| Previous changeset 14:85ca751407c3 (2018-06-12) Next changeset 16:c9ecd2a96ecf (2018-08-28) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 999eca8a05f17ae567f99b8ca3394f2105491173 |
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modified:
gbk2fa.py snpEff_create_db.xml snpEff_macros.xml |
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added:
test-data/pBR322.gbk.gz test-data/pBR322.gff3 test-data/pBR322_test1.fna test-data/pBR322_test2.fna test-data/pBR322_test2.fna.gz |
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removed:
test-data/pBR322.fna |
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| diff -r 85ca751407c3 -r 479c4f2f4826 gbk2fa.py --- a/gbk2fa.py Tue Jun 12 17:31:21 2018 -0400 +++ b/gbk2fa.py Mon Jul 09 13:22:58 2018 -0400 |
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| @@ -22,7 +22,7 @@ f_type = magic.from_file(args.genbank_file, mime=True) if f_type == 'text/plain': input_handle = open(gbk_filename, "r") - elif f_type == 'application/gzip': + elif f_type == 'application/gzip' or f_type == 'application/x-gzip': input_handle = gzip.open(gbk_filename, "rt") elif f_type == 'application/x-bzip2': input_handle = bz2.open(gbk_filename, "rt") |
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| diff -r 85ca751407c3 -r 479c4f2f4826 snpEff_create_db.xml --- a/snpEff_create_db.xml Tue Jun 12 17:31:21 2018 -0400 +++ b/snpEff_create_db.xml Mon Jul 09 13:22:58 2018 -0400 |
| [ |
| b'@@ -1,5 +1,5 @@\n-<tool id="snpEff_build_gb" name="SnpEff build:" version="@wrapper_version@.galaxy2">\n- <description> database from Genbank record</description>\n+<tool id="snpEff_build_gb" name="SnpEff build:" version="@wrapper_version@.galaxy3">\n+ <description> database from Genbank or GFF record</description>\n <macros>\n <import>snpEff_macros.xml</import>\n </macros>\n@@ -14,22 +14,42 @@\n <expand macro="version_command" />\n <command><![CDATA[\n \n- #if str( $fasta.fasta_selector ) == "yes":\n- python3 \'$__tool_directory__/gbk2fa.py\' \'${input_gbk}\' \'${output_fasta}\'\n- #if $fasta.remove_version:\n- \'${fasta.remove_version}\'\n+ #if str( $input_type.input_type_selector ) == "gb":\n+ #if str( $input_type.fasta ) == "yes":\n+ python3 \'$__tool_directory__/gbk2fa.py\' \'${input_type.input_gbk}\' \'${output_fasta}\'\n+ #if $input_type.remove_version:\n+ \'${input_type.remove_version}\'\n+ #end if\n+ &&\n #end if\n- &&\n #end if\n \n mkdir -p \'${snpeff_output.files_path}\'/\'${genome_version}\' &&\n \n- ln -s \'${input_gbk}\' \'${snpeff_output.files_path}\'/\'${genome_version}\'/genes.gbk &&\n+ #if str( $input_type.input_type_selector ) == "gb":\n+ #if $input_type.input_gbk.is_of_type("genbank"):\n+ ln -s \'${input_type.input_gbk}\' \'${snpeff_output.files_path}\'/\'${genome_version}\'/genes.gbk &&\n+ #elif $input_type.input_gbk.is_of_type("genbank.gz"):\n+ ln -s \'${input_type.input_gbk}\' \'${snpeff_output.files_path}\'/\'${genome_version}\'/genes.gbk.gz &&\n+ #end if\n+ #elif str( $input_type.input_type_selector ) == "gff":\n+ #if $input_type.input_fasta.is_of_type("fasta"):\n+ ln -s \'${input_type.input_fasta}\' \'${snpeff_output.files_path}\'/\'${genome_version}\'/sequences.fa &&\n+ #elif $input_type.input_fasta.is_of_type("fasta.gz"):\n+ ln -s \'${input_type.input_fasta}\' \'${snpeff_output.files_path}\'/\'${genome_version}\'/sequences.fa.gz &&\n+ #end if\n+ ln -s \'${input_type.input_gff}\' \'${snpeff_output.files_path}\'/\'${genome_version}\'/genes.gff &&\n+ #end if\n \n snpEff @java_options@ build -v\n -configOption \'${genome_version}\'.genome=\'${genome_version}\'\n -configOption \'${genome_version}\'.codonTable=\'${codon_table}\'\n- -genbank -dataDir \'${snpeff_output.files_path}\' \'${genome_version}\' &&\n+ #if str( $input_type.input_type_selector ) == "gb":\n+ -genbank\n+ #elif str( $input_type.input_type_selector ) == "gff":\n+ -gff3\n+ #end if\n+ -dataDir \'${snpeff_output.files_path}\' \'${genome_version}\' &&\n echo "${genome_version}.genome : ${genome_version}" >> \'${snpeff_output.files_path}\'/snpEff.config &&\n echo "${genome_version}.codonTable : ${codon_table}" >> \'${snpeff_output.files_path}\'/snpEff.config\n \n@@ -38,7 +58,24 @@\n <param name="genome_version" type="text" value="" label="Name for the database" help="for E. coli K12 you may want to use \'EcK12\' etc.">\n <validator type="regex" message="A genome version name is required">\\S+</validator>\n </param>\n- <param name="input_gbk" type="data" format="genbank,genbank.gz" label="Genbank dataset to build database from" help="This Genbank file will be used to generate snpEff database"/>\n+ <conditional name="input_type">\n+ <param name="input_type_selector" type="select" display="radio" label="Input annotations are in" help="Specify format for annotations you are using to create SnpEff database">\n+ <option value="gb" selected="true">GenBank</option>\n+ <option value="gff">GFF</option>\n+ </param>\n+ <when value="gb">\n+ <param name="input_gbk" type="data" format="genbank,genbank.gz" label="Genbank'..b"nes) together with sequences. This ensures that these two are in sync with each other. \n+ #. When you are analyzing small genomes (or not so small) it is much more convenient to create a database on the fly and use it.\n+\n+ .. class:: warningmark\n+\n+ SnpEff errors out on highly fragmented genomes containing multiple scaffolds. This is because a single gene may be split between multiple scaffolds causing SnpEff to crash. If this is happening use GFF route described below. \n+\n+-------\n+\n+**Genbank usage scenario**\n+\n+Suppose you have a series of Illumina reads from an experiment involving *E. coli* K-12 MG1655. You want to map these reads to the reference genome of K-12 MG1655, call variants, and annotate them using snpEff. This tool enables you to follow the following analysis steps:\n+\n+ #. Go to `NCBI <http://www.ncbi.nlm.nih.gov>`_ page for K-12 MG1655 genome (note that all NCBI genomes have similar list of files associated with them).\n+ #. Copy URL for file with extension `gbff.gz` \n+ #. Paste the URL into upload tool and set datatype to `genbank.gz`.\n+ #. Use this tool to generate a snpEff database and FASTA sequences from the dataset you've uploaded during the previous step.\n+ #. Use your Illumina reads to map against FASTA dataset generated in the previous step using BWA-MEM.\n+ #. Call variants using **Freebayes**.\n+ #. Annotate vcf output of Freebayes with **SnpEff eff** using database generated at step 2 (using *Custom* option for **Genome source** parameter).\n+\n+In this scenario Genbank dataset is used twice. First, it is used to produce FASTA sequences that are using by BWA to map against. Second, it is used to create snpEff database. This guarantees that you will not have any issues related to reference sequence naming.\n \n -------\n \n .. class:: infomark\n \n-**The usage scenario**\n+**Working with GFF files**\n+\n+Alternatively you can create a SnpEff database from `GFF3 <https://en.wikipedia.org/wiki/General_feature_format>`_ files downloaded from NCBI or any other source. Using GFF dataset for building SnpEff database requires two inputs:\n \n-Suppose you have a series of Illumina reads from an experiment involving *E. coli* K-12 MG1655. You want to map these reads to the reference genome of K-12 MG1655, call variants, and annotate them using snpEff. This tool enables you to follow the following analysis steps:\n+ #. The GFF file itself\n+ #. A genome in FASTA format\n+\n+The GFF file contains coordinates of various features, but does not contain underlying sequences. This is why a FASTA file needs to be provided as well.\n+\n+------\n \n- #. Download genome from `NCBI <https://www.ncbi.nlm.nih.gov>`_ into Galaxy.\n- #. Use this tool to generate a snpEff database and FASTA sequences from the file you downloaded at step 1.