAGCGTGCCGGTGGGCGGGCTGTTATTC\r\n+TGGAGGTCAGTGGACGCTGGATGGAAGCGGCAGAAGCATGGCGACGGGCTGCCTGTATAGCTCCCCGGAC\r\n+AGACTGGCAGCAGTTTGCCCGAAAAAGGGCTGAACACTGCCACCGGCGCTGCCGGGGTAGGGTGTAACGA\r\n+AAAAAGCAGCCTTCATTACTCCAGGGATTCAGAAGGCTGAATAATGCATGAGATTTGCTTTTTTTAATAT\r\n+CCAGTCGGGCAGTATGGCCGGACAGTTCTGAGTAGCACGGAGTTTTTTCCGTATTAAGTCGTGATTTTAT\r\n+ATTTTGTGATTAATTTCACAAAATAAGGTGTTGTTCAGTGTGTGCTGCGATATTCAGGATTGCCTGAAAT\r\n+ACAGGTGCCATTTATCTGATATGGAGAATAACATGAGGAAATATATTCCACTGGTATTATTTATCTTTTC\r\n+ATGGCCGGTATTGTCTGCAGATATTCATGGACGGGTTGTTCGTGTACTGGACGGTGATACCATCGAGGTA\r\n+ATGGACTCACTGAAGGCAGTGCGGATCAGGCTGGTAAATATTGATGCACCGGAAAAGAAACAGGATTATG\r\n+GCCGGTGGTCGACAGATATGATGAAATCACTGGTTGCAGGAAAAACGATTACCGTCACATATTTTCAGCG\r\n+AGATCGTTATGGTCGTATTCTCGGGCAGGTTTATGCACCAGACGGAATGAATGTTAATCAGTTTATGGTC\r\n+CGGGCCGGGGGTGCCTGGGTATATGAGCAGTACAACACAGATCCCGTGCTGCCTGTCCTTCAGAACGAAG\r\n+CCAGACAACAAAAACGTGGGCTCTGGTCAGATGCTGATCCGGTTCCACCCTGGATATGGAGACACCGTAA\r\n+ATAAAGCGATGGCAATCTTATCATTCATCTGTTCTCAGCGGGAATAAAAATGGCAAAAACAAAACAGGAA\r\n+TGGCTGTATCCGTTACGGCGATGTTCATCAGTTAATTAATACGCTGGGAAAAATTATTCATAAAAACAGA\r\n+GACAGTTTATCGGCCAGTGAATGTGAATCATTTAATCCAGCAGCAGACCACCGGTTAGTGGAATTAATCA\r\n+CCGGAAAGTTATATGACAGGATACCAAAAGATATATGGAAATATGTAAGGTAATAATTCAGCACAATTAA\r\n+TTGCCAGGAGCAGATAAATAATGAAGTTGATTATTTTTATTCTCATTGTTCTGATTATTGCAGCGTTACT\r\n+TATCCGGATCATCCTCAGAAGTGTAAATCAGCATTCTCCTTTGCTGATGCAATTGCATGCGGCAGGTATA\r\n+CGGACCGGTGATGCAGAACGAATACTGTCCGGCGGTGAATACTGGCAACGTCAGAAGACGCTGCTGACAG\r\n+AAAGGGAAGTCAGTTTTATGAAAGGACTGTTCAGAATTGTGGATATGAAGCGGTGGTATCTGTGTCCGCA\r\n+GGTACGGGTCGCGGATATCGTCCAGCTGAACGGGAATATCCGGCCACGATCACGCCAGTGGTGGCAGTTA\r\n+TTCAGGATGGTGTCTCAGTGGCATGTTGATGTGGTTATCGTTGAGCGGTGTTCGTTCAGTATTGTTGCTG\r\n+CAGTAGAGCTGGATGATGCCAGCCATTTACGACCGGAACGCAGACGCCGGGATATTCTTCTGGAAGAGGT\r\n+TCTGAGGCAGGCTGGTATTCCGTTGCTCAGAAGCCACGATGCCAGAAAACTGCTGCAGATGACCGGAGAA\r\n+TGGCTGAATACAACAGGGGCTGCTCAGCAGTCACCGGAACATCGTAGCTGACGCCTTCGCGTTGCTCAGT\r\n+TGTCCAACCCCGGAAACGGGAAAAAGCAAGTTTTCCCCGCTCCCGGCGTTTCTGTAACAAAAACAGGTAA\r\n+ATGGGGGTAATAGTCAGCAACAGGGAATGTGGTATTATCGCGGCGGGTGTCTGAGCCTTTCTGGTTCAGG\r\n+CAAGACGCAGGTACCAGAAATGCGAAGACCCCACTCGTTAATCCATTAACTCGTGAGGTCTGCATGAAGT\r\n+TCCTAGCAGTTCTGATTGTAGCCTCTTCCTTGCAGAGAGGTCAAAGTTTATGACGAAATATGCCCTTATC\r\n+GGGTTGCTCGCCGTGTGTGCCACGGTGTTGTGTTTTTCACTGATATTCAGGGAACGGTTATGTGAACTGA\r\n+ATATTCACAGGGGAAATACAGTGGTGCAGGTTACTTTGGCCTACGAAGCACGGAAGTAAGCTGCCGGGCG\r\n+GGGACGGAAGTCCCCGCTTTCCGGAAGTGTGAGGTATTTCAGGGGCAGACACCCGACATGCCAGAAACAG\r\n+CCGGTCCCGCCCGGGGCCGGCACCCGGGTTAAGGCATTTCCTGTTTTTCAGCCATTTCGCAACAAAATTC\r\n+ACACTAAACGACGGTAATTCCTGTTGATTTGTGCGCCAACACAGATCTTCGTCACAATTCTCAAGTCGCT\r\n+GATTTCAAAAAACTGTAGTATCCTCTGCGAAACGATCCCTGTTTAAGTATTGAGGAGGCGAGATGTCACA\r\n+GACAGAAAATGCAGTGACTTCCTCATCTGGCGTAAAGCGAGCATACAGAAAAGGTAATCCTCTGACACTT\r\n+GCAGAACGTCAGCAGGCATCCCTGGCAAGAAAACGAGCTACACATAAAGAACTCAGAGTGTTCATTCCTG\r\n+CTGCGTTAAAAGCGCAATTGCAGGAGATGTGTGAAGCTGAGGGCGTTACCCAGGCTGAGATGATTGCCGA\r\n+ACTGATAAAGCAGAAGAGTGCTTTTAGCTAACTAGAATGTAGCGACATCACATTCTTGCCTGTTTCCGGT\r\n+GTGCGTGATAGATTGCTGATCGTTTAAGGAATTTTGTGGCTGGCCACGCCATAAGGTGGCAGGGAACTGG\r\n+TTCTGATGTGGATGTACAGGAGCCAGAAAAGCGAAAACCCCGATAATCTTTCTATGTTTGGCGACGAAGA\r\n+AGATTACCGGGGCCATCTAAAAACCGCATAGAAGCTGTTGCTCTATGCGGGGAGTATAGTTATATGCCCG\r\n+GAAAAGTTCAAGACTTCTTTCTGTGCTCACTCCTTCTGTGCAACATAAGTGCAGGATGGTGTGACTGATC\r\n+TTCAACAAACGTATTACCGCCAGGTA'..b'GAACCGGCCACCCTGCCTGTGGCTGATTCACCGTTCACGGCACTGAAGCTGGA\r\n+GAACGGCTGGGTGGAAACGCCCGGGCATTCCGTCAGCGACAGTGCGAAGGTTTTTGCCTCCGTCACACAG\r\n+ATGGCAATGGACAACGCCACCCTGAACGGTCTGGCCCGCAGCGGTCGTGATGTCCGGCTGTATTCCTCAC\r\n+TGGATGAAACCCGTACTGCGGAAAAACTTGCCCGCCATCCCTCCTTTACGGTGGTTTCTGAGCAGATAAA\r\n+GGCGCGTGCCGGTGAGACATTGCTGGAAACCGCTATCAGTCTGCAGAAAGCCGGGCTTCACACGCCGGCA\r\n+CAGCAGGCTATTCATCTGGCGCTTCCTGTGGTGGAAAGTAAAAACCTGGCCTTCAGCATGGTGGACCTGC\r\n+TGACAGAGGCGAAGTCGTTTGCTGCAGAAGGAACCAGTTTTACTGAACTGGGAGGGGAAATCAATGCGCA\r\n+GATAAAACGCGGTGATTTACTGTATGTGGATGTGGCAAAAGGCTATGGCACAGGCCTGCTGGTTTCCCGT\r\n+GCGTCGTATGAGGCAGAAAAGAGCATTCTTCGCCATATTCTCGAAGGTAAGGAGGCGGTCACGCCGCTGA\r\n+TGGAGAGAGTACCTGGCGAACTCATGGAGAAACTGACATCAGGACAGCGTGCCGCTACCCGCATGATACT\r\n+GGAAACGTCCGACCGTTTCACGGTGGTGCAGGGCTATGCCGGTGTGGGTAAGACCACACAGTTCCGGGCG\r\n+GTGATGTCAGCCGTGAACATGCTGCCGGAGAGTGAACGTCCCCGTGTCGTGGGGCTGGGGCCCACGCACC\r\n+GTGCGGTCGGTGAGATGCGCAGCGCCGGCGTGGATGCACAGACGCTGGCGTCCTTTCTGCATGACACGCA\r\n+GCTGCTGCAGCGCAGCGGAGAAACGCCGAATTTCAGCAACACGCTGTTCCTGCTCGATGAGAGCTCTATG\r\n+GTGGGCAATACCGACATGGCACGGGCATACGCCCTGATTGCGGCCGGTGGCGGTCGTGCCGTGGCCCGTG\r\n+GTGACACGGACCAGTTGCAGGCCATCGCGCCCGGTCAGCCTTTCCGTCTCCAGCAGACGCGCAGTGCTGC\r\n+CGATGTGGCCATCATGAAGGAGATTGTGCGCCAGACGCCGGAGCTGCGGGAGGCGGTATACAGCCTGATT\r\n+AACCGGGATGTGGAAAGGGCACTGTCCGGGCTTGAGAGTGTGAAACCGTCTCAGGTGCCACGTCAGGAGG\r\n+GCGCATGGGTACCGGAGCACTCCGTGACGGAGTTCAGTCACAGCCAGGAAGCGAAACTGGCAGAAGCGCA\r\n