| Next changeset 1:85c57cc9b558 (2019-12-02) |
|
Commit message:
"planemo upload commit fadaff2d55736bf8c580541d6089c83cd4106a1f" |
|
added:
README.txt breseq.xml macros.xml test-data/gdout.txt test-data/gdtoolsout.html test-data/genbank_files.loc test-data/lambda.gbk test-data/lambda.short_sequence_repeats.fastq test-data/log.txt test-data/out.tar.gz test-data/report.html tool-data/genbank_files.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
| b |
| diff -r 000000000000 -r f848a7f97332 README.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.txt Thu Oct 31 19:40:40 2019 -0400 |
| b |
| @@ -0,0 +1,1 @@ +In order to properly view breseq's html output in Galaxy, breseq needs to be whitelisted. Otherwise, the results will not be displayed properly and interactive controls will not function. \ No newline at end of file |
| b |
| diff -r 000000000000 -r f848a7f97332 breseq.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/breseq.xml Thu Oct 31 19:40:40 2019 -0400 |
| [ |
| b'@@ -0,0 +1,354 @@\n+<tool id="breseq" name="breseq" version="@PACKAGE_VERSION@+@GALAXY_VERSION@">\n+\n+ <description>find mutations in haploid microbial genomes</description>\n+\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+\n+ <requirements>\n+ <requirement type="package" version="0.34.0">breseq</requirement>\n+ </requirements>\n+\n+ <version_command>breseq --version</version_command>\n+\n+ <command detect_errors="aggressive">\n+ <![CDATA[\n+ #set $ref_opts = ""\n+ #for $i, $r in enumerate( $references ):\n+ #if str($references[$i].reference.source) == "history":\n+ #for $ref in $references[$i].reference.own_genome:\n+ #if $ref\n+ #set $ref_opts = $ref_opts + " --reference \'" + str($ref) + "\'"\n+ #end if\n+ #end for\n+ #else:\n+ #set $ref_opts = $ref_opts + " --reference \'" + $references[$i].reference.fixed_genome.fields.path + "\'"\n+ #end if\n+ #end for\n+\n+ #if str($run.mode) == \'detect\'\n+ breseq\n+\n+ --num-processors \\${GALAXY_SLOTS:-4}\n+\n+ -o results\n+\n+ $ref_opts\n+\n+ #for $s in $run.fastqs:\n+ ${s}\n+ #end for\n+\n+ #if $run.name\n+ --name \'$run.name\'\n+ #end if\n+\n+ $run.polymorphism_prediction\n+ $run.predict_junctions\n+\n+ #if \'gd\' in str($run.output_options.formats).split(\',\'):\n+ && cp results/output/output.gd \'$output\'\n+ #end if\n+\n+ #if \'html\' in str($run.output_options.formats).split(\',\'):\n+ && cp results/output/index.html \'$report\'\n+ && mkdir $report.extra_files_path\n+ && cp -R results/output/* $report.extra_files_path\n+ #end if\n+\n+ #if \'zip\' in str($run.output_options.formats).split(\',\'):\n+ && tar -zcf \'$zip_output\' results\n+ #end if\n+\n+ #if \'log\' in str($run.output_options.formats).split(\',\'):\n+ && cp results/output/log.txt \'$log\'\n+ #end if\n+ #else\n+ #set $first = 1\n+ #for $o in str($run.output_options.formats).split(\',\'):\n+\n+ #if $first == 0\n+ &&\n+ #end if\n+ #set $first = 0\n+\n+ gdtools ANNOTATE\n+\n+ --format \'$o\'\n+\n+ -o\n+ #if $o == \'html\':\n+ \'$annreport\'\n+ #else if $o == \'gd\':\n+ \'$genomediff\'\n+ #else if $o == \'tsv\':\n+ \'$tabdelim\'\n+ #else if $o == \'phylip\':\n+ \'$phylipout\'\n+ #else if $o == \'json\':\n+ \'$jsonout\'\n+ #end if\n+\n+ $ref_opts\n+\n+ #for $s in $run.gds:\n+ ${s}\n+ #end for\n+ #end for\n+ #end if\n+ ]]>\n+ </command>\n+\n+ <inputs>\n+ <repeat name="references" title="Reference Genome" min="1">\n+ <conditional name="reference">\n+ <param name="source" type="select" label="Reference source" >\n+ <option value="builtin">built-in</option>\n+ <option value="history" selected="true">history</option>\n+ </param>\n+ <when value="builtin">\n+ <param name="fixed_genome" argument="--reference" type="select" optional="false" label="Galaxy Built-in Reference(s)">\n+ <options from_data_table="genbank_files">\n+ <fi'..b'<output name="output" file="gdout.txt" lines_diff="8" />\n+ </test>\n+ <test>\n+ <repeat name="references">\n+ <conditional name="reference">\n+ <param name="source" value="history" />\n+ <param name="own_genome" value="lambda.gbk" />\n+ </conditional>\n+ </repeat>\n+ <conditional name="run">\n+ <param name="mode" value="annotate" />\n+ <param name="gds" value="gdout.txt" />\n+ <section name="output_options">\n+ <param name="formats" value="html" />\n+ </section>\n+ </conditional>\n+\n+ <output name="annreport" file="gdtoolsout.html" compare="sim_size" delta="100" />\n+ </test>\n+ </tests>\n+\n+ <help>\n+ <![CDATA[\n+**Detect Variants**\n+\n+breseq (pronounced: \\\\br\xc4\x93z-\xcb\x88s\xc4\x93k\\\\ or breeze-seq) is a computational pipeline for\n+the analysis of short-read re-sequencing data (e.g. Illumina, 454, IonTorrent,\n+etc.). It uses reference-based alignment approaches to predict mutations in a\n+sample relative to an already sequenced genome. breseq is intended for microbial\n+genomes (<10 Mb) and re-sequenced samples that are only slightly diverged from\n+the reference sequence (<1 mutation per 1000 bp).\n+\n+breseq\'s primary advantages over other software programs are that it can:\n+\n+- Accurately predict new sequence junctions, such as those associated with mobile element insertions.\n+- Integrate multiple sources of evidence for genetic changes into mutation predictions.\n+- Produce annotated output describing biologically relevant mutational events.\n+\n+breseq was initially developed to analyze data from the Lenski long-term\n+evolution experiment with `E. coli`_. References: barrick2009a_ barrick2009b_.\n+\n+.. _`E. coli`: http://myxo.css.msu.edu/ecoli/\n+.. _barrick2009a: http://barricklab.org/twiki/pub/Lab/ToolsBacterialGenomeResequencing/documentation/references.html#barrick2009a\n+.. _barrick2009b: http://barricklab.org/twiki/pub/Lab/ToolsBacterialGenomeResequencing/documentation/references.html#barrick2009b\n+\n+However, breseq may be generally useful to researchers who are:\n+\n+- Tracking mutations over time in microbial evolution experiments.\n+- Checking strains for unwanted second-site mutations after genetic manipulations.\n+- Identifying mutations that occur during strain improvement or after long-term culture of engineered strains.\n+- Discovering what mutations arise in pathogens during infection or cause antibiotic resistance.\n+\n+\n+*Inputs*\n+\n+Breseq accepts files in FASTQ format. It does not take pair-end information into\n+account.\n+\n+You can either run in clonal (consensus) mode or search for polymorphisms in a\n+population.\n+\n+You can also select an external sequence (eg. a transposon) to detect for\n+insertions or horizontal transfer.\n+\n+\n+*Outputs*\n+\n+Breseq outputs a number of files. These are all condensed in a single zipped\n+file.\n+\n+It contains output files with the final results, accessible through\n+``output/index.html``\n+\n+It also contains data files with accessory data, including:\n+\n+- ``data/reference.fasta`` (file with reference genome: can be used in eg. IGV browser)\n+- ``data/reference.gff`` (file with genomic annotations: can be used in eg. IGV browser)\n+- ``data/areference.bam`` (file with read alignments: can be used in eg. IGV browser)\n+- ``data/unmatched.