\n- #. Use your Illumina reads to map against FASTA dataset generated in the previous step using BWA-MEM.\n- #. Call variants using **Freebayes**.\n- #. Annotate vcf output of Freebayes with **SnpEff eff** using database generated at step 2 (using *Custom* option for **Genome source** parameter).\n+**GFF usage scenario** \n+\n+The following example also uses *E. coli* K-12 MG1655:\n \n-In this scenario Genbank dataset is used twice. First, it is used to produce FASTA sequences that are using by BWA to map against. Second, it is used to create snpEff database. This guarantees that you will not have any issues related to reference sequence naming.\n+#. Go to `NCBI <http://www.ncbi.nlm.nih.gov>`_ page for K-12 MG1655 genome.\n+#. Copy URLs for files with `gff.gz` and `fna.gz` extensions. The first file contains annotations in GFF3 format. The second file contains entire genome as a FASTA record.\n+#. Paste URLs into upload tool and set datatypes to `gff3` and `fasta.gz` for annotations and genome, respectively.\n+#. Use this tool to generate a snpEff database from the GFF dataset.\n+#. Map your reads against the FASTA dataset and continue as described in the above example.\n+\n \n @snpeff_in_galaxy_info@\n @external_documentation@\n" |
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| diff -r 85ca751407c3 -r 479c4f2f4826 snpEff_macros.xml --- a/snpEff_macros.xml Tue Jun 12 17:31:21 2018 -0400 +++ b/snpEff_macros.xml Mon Jul 09 13:22:58 2018 -0400 |
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| @@ -54,11 +54,11 @@ In cases when you are dealing with bacterial or viral (or, frankly, any other) genomes it may be easier to create database yourself. For this you need: - #. Download Genbank record corresponding to your genome of interest from NCBI. + #. Download Genbank record corresponding to your genome of interest from NCBI or use annotations in GFF format accompanied by the corresponding genome in FASTA format. #. Use **SnpEff build** to create the database. #. Use the database in **SnpEff eff** (using *Custom* option for **Genome source** parameter). -Creating custom database has one benefit. The **SnpEff build** tool normally produces two outputs: (1) a SnpEff database and (2) FASTA file containing sequences from the Genbank file. If you are performing your experiment from the beginning by mapping reads against a genome and finding variants before annotating them with SnpEff you can use **this FASTA file** as a reference to map your reads against. This will guarantee that you will not have any issues related to reference sequence naming -- the most common source of SnpEff errors. +Creating custom database has one major advantage. It guaranteess that you will not have any issues related to reference sequence naming -- the most common source of SnpEff errors. </token> |
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| diff -r 85ca751407c3 -r 479c4f2f4826 test-data/pBR322.fna --- a/test-data/pBR322.fna Tue Jun 12 17:31:21 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,2 +0,0 @@ ->J01749 -TTCTCATGTTTGACAGCTTATCATCGATAAGCTTTAATGCGGTAGTTTATCACAGTTAAATTGCTAACGCAGTCAGGCACCGTGTATGAAATCTAACAATGCGCTCATCGTCATCCTCGGCACCGTCACCCTGGATGCTGTAGGCATAGGCTTGGTTATGCCGGTACTGCCGGGCCTCTTGCGGGATATCGTCCATTCCGACAGCATCGCCAGTCACTATGGCGTGCTGCTAGCGCTATATGCGTTGATGCAATTTCTATGCGCACCCGTTCTCGGAGCACTGTCCGACCGCTTTGGCCGCCGCCCAGTCCTGCTCGCTTCGCTACTTGGAGCCACTATCGACTACGCGATCATGGCGACCACACCCGTCCTGTGGATCCTCTACGCCGGACGCATCGTGGCCGGCATCACCGGCGCCACAGGTGCGGTTGCTGGCGCCTATATCGCCGACATCACCGATGGGGAAGATCGGGCTCGCCACTTCGGGCTCATGAGCGCTTGTTTCGGCGTGGGTATGGTGGCAGGCCCCGTGGCCGGGGGACTGTTGGGCGCCATCTCCTTGCATGCACCATTCCTTGCGGCGGCGGTGCTCAACGGCCTCAACCTACTACTGGGCTGCTTCCTAATGCAGGAGTCGCATAAGGGAGAGCGTCGACCGATGCCCTTGAGAGCCTTCAACCCAGTCAGCTCCTTCCGGTGGGCGCGGGGCATGACTATCGTCGCCGCACTTATGACTGTCTTCTTTATCATGCAACTCGTAGGACAGGTGCCGGCAGCGCTCTGGGTCATTTTCGGCGAGGACCGCTTTCGCTGGAGCGCGACGATGATCGGCCTGTCGCTTGCGGTATTCGGAATCTTGCACGCCCTCGCTCAAGCCTTCGTCACTGGTCCCGCCACCAAACGTTTCGGCGAGAAGCAGGCCATTATCGCCGGCATGGCGGCCGACGCGCTGGGCTACGTCTTGCTGGCGTTCGCGACGCGAGGCTGGATGGCCTTCCCCATTATGATTCTTCTCGCTTCCGGCGGCATCGGGATGCCCGCGTTGCAGGCCATGCTGTCCAGGCAGGTAGATGACGACCATCAGGGACAGCTTCAAGGATCGCTCGCGGCTCTTACCAGCCTAACTTCGATCACTGGACCGCTGATCGTCACGGCGATTTATGCCGCCTCGGCGAGCACATGGAACGGGTTGGCATGGATTGTAGGCGCCGCCCTATACCTTGTCTGCCTCCCCGCGTTGCGTCGCGGTGCATGGAGCCGGGCCACCTCGACCTGAATGGAAGCCGGCGGCACCTCGCTAACGGATTCACCACTCCAAGAATTGGAGCCAATCAATTCTTGCGGAGAACTGTGAATGCGCAAACCAACCCTTGGCAGAACATATCCATCGCGTCCGCCATCTCCAGCAGCCGCACGCGGCGCATCTCGGGCAGCGTTGGGTCCTGGCCACGGGTGCGCATGATCGTGCTCCTGTCGTTGAGGACCCGGCTAGGCTGGCGGGGTTGCCTTACTGGTTAGCAGAATGAATCACCGATACGCGAGCGAACGTGAAGCGACTGCTGCTGCAAAACGTCTGCGACCTGAGCAACAACATGAATGGTCTTCGGTTTCCGTGTTTCGTAAAGTCTGGAAACGCGGAAGTCAGCGCCCTGCACCATTATGTTCCGGATCTGCATCGCAGGATGCTGCTGGCTACCCTGTGGAACACCTACATCTGTATTAACGAAGCGCTGGCATTGACCCTGAGTGATTTTTCTCTGGTCCCGCCGCATCCATACCGCCAGTTGTTTACCCTCACAACGTTCCAGTAACCGGGCATGTTCATCATCAGTAACCCGTATCGTGAGCATCCTCTCTCGTTTCATCGGTATCATTACCCCCATGAACAGAAATCCCCCTTACACGGAGGCATCAGTGACCAAACAGGAAAAAACCGCCCTTAACATGGCCCGCTTTATCAGAAGCCAGACATTAACGCTTCTGGAGAAACTCAACGAGCTGGACGCGGATGAACAGGCAGACATCTGTGAATCGCTTCACGACCACGCTGATGAGCTTTACCGCAGCTGCCTCGCGCGTTTCGGTGATGACGGTGAAAACCTCTGACACATGCAGCTCCCGGAGACGGTCACAGCTTGTCTGTAAGCGGATGCCGGGAGCAGACAAGCCCGTCAGGGCGCGTCAGCGGGTGTTGGCGGGTGTCGGGGCGCAGCCATGACCCAGTCACGTAGCGATAGCGGAGTGTATACTGGCTTAACTATGCGGCATCAGAGCAGATTGTACTGAGAGTGCACCATATGCGGTGTGAAATACCGCACAGATGCGTAAGGAGAAAATACCGCATCAGGCGCTCTTCCGCTTCCTCGCTCACTGACTCGCTGCGCTCGGTCGTTCGGCTGCGGCGAGCGGTATCAGCTCACTCAAAGGCGGTAATACGGTTATCCACAGAATCAGGGGATAACGCAGGAAAGAACATGTGAGCAAAAGGCCAGCAAAAGGCCAGGAACCGTAAAAAGGCCGCGTTGCTGGCGTTTTTCCATAGGCTCCGCCCCCCTGACGAGCATCACAAAAATCGACGCTCAAGTCAGAGGTGGCGAAACCCGACAGGACTATAAAGATACCAGGCGTTTCCCCCTGGAAGCTCCCTCGTGCGCTCTCCTGTTCCGACCCTGCCGCTTACCGGATACCTGTCCGCCTTTCTCCCTTCGGGAAGCGTGGCGCTTTCTCATAGCTCACGCTGTAGGTATCTCAGTTCGGTGTAGGTCGTTCGCTCCAAGCTGGGCTGTGTGCACGAACCCCCCGTTCAGCCCGACCGCTGCGCCTTATCCGGTAACTATCGTCTTGAGTCCAACCCGGTAAGACACGACTTATCGCCACTGGCAGCAGCCACTGGTAACAGGATTAGCAGAGCGAGGTATGTAGGCGGTGCTACAGAGTTCTTGAAGTGGTGGCCTAACTACGGCTACACTAGAAGGACAGTATTTGGTATCTGCGCTCTGCTGAAGCCAGTTACCTTCGGAAAAAGAGTTGGTAGCTCTTGATCCGGCAAACAAACCACCGCTGGTAGCGGTGGTTTTTTTGTTTGCAAGCAGCAGATTACGCGCAGAAAAAAAGGATCTCAAGAAGATCCTTTGATCTTTTCTACGGGGTCTGACGCTCAGTGGAACGAAAACTCACGTTAAGGGATTTTGGTCATGAGATTATCAAAAAGGATCTTCACCTAGATCCTTTTAAATTAAAAATGAAGTTTTAAATCAATCTAAAGTATATATGAGTAAACTTGGTCTGACAGTTACCAATGCTTAATCAGTGAGGCACCTATCTCAGCGATCTGTCTATTTCGTTCATCCATAGTTGCCTGACTCCCCGTCGTGTAGATAACTACGATACGGGAGGGCTTACCATCTGGCCCCAGTGCTGCAATGATACCGCGAGACCCACGCTCACCGGCTCCAGATTTATCAGCAATAAACCAGCCAGCCGGAAGGGCCGAGCGCAGAAGTGGTCCTGCAACTTTATCCGCCTCCATCCAGTCTATTAATTGTTGCCGGGAAGCTAGAGTAAGTAGTTCGCCAGTTAATAGTTTGCGCAACGTTGTTGCCATTGCTGCAGGCATCGTGGTGTCACGCTCGTCGTTTGGTATGGCTTCATTCAGCTCCGGTTCCCAACGATCAAGGCGAGTTACATGATCCCCCATGTTGTGCAAAAAAGCGGTTAGCTCCTTCGGTCCTCCGATCGTTGTCAGAAGTAAGTTGGCCGCAGTGTTATCACTCATGGTTATGGCAGCACTGCATAATTCTCTTACTGTCATGCCATCCGTAAGATGCTTTTCTGTGACTGGTGAGTACTCAACCAAGTCATTCTGAGAATAGTGTATGCGGCGACCGAGTTGCTCTTGCCCGGCGTCAACACGGGATAATACCGCGCCACATAGCAGAACTTTAAAAGTGCTCATCATTGGAAAACGTTCTTCGGGGCGAAAACTCTCAAGGATCTTACCGCTGTTGAGATCCAGTTCGATGTAACCCACTCGTGCACCCAACTGATCTTCAGCATCTTTTACTTTCACCAGCGTTTCTGGGTGAGCAAAAACAGGAAGGCAAAATGCCGCAAAAAAGGGAATAAGGGCGACACGGAAATGTTGAATACTCATACTCTTCCTTTTTCAATATTATTGAAGCATTTATCAGGGTTATTGTCTCATGAGCGGATACATATTTGAATGTATTTAGAAAAATAAACAAATAGGGGTTCCGCGCACATTTCCCCGAAAAGTGCCACCTGACGTCTAAGAAACCATTATTATCATGACATTAACCTATAAAAATAGGCGTATCACGAGGCCCTTTCGTCTTCAAGAA |
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| diff -r 85ca751407c3 -r 479c4f2f4826 test-data/pBR322.gbk.gz |
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| Binary file test-data/pBR322.gbk.gz has changed |