+GCAGAAGGCGATGCTGAAAGGTGAGGCTTTTCCGGATATTCCCATGACACTGTATGAAGCCATTGTCCGC\r\n+GATTATACCGGCAGGACGCCGGAAGCACGGGAGCAGACGCTGATTGTCACGCATCTGAATGAGGACCGGC\r\n+GCGTACTGAACAGCATGATTCATGATGCACGGGAAAAGGCCGGTGAGCTGGGAAAAGAGCAGGTCATGGT\r\n+GCCTGTCCTGAACACAGCGAATATACGCGACGGGGAGTTGCGTCGTCTCTCCACCTGGGAGACACATCGG\r\n+GACGCACTTGCCCTGGTGGATAATGTGTATCACCGGATTGCCGGTATCAGCAAGGATGACGGGCTGATAA\r\n+CCCTGCAGGATGCGGAAGGTAACACGCGGCTGATTTCGCCCCGGGAGGCGGTGGCTGAAGGCGTCACACT\r\n+GTACACTCCGGACACCATCCGGGTGGGAACCGGTGACCGGATGCGCTTCACGAAGAGTGACCGGGAGCGC\r\n+GGTTATGTGGCCAACAGCGTCTGGACGGTGACAGCAGTTTCCGGTGACAGTGTCACGCTGTCGGACGGAC\r\n+AGCAGACCCGGGTGATTCGCTCCGGTCAGGAGCGGGCAGAGCAACATATTGACCTGGCCTATGCCATCAC\r\n+CGCCCACGGTGCGCAGGGGGCAAGTGAAACCTTTGCCATTGCGCTTGAAGGCACGGAAGGTAACCGGAAA\r\n+CAGATGGCCGGCTTTGAGTCAGCCTACGTGGCCCTGTCGCGTATGAAGCAGCATGTGCAGGTGTATACCG\r\n+ATAACCGTCAGGGCTGGACGGATGCCATTAACAATGCCGTACAGAAAGGAACTGCCCACGATGTGCTTGA\r\n+GCCGAAATCGGACCGGGAGGTCATGAATGCAGAGCGGCTGTTCAGTACGGCGCGGGAGTTGCGGGACGTG\r\n+GCGGCCGGCCGTGCCGTTCTCCGTCAGGCAGGGCTGGCCGGGGGAGACAGTCCTGCACGGTTTATTGCAC\r\n+CCGGGCGAAAATATCCGCAGCCGTATGTGGCACTGCCGGCTTTTGACCGTAACGGCAAGTCAGCTGGTAT\r\n+CTGGCTGAACCCGCTGACCACGGATGACGGAAACGGACTGCGGGGCTTCAGTGGTGAAGGCCGGGTGAAA\r\n+GGCAGCGGGGATGCGCAGTTCGTGGCCCTGCAGGGCAGCCGTAACGGAGAGAGCCTGCTGACTGATAATA\r\n+TGCAGGATGGTGTCCGGATTGCCCGTGATAATCCTGACAGCGGTGTGGTGGTAAGAATCGCCGGTGAAGG\r\n+TCGTCCGTGGAATCCCGGTACCATCACCGGTGGTCGCGTGTGGGGGGATATCCCGGACAACAGCGTTCAG\r\n+CCGGGAGCCGGAAATGGCGAACCGGTCACGGCAGAGGTACTGGCACAGCGGCAGGCTGAAGAGGCCATCC\r\n+GCCGTGAAACGGAACGCCGTGCGGATGAAATTGTCCGTAAAATGGCAGAGAACAAACCTGACCTGCCGGA\r\n+CGGCAAAACAGAGCAGGCTGTCAGGGATATTGCCGGGCTGGAGCGTGACCGGTCTGCCATATCTGAACGG\r\n+GAAGCCGCGCTGCCGGAGAGTGTACTGCGTGAACCACAGCGGGTGCGGGAAGCGGTCCGGGAGGTTGCCC\r\n+GGGAAAATCTGCTGCAGGAGCGACTGCAGCAGATGGAGCGGGATATGGTTCGTGACCTGCAGAAAGAGAA\r\n+AACCCTGGGCGGAGACTGATACAGGAAGATAAACGCTGATGACAACGGATAACACGAACACAACACGTAA\r\n+TGATTCACTGGCTGCCCGGACCGATACCTGGTTGCAGTCGTTGCTGGTCTGGTCACCCGGACAGCGGGAT\r\n+ATCATCAAAACGGTGGCACTGGTGCTGATGGTTCTGGACCATGCAAACCGCATTCTGCATCTGGACCAGT\r\n+CGTGGATGTTTCTGGTCGGGCGTGGGGCCTTTCCGCTGTTTGCGCTGGTCTGGGGACTGAATCTGTCCCG\r\n+TGATGCGCATATCCGGCAACCGGCCATTAACCGGCTGTGGGGATGGGCTGTGATTGCCCAGTTCGCGTAT\r\n+TACGTTGCCGGCTTTCCCTGGTATGAGGGGAATATCCTGTTTGCCTTTGCAGTGGCGGCACAGGTGCTGA\r\n+CGTGGTGTGAGACGCGCAGCCTGTGGCGTACTGCCGCGGCCATACTCCTGATGGCATTGTGGGGGCCTTT\r\n+GTCCGGCACCAGTTACGGCATTGCCGGGCTGCTGATGCTGGCGGTCAGTCACCGGCTGTACCGGGCGGAA\r\n+GACAGAACGGAACGTCTGGCGCTGGTTGCATGCCTGCTGGCCGTGATTCCGGCACTTAACCTTGCCTCCA\r\n+GTGATGCGGCGGCTGTAGCTGGTCTTGTGATGACGGTGCTGACCGTTGGTCTGGTGTCGTGTGCAGGGAA\r\n+ATCATTACCCCGTTTCTGGCCCGGGGATTTTTTCCTGACGTTCTATGCCTGTCATCTGGCTGTGCTGGGC\r\n+GTTCTGGCGCTGTGACGGGTGTGGTATCTTTGGCCGCAAGAGGATGATTCGTCAGAGGCAGAACACAGC\r\n+\r\n' |
| b |
| diff -r 000000000000 -r 6dcb66689a7d pmlst/tmp_pMLST/tmp/out_inchi2.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pmlst/tmp_pMLST/tmp/out_inchi2.xml Wed Aug 25 21:12:34 2021 +0000 |
| b |
| @@ -0,0 +1,44 @@ +<?xml version="1.0"?> +<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd"> +<BlastOutput> + <BlastOutput_program>blastn</BlastOutput_program> + <BlastOutput_version>BLASTN 2.11.0+</BlastOutput_version> + <BlastOutput_reference>Zheng Zhang, Scott Schwartz, Lukas Wagner, and Webb Miller (2000), "A greedy algorithm for aligning DNA sequences", J Comput Biol 2000; 7(1-2):203-14.</BlastOutput_reference> + <BlastOutput_db></BlastOutput_db> + <BlastOutput_query-ID>Query_1</BlastOutput_query-ID> + <BlastOutput_query-def>pSFO157</BlastOutput_query-def> + <BlastOutput_query-len>121239</BlastOutput_query-len> + <BlastOutput_param> + <Parameters> + <Parameters_expect>10</Parameters_expect> + <Parameters_sc-match>1</Parameters_sc-match> + <Parameters_sc-mismatch>-2</Parameters_sc-mismatch> + <Parameters_gap-open>0</Parameters_gap-open> + <Parameters_gap-extend>0</Parameters_gap-extend> + <Parameters_filter>m;</Parameters_filter> + </Parameters> + </BlastOutput_param> +<BlastOutput_iterations> +<Iteration> + <Iteration_iter-num>1</Iteration_iter-num> + <Iteration_query-ID>Query_1</Iteration_query-ID> + <Iteration_query-def>pSFO157</Iteration_query-def> + <Iteration_query-len>121239</Iteration_query-len> +<Iteration_hits> +</Iteration_hits> + <Iteration_stat> + <Statistics> + <Statistics_db-num>0</Statistics_db-num> + <Statistics_db-len>0</Statistics_db-len> + <Statistics_hsp-len>20</Statistics_hsp-len> + <Statistics_eff-space>701858010</Statistics_eff-space> + <Statistics_kappa>0.46</Statistics_kappa> + <Statistics_lambda>1.28</Statistics_lambda> + <Statistics_entropy>0.85</Statistics_entropy> + </Statistics> + </Iteration_stat> + <Iteration_message>No hits found</Iteration_message> +</Iteration> +</BlastOutput_iterations> +</BlastOutput> + |