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| diff -r 85ca751407c3 -r 479c4f2f4826 test-data/pBR322.gff3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pBR322.gff3 Mon Jul 09 13:22:58 2018 -0400 |
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| @@ -0,0 +1,51 @@ +##sequence-region J01749.1 1 4361 +##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=47470 +J01749.1 Genbank region 1 4361 . + . ID=id-1;Dbxref=taxon:47470;Is_circular=true;gbkey=Src;mol_type=other DNA;tissue-lib=ATCC 31344%2C ATCC 37017 +J01749.1 Genbank region 1 1762 . + . ID=id-J01749.1:1..1762;gbkey=Src +J01749.1 Genbank binding_site 24 27 . + . ID=id-J01749.1:24..27;bound_moiety=echinomycin;gbkey=misc_binding +J01749.1 Genbank promoter 27 33 . - . ID=id-J01749.1:27..33;Note=promoter P1 (6);gbkey=promoter +J01749.1 Genbank binding_site 39 42 . + . ID=id-J01749.1:39..42;bound_moiety=echinomycin;gbkey=misc_binding +J01749.1 Genbank promoter 43 49 . + . ID=id-J01749.1:43..49;Note=promoter P2 (6);gbkey=promoter +J01749.1 Genbank binding_site 53 56 . + . ID=id-J01749.1:53..56;bound_moiety=echinomycin;gbkey=misc_binding +J01749.1 Genbank binding_site 67 70 . + . ID=id-J01749.1:67..70;bound_moiety=echinomycin;gbkey=misc_binding +J01749.1 Genbank binding_site 80 83 . + . ID=id-J01749.1:80..83;bound_moiety=echinomycin;gbkey=misc_binding +J01749.1 Genbank gene 86 1276 . + . ID=gene-tet;Name=tet;gbkey=Gene;gene=tet +J01749.1 Genbank CDS 86 1276 . + 0 ID=cds-AAB59735.1;Parent=gene-tet;Dbxref=NCBI_GP:AAB59735.1;Name=AAB59735.1;gbkey=CDS;gene=tet;product=tetracycline resistance protein;protein_id=AAB59735.1;transl_table=11 +J01749.1 Genbank binding_site 411 414 . + . ID=id-tet;bound_moiety=echinomycin;gbkey=misc_binding;gene=tet +J01749.1 Genbank binding_site 469 472 . + . ID=id-tet-2;bound_moiety=echinomycin;gbkey=misc_binding;gene=tet +J01749.1 Genbank sequence_difference 426 426 . + . ID=id-tet-3;Note=conflict;gbkey=misc_difference;gene=tet;replace= +J01749.1 Genbank sequence_feature 146 147 . + . ID=id-tet-4;Note=Endo.Sce I cleavage site coordinated with site at base 142 (10);gbkey=misc_feature;gene=tet +J01749.1 Genbank region 526 528 . + . ID=id-tet-5;gbkey=old_sequence;gene=tet +J01749.1 Genbank sequence_feature 141 142 . - . ID=id-J01749.1:141..142;Note=Endo.Sce I cleavage site coordinated with site at base 146 (10);gbkey=misc_feature +J01749.1 Genbank direct_repeat 1515 1519 . - . ID=id-J01749.1:1515..1519;Note=gamma-delta insertion target sequence;gbkey=repeat_region;rpt_type=direct +J01749.1 Genbank sequence_feature 1636 1762 . + . ID=id-J01749.1:1636..1762;Note=from pSC101 (bp 1860-1986);gbkey=misc_feature +J01749.1 Genbank direct_repeat 1788 1792 . - . ID=id-J01749.1:1788..1792;Note=gamma-delta insertion target sequence;gbkey=repeat_region;rpt_type=direct +J01749.1 Genbank sequence_difference 1891 1892 . + . ID=id-J01749.1:1891..1892;Note=conflict;gbkey=misc_difference;replace=att +J01749.1 Genbank region 1892 1893 . + . ID=id-J01749.1:1892..1893;gbkey=old_sequence +J01749.1 Genbank region 1905 1910 . + . ID=id-J01749.1:1905..1910;gbkey=RBS +J01749.1 Genbank region 1905 1909 . + . ID=id-J01749.1:1905..1909;Note=Shine-Dalgarno sequence;gbkey=RBS +J01749.1 Genbank sequence_difference 1913 1914 . + . ID=id-J01749.1:1913..1914;Note=conflict;gbkey=misc_difference;replace=caa +J01749.1 Genbank region 1914 1915 . + . ID=id-J01749.1:1914..1915;gbkey=old_sequence +J01749.1 Genbank CDS 1915 2106 . + 0 ID=cds-AAB59736.1;Dbxref=NCBI_GP:AAB59736.1;Name=AAB59736.1;gbkey=CDS;product=ROP protein;protein_id=AAB59736.1;transl_table=11 +J01749.1 Genbank sequence_feature 2011 2167 . + . ID=id-J01749.1:2011..2167;Note=H-strand Y effector site;gbkey=misc_feature +J01749.1 Genbank direct_repeat 2245 2249 . - . ID=id-J01749.1:2245..2249;Note=gamma-delta insertion target sequence;gbkey=repeat_region;rpt_type=direct +J01749.1 Genbank sequence_feature 2351 2414 . - . ID=id-J01749.1:2351..2414;Note=L-strand Y effector site;gbkey=misc_feature +J01749.1 Genbank binding_site 2439 2447 . + . ID=id-J01749.1:2439..2447;bound_moiety=dnaA;gbkey=misc_binding +J01749.1 Genbank origin_of_replication 2535 2535 . + . ID=id-J01749.1:2535..2535;gbkey=rep_origin +J01749.1 Genbank region 2729 2730 . + . ID=id-J01749.1:2729..2730;Note=revision according to (17);gbkey=old_sequence;replace=at +J01749.1 Genbank region 2729 2729 . + . ID=id-J01749.1:2729..2729;gbkey=old_sequence +J01749.1 Genbank region 2730 2730 . + . ID=id-J01749.1:2730..2730;Note=revision according to (16);gbkey=old_sequence;replace=t +J01749.1 Genbank mobile_genetic_element 3148 4361 . + . ID=id-J01749.1:3148..4361;gbkey=mobile_element;mobile_element_type=transposon:Tn3 +J01749.1 Genbank inverted_repeat 3148 3185 . + . ID=id-J01749.1:3148..3185;Note=corresponds to one of the 38bp repeats found in Tn3 (bp 1-38 and complement (4920-4957));gbkey=repeat_region;rpt_type=inverted +J01749.1 Genbank gene 3293 4153 . - . ID=gene-bla;Name=bla;gbkey=Gene;gene=bla +J01749.1 Genbank CDS 3293 4153 . - 0 ID=cds-AAB59737.1;Parent=gene-bla;Dbxref=NCBI_GP:AAB59737.1;Name=AAB59737.1;Note=E-286;gbkey=CDS;gene=bla;product=beta-lactamase;protein_id=AAB59737.1;transl_table=11 +J01749.1 Genbank region 4161 4165 . - . ID=id-J01749.1:4161..4165;Note=Shine-Dalgarno sequence;gbkey=RBS +J01749.1 Genbank promoter 4188 4194 . - . ID=id-J01749.1:4188..4194;Note=promoter P3 (6);gbkey=promoter +J01749.1 Genbank binding_site 4268 4271 . - . ID=id-J01749.1:4268..4271;bound_moiety=echinomycin;gbkey=misc_binding +J01749.1 Genbank binding_site 4280 4283 . - . ID=id-J01749.1:4280..4283;bound_moiety=echinomycin;gbkey=misc_binding +J01749.1 Genbank binding_site 4285 4288 . - . ID=id-J01749.1:4285..4288;bound_moiety=echinomycin;gbkey=misc_binding +J01749.1 Genbank binding_site 4296 4299 . - . ID=id-J01749.1:4296..4299;bound_moiety=echinomycin;gbkey=misc_binding +J01749.1 Genbank binding_site 4311 4314 . - . ID=id-J01749.1:4311..4314;bound_moiety=echinomycin;gbkey=misc_binding +J01749.1 Genbank binding_site 4317 4320 . - . ID=id-J01749.1:4317..4320;bound_moiety=echinomycin;gbkey=misc_binding +J01749.1 Genbank binding_site 4331 4334 . - . ID=id-J01749.1:4331..4334;bound_moiety=echinomycin;gbkey=misc_binding + |
| b |
| diff -r 85ca751407c3 -r 479c4f2f4826 test-data/pBR322_test1.fna --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pBR322_test1.fna Mon Jul 09 13:22:58 2018 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>J01749 +TTCTCATGTTTGACAGCTTATCATCGATAAGCTTTAATGCGGTAGTTTATCACAGTTAAATTGCTAACGCAGTCAGGCACCGTGTATGAAATCTAACAATGCGCTCATCGTCATCCTCGGCACCGTCACCCTGGATGCTGTAGGCATAGGCTTGGTTATGCCGGTACTGCCGGGCCTCTTGCGGGATATCGTCCATTCCGACAGCATCGCCAGTCACTATGGCGTGCTGCTAGCGCTATATGCGTTGATGCAATTTCTATGCGCACCCGTTCTCGGAGCACTGTCCGACCGCTTTGGCCGCCGCCCAGTCCTGCTCGCTTCGCTACTTGGAGCCACTATCGACTACGCGATCATGGCGACCACACCCGTCCTGTGGATCCTCTACGCCGGACGCATCGTGGCCGGCATCACCGGCGCCACAGGTGCGGTTGCTGGCGCCTATATCGCCGACATCACCGATGGGGAAGATCGGGCTCGCCACTTCGGGCTCATGAGCGCTTGTTTCGGCGTGGGTATGGTGGCAGGCCCCGTGGCCGGGGGACTGTTGGGCGCCATCTCCTTGCATGCACCATTCCTTGCGGCGGCGGTGCTCAACGGCCTCAACCTACTACTGGGCTGCTTCCTAATGCAGGAGTCGCATAAGGGAGAGCGTCGACCGATGCCCTTGAGAGCCTTCAACCCAGTCAGCTCCTTCCGGTGGGCGCGGGGCATGACTATCGTCGCCGCACTTATGACTGTCTTCTTTATCATGCAACTCGTAGGACAGGTGCCGGCAGCGCTCTGGGTCATTTTCGGCGAGGACCGCTTTCGCTGGAGCGCGACGATGATCGGCCTGTCGCTTGCGGTATTCGGAATCTTGCACGCCCTCGCTCAAGCCTTCGTCACTGGTCCCGCCACCAAACGTTTCGGCGAGAAGCAGGCCATTATCGCCGGCATGGCGGCCGACGCGCTGGGCTACGTCTTGCTGGCGTTCGCGACGCGAGGCTGGATGGCCTTCCCCATTATGATTCTTCTCGCTTCCGGCGGCATCGGGATGCCCGCGTTGCAGGCCATGCTGTCCAGGCAGGTAGATGACGACCATCAGGGACAGCTTCAAGGATCGCTCGCGGCTCTTACCAGCCTAACTTCGATCACTGGACCGCTGATCGTCACGGCGATTTATGCCGCCTCGGCGAGCACATGGAACGGGTTGGCATGGATTGTAGGCGCCGCCCTATACCTTGTCTGCCTCCCCGCGTTGCGTCGCGGTGCATGGAGCCGGGCCACCTCGACCTGAATGGAAGCCGGCGGCACCTCGCTAACGGATTCACCACTCCAAGAATTGGAGCCAATCAATTCTTGCGGAGAACTGTGAATGCGCAAACCAACCCTTGGCAGAACATATCCATCGCGTCCGCCATCTCCAGCAGCCGCACGCGGCGCATCTCGGGCAGCGTTGGGTCCTGGCCACGGGTGCGCATGATCGTGCTCCTGTCGTTGAGGACCCGGCTAGGCTGGCGGGGTTGCCTTACTGGTTAGCAGAATGAATCACCGATACGCGAGCGAACGTGAAGCGACTGCTGCTGCAAAACGTCTGCGACCTGAGCAACAACATGAATGGTCTTCGGTTTCCGTGTTTCGTAAAGTCTGGAAACGCGGAAGTCAGCGCCCTGCACCATTATGTTCCGGATCTGCATCGCAGGATGCTGCTGGCTACCCTGTGGAACACCTACATCTGTATTAACGAAGCGCTGGCATTGACCCTGAGTGATTTTTCTCTGGTCCCGCCGCATCCATACCGCCAGTTGTTTACCCTCACAACGTTCCAGTAACCGGGCATGTTCATCATCAGTAACCCGTATCGTGAGCATCCTCTCTCGTTTCATCGGTATCATTACCCCCATGAACAGAAATCCCCCTTACACGGAGGCATCAGTGACCAAACAGGAAAAAACCGCCCTTAACATGGCCCGCTTTATCAGAAGCCAGACATTAACGCTTCTGGAGAAACTCAACGAGCTGGACGCGGATGAACAGGCAGACATCTGTGAATCGCTTCACGACCACGCTGATGAGCTTTACCGCAGCTGCCTCGCGCGTTTCGGTGATGACGGTGAAAACCTCTGACACATGCAGCTCCCGGAGACGGTCACAGCTTGTCTGTAAGCGGATGCCGGGAGCAGACAAGCCCGTCAGGGCGCGTCAGCGGGTGTTGGCGGGTGTCGGGGCGCAGCCATGACCCAGTCACGTAGCGATAGCGGAGTGTATACTGGCTTAACTATGCGGCATCAGAGCAGATTGTACTGAGAGTGCACCATATGCGGTGTGAAATACCGCACAGATGCGTAAGGAGAAAATACCGCATCAGGCGCTCTTCCGCTTCCTCGCTCACTGACTCGCTGCGCTCGGTCGTTCGGCTGCGGCGAGCGGTATCAGCTCACTCAAAGGCGGTAATACGGTTATCCACAGAATCAGGGGATAACGCAGGAAAGAACATGTGAGCAAAAGGCCAGCAAAAGGCCAGGAACCGTAAAAAGGCCGCGTTGCTGGCGTTTTTCCATAGGCTCCGCCCCCCTGACGAGCATCACAAAAATCGACGCTCAAGTCAGAGGTGGCGAAACCCGACAGGACTATAAAGATACCAGGCGTTTCCCCCTGGAAGCTCCCTCGTGCGCTCTCCTGTTCCGACCCTGCCGCTTACCGGATACCTGTCCGCCTTTCTCCCTTCGGGAAGCGTGGCGCTTTCTCATAGCTCACGCTGTAGGTATCTCAGTTCGGTGTAGGTCGTTCGCTCCAAGCTGGGCTGTGTGCACGAACCCCCCGTTCAGCCCGACCGCTGCGCCTTATCCGGTAACTATCGTCTTGAGTCCAACCCGGTAAGACACGACTTATCGCCACTGGCAGCAGCCACTGGTAACAGGATTAGCAGAGCGAGGTATGTAGGCGGTGCTACAGAGTTCTTGAAGTGGTGGCCTAACTACGGCTACACTAGAAGGACAGTATTTGGTATCTGCGCTCTGCTGAAGCCAGTTACCTTCGGAAAAAGAGTTGGTAGCTCTTGATCCGGCAAACAAACCACCGCTGGTAGCGGTGGTTTTTTTGTTTGCAAGCAGCAGATTACGCGCAGAAAAAAAGGATCTCAAGAAGATCCTTTGATCTTTTCTACGGGGTCTGACGCTCAGTGGAACGAAAACTCACGTTAAGGGATTTTGGTCATGAGATTATCAAAAAGGATCTTCACCTAGATCCTTTTAAATTAAAAATGAAGTTTTAAATCAATCTAAAGTATATATGAGTAAACTTGGTCTGACAGTTACCAATGCTTAATCAGTGAGGCACCTATCTCAGCGATCTGTCTATTTCGTTCATCCATAGTTGCCTGACTCCCCGTCGTGTAGATAACTACGATACGGGAGGGCTTACCATCTGGCCCCAGTGCTGCAATGATACCGCGAGACCCACGCTCACCGGCTCCAGATTTATCAGCAATAAACCAGCCAGCCGGAAGGGCCGAGCGCAGAAGTGGTCCTGCAACTTTATCCGCCTCCATCCAGTCTATTAATTGTTGCCGGGAAGCTAGAGTAAGTAGTTCGCCAGTTAATAGTTTGCGCAACGTTGTTGCCATTGCTGCAGGCATCGTGGTGTCACGCTCGTCGTTTGGTATGGCTTCATTCAGCTCCGGTTCCCAACGATCAAGGCGAGTTACATGATCCCCCATGTTGTGCAAAAAAGCGGTTAGCTCCTTCGGTCCTCCGATCGTTGTCAGAAGTAAGTTGGCCGCAGTGTTATCACTCATGGTTATGGCAGCACTGCATAATTCTCTTACTGTCATGCCATCCGTAAGATGCTTTTCTGTGACTGGTGAGTACTCAACCAAGTCATTCTGAGAATAGTGTATGCGGCGACCGAGTTGCTCTTGCCCGGCGTCAACACGGGATAATACCGCGCCACATAGCAGAACTTTAAAAGTGCTCATCATTGGAAAACGTTCTTCGGGGCGAAAACTCTCAAGGATCTTACCGCTGTTGAGATCCAGTTCGATGTAACCCACTCGTGCACCCAACTGATCTTCAGCATCTTTTACTTTCACCAGCGTTTCTGGGTGAGCAAAAACAGGAAGGCAAAATGCCGCAAAAAAGGGAATAAGGGCGACACGGAAATGTTGAATACTCATACTCTTCCTTTTTCAATATTATTGAAGCATTTATCAGGGTTATTGTCTCATGAGCGGATACATATTTGAATGTATTTAGAAAAATAAACAAATAGGGGTTCCGCGCACATTTCCCCGAAAAGTGCCACCTGACGTCTAAGAAACCATTATTATCATGACATTAACCTATAAAAATAGGCGTATCACGAGGCCCTTTCGTCTTCAAGAA |
| b |
| diff -r 85ca751407c3 -r 479c4f2f4826 test-data/pBR322_test2.fna --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pBR322_test2.fna Mon Jul 09 13:22:58 2018 -0400 |
| b |
| @@ -0,0 +1,65 @@ +>J01749.1 Cloning vector pBR322, complete sequence +TTCTCATGTTTGACAGCTTATCATCGATAAGCTTTAATGCGGTAGTTTATCACAGTTAAATTGCTAACGC +AGTCAGGCACCGTGTATGAAATCTAACAATGCGCTCATCGTCATCCTCGGCACCGTCACCCTGGATGCTG +TAGGCATAGGCTTGGTTATGCCGGTACTGCCGGGCCTCTTGCGGGATATCGTCCATTCCGACAGCATCGC +CAGTCACTATGGCGTGCTGCTAGCGCTATATGCGTTGATGCAATTTCTATGCGCACCCGTTCTCGGAGCA +CTGTCCGACCGCTTTGGCCGCCGCCCAGTCCTGCTCGCTTCGCTACTTGGAGCCACTATCGACTACGCGA +TCATGGCGACCACACCCGTCCTGTGGATCCTCTACGCCGGACGCATCGTGGCCGGCATCACCGGCGCCAC +AGGTGCGGTTGCTGGCGCCTATATCGCCGACATCACCGATGGGGAAGATCGGGCTCGCCACTTCGGGCTC +ATGAGCGCTTGTTTCGGCGTGGGTATGGTGGCAGGCCCCGTGGCCGGGGGACTGTTGGGCGCCATCTCCT +TGCATGCACCATTCCTTGCGGCGGCGGTGCTCAACGGCCTCAACCTACTACTGGGCTGCTTCCTAATGCA +GGAGTCGCATAAGGGAGAGCGTCGACCGATGCCCTTGAGAGCCTTCAACCCAGTCAGCTCCTTCCGGTGG +GCGCGGGGCATGACTATCGTCGCCGCACTTATGACTGTCTTCTTTATCATGCAACTCGTAGGACAGGTGC +CGGCAGCGCTCTGGGTCATTTTCGGCGAGGACCGCTTTCGCTGGAGCGCGACGATGATCGGCCTGTCGCT +TGCGGTATTCGGAATCTTGCACGCCCTCGCTCAAGCCTTCGTCACTGGTCCCGCCACCAAACGTTTCGGC +GAGAAGCAGGCCATTATCGCCGGCATGGCGGCCGACGCGCTGGGCTACGTCTTGCTGGCGTTCGCGACGC +GAGGCTGGATGGCCTTCCCCATTATGATTCTTCTCGCTTCCGGCGGCATCGGGATGCCCGCGTTGCAGGC +CATGCTGTCCAGGCAGGTAGATGACGACCATCAGGGACAGCTTCAAGGATCGCTCGCGGCTCTTACCAGC +CTAACTTCGATCACTGGACCGCTGATCGTCACGGCGATTTATGCCGCCTCGGCGAGCACATGGAACGGGT +TGGCATGGATTGTAGGCGCCGCCCTATACCTTGTCTGCCTCCCCGCGTTGCGTCGCGGTGCATGGAGCCG +GGCCACCTCGACCTGAATGGAAGCCGGCGGCACCTCGCTAACGGATTCACCACTCCAAGAATTGGAGCCA +ATCAATTCTTGCGGAGAACTGTGAATGCGCAAACCAACCCTTGGCAGAACATATCCATCGCGTCCGCCAT +CTCCAGCAGCCGCACGCGGCGCATCTCGGGCAGCGTTGGGTCCTGGCCACGGGTGCGCATGATCGTGCTC +CTGTCGTTGAGGACCCGGCTAGGCTGGCGGGGTTGCCTTACTGGTTAGCAGAATGAATCACCGATACGCG +AGCGAACGTGAAGCGACTGCTGCTGCAAAACGTCTGCGACCTGAGCAACAACATGAATGGTCTTCGGTTT +CCGTGTTTCGTAAAGTCTGGAAACGCGGAAGTCAGCGCCCTGCACCATTATGTTCCGGATCTGCATCGCA +GGATGCTGCTGGCTACCCTGTGGAACACCTACATCTGTATTAACGAAGCGCTGGCATTGACCCTGAGTGA +TTTTTCTCTGGTCCCGCCGCATCCATACCGCCAGTTGTTTACCCTCACAACGTTCCAGTAACCGGGCATG +TTCATCATCAGTAACCCGTATCGTGAGCATCCTCTCTCGTTTCATCGGTATCATTACCCCCATGAACAGA +AATCCCCCTTACACGGAGGCATCAGTGACCAAACAGGAAAAAACCGCCCTTAACATGGCCCGCTTTATCA +GAAGCCAGACATTAACGCTTCTGGAGAAACTCAACGAGCTGGACGCGGATGAACAGGCAGACATCTGTGA +ATCGCTTCACGACCACGCTGATGAGCTTTACCGCAGCTGCCTCGCGCGTTTCGGTGATGACGGTGAAAAC +CTCTGACACATGCAGCTCCCGGAGACGGTCACAGCTTGTCTGTAAGCGGATGCCGGGAGCAGACAAGCCC +GTCAGGGCGCGTCAGCGGGTGTTGGCGGGTGTCGGGGCGCAGCCATGACCCAGTCACGTAGCGATAGCGG +AGTGTATACTGGCTTAACTATGCGGCATCAGAGCAGATTGTACTGAGAGTGCACCATATGCGGTGTGAAA +TACCGCACAGATGCGTAAGGAGAAAATACCGCATCAGGCGCTCTTCCGCTTCCTCGCTCACTGACTCGCT +GCGCTCGGTCGTTCGGCTGCGGCGAGCGGTATCAGCTCACTCAAAGGCGGTAATACGGTTATCCACAGAA +TCAGGGGATAACGCAGGAAAGAACATGTGAGCAAAAGGCCAGCAAAAGGCCAGGAACCGTAAAAAGGCCG +CGTTGCTGGCGTTTTTCCATAGGCTCCGCCCCCCTGACGAGCATCACAAAAATCGACGCTCAAGTCAGAG +GTGGCGAAACCCGACAGGACTATAAAGATACCAGGCGTTTCCCCCTGGAAGCTCCCTCGTGCGCTCTCCT +GTTCCGACCCTGCCGCTTACCGGATACCTGTCCGCCTTTCTCCCTTCGGGAAGCGTGGCGCTTTCTCATA +GCTCACGCTGTAGGTATCTCAGTTCGGTGTAGGTCGTTCGCTCCAAGCTGGGCTGTGTGCACGAACCCCC +CGTTCAGCCCGACCGCTGCGCCTTATCCGGTAACTATCGTCTTGAGTCCAACCCGGTAAGACACGACTTA +TCGCCACTGGCAGCAGCCACTGGTAACAGGATTAGCAGAGCGAGGTATGTAGGCGGTGCTACAGAGTTCT +TGAAGTGGTGGCCTAACTACGGCTACACTAGAAGGACAGTATTTGGTATCTGCGCTCTGCTGAAGCCAGT +TACCTTCGGAAAAAGAGTTGGTAGCTCTTGATCCGGCAAACAAACCACCGCTGGTAGCGGTGGTTTTTTT +GTTTGCAAGCAGCAGATTACGCGCAGAAAAAAAGGATCTCAAGAAGATCCTTTGATCTTTTCTACGGGGT +CTGACGCTCAGTGGAACGAAAACTCACGTTAAGGGATTTTGGTCATGAGATTATCAAAAAGGATCTTCAC +CTAGATCCTTTTAAATTAAAAATGAAGTTTTAAATCAATCTAAAGTATATATGAGTAAACTTGGTCTGAC +AGTTACCAATGCTTAATCAGTGAGGCACCTATCTCAGCGATCTGTCTATTTCGTTCATCCATAGTTGCCT +GACTCCCCGTCGTGTAGATAACTACGATACGGGAGGGCTTACCATCTGGCCCCAGTGCTGCAATGATACC +GCGAGACCCACGCTCACCGGCTCCAGATTTATCAGCAATAAACCAGCCAGCCGGAAGGGCCGAGCGCAGA +AGTGGTCCTGCAACTTTATCCGCCTCCATCCAGTCTATTAATTGTTGCCGGGAAGCTAGAGTAAGTAGTT +CGCCAGTTAATAGTTTGCGCAACGTTGTTGCCATTGCTGCAGGCATCGTGGTGTCACGCTCGTCGTTTGG +TATGGCTTCATTCAGCTCCGGTTCCCAACGATCAAGGCGAGTTACATGATCCCCCATGTTGTGCAAAAAA +GCGGTTAGCTCCTTCGGTCCTCCGATCGTTGTCAGAAGTAAGTTGGCCGCAGTGTTATCACTCATGGTTA +TGGCAGCACTGCATAATTCTCTTACTGTCATGCCATCCGTAAGATGCTTTTCTGTGACTGGTGAGTACTC +AACCAAGTCATTCTGAGAATAGTGTATGCGGCGACCGAGTTGCTCTTGCCCGGCGTCAACACGGGATAAT +ACCGCGCCACATAGCAGAACTTTAAAAGTGCTCATCATTGGAAAACGTTCTTCGGGGCGAAAACTCTCAA +GGATCTTACCGCTGTTGAGATCCAGTTCGATGTAACCCACTCGTGCACCCAACTGATCTTCAGCATCTTT +TACTTTCACCAGCGTTTCTGGGTGAGCAAAAACAGGAAGGCAAAATGCCGCAAAAAAGGGAATAAGGGCG +ACACGGAAATGTTGAATACTCATACTCTTCCTTTTTCAATATTATTGAAGCATTTATCAGGGTTATTGTC +TCATGAGCGGATACATATTTGAATGTATTTAGAAAAATAAACAAATAGGGGTTCCGCGCACATTTCCCCG +AAAAGTGCCACCTGACGTCTAAGAAACCATTATTATCATGACATTAACCTATAAAAATAGGCGTATCACG +AGGCCCTTTCGTCTTCAAGAA + |
| b |
| diff -r 85ca751407c3 -r 479c4f2f4826 test-data/pBR322_test2.fna.gz |
| b |
| Binary file test-data/pBR322_test2.fna.gz has changed |