*`` (files with read that failed to align: can be used to build an assembly or to eg. blast against NCBI)\n+\n+\n+----\n+\n+**Annotate Variants**\n+\n+Annotate a GenomeDiff file (generated by breseq) with information about\n+mutations (what genes they affect, amino acid substitutions, etc.) If multiple\n+input files are provided, then also COMPARE the frequencies for identical\n+mutations across samples.\n+ ]]>\n+ </help>\n+\n+ <citations>\n+ <citation type="doi">10.1007/978-1-4939-0554-6_12</citation>\n+ </citations>\n+\n+</tool>\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r f848a7f97332 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu Oct 31 19:40:40 2019 -0400 |
| b |
| @@ -0,0 +1,14 @@ +<macros> + <token name="@PACKAGE_VERSION@" >0.34.0</token> + <token name="@GALAXY_VERSION@" >1</token> + <xml name="annotate_format_opts"> + <section name="output_options" title="Output Options" expanded="false"> + <param argument="--format" name="formats" type="select" multiple="true" optional="false" display="checkboxes" label="Output Formats" help="Note, this tool will run as many times (serially) as the number of output formats selected."> + <yield /> + <option value="tsv">Annotated Variants (Tabular)</option> + <option value="json">Annotated Variants (Json)</option> + <option value="html">Report (Webpage)</option> + </param> + </section> + </xml> +</macros> |
| b |
| diff -r 000000000000 -r f848a7f97332 test-data/gdout.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gdout.txt Thu Oct 31 19:40:40 2019 -0400 |
| b |
| @@ -0,0 +1,31 @@ +#=GENOME_DIFF 1.0 +#=TITLE smallest +#=CREATED 16:09:36 17 Oct 2019 +#=PROGRAM breseq 0.34.0 +#=COMMAND breseq --num-processors 1 -o results --reference /private/var/folders/8d/z84mms353qb2n0r3n2jhww0m0000gq/T/tmpYSLdP2/files/000/dataset_3.dat /private/var/folders/8d/z84mms353qb2n0r3n2jhww0m0000gq/T/tmpYSLdP2/files/000/dataset_1.dat --name smallest +#=REFSEQ /private/var/folders/8d/z84mms353qb2n0r3n2jhww0m0000gq/T/tmpYSLdP2/files/000/dataset_3.dat +#=READSEQ /private/var/folders/8d/z84mms353qb2n0r3n2jhww0m0000gq/T/tmpYSLdP2/files/000/dataset_1.dat +#=CONVERTED-BASES 250000 +#=CONVERTED-READS 5000 +#=INPUT-BASES 250000 +#=INPUT-READS 5000 +#=MAPPED-BASES 243031 +#=MAPPED-READS 4872 +INS 1 11 NC_001416 41405 GCGGCGGCG repeat_length=3 repeat_new_copies=5 repeat_ref_copies=2 repeat_seq=GCG +DEL 2 8,12 NC_001416 41601 3 repeat_length=3 repeat_new_copies=1 repeat_ref_copies=2 repeat_seq=AAC +INS 3 13 NC_001416 41716 TTTT repeat_length=1 repeat_new_copies=9 repeat_ref_copies=5 repeat_seq=T +DEL 4 9,14 NC_001416 44075 4 repeat_length=4 repeat_new_copies=1 repeat_ref_copies=2 repeat_seq=CAAA +SNP 5 6 NC_001416 47317 T +RA 6 . NC_001416 47317 0 N T consensus_score=103.5 frequency=1 major_base=T major_cov=17/17 major_frequency=1.000e+00 minor_base=N minor_cov=0/0 new_cov=17/17 polymorphism_frequency=1.000e+00 polymorphism_score=NA prediction=consensus ref_cov=0/0 total_cov=17/17 +MC 7 . NC_001416 1 38810 0 0 left_inside_cov=0 left_outside_cov=NA right_inside_cov=10 right_outside_cov=13 +MC 8 . NC_001416 41601 41603 0 0 left_inside_cov=0 left_outside_cov=29 right_inside_cov=0 right_outside_cov=28 +MC 9 . NC_001416 44075 44078 0 0 left_inside_cov=0 left_outside_cov=28 right_inside_cov=0 right_outside_cov=27 +MC 10 . NC_001416 48475 48502 0 0 left_inside_cov=10 left_outside_cov=12 right_inside_cov=0 right_outside_cov=NA +JC 11 . NC_001416 41398 1 NC_001416 41405 -1 -1 alignment_overlap=-1 coverage_minus=6 coverage_plus=18 flanking_left=50 flanking_right=50 frequency=1 junction_possible_overlap_registers=48 key=NC_001416__41398__1__NC_001416__41405__-1__-1__C__50__50__0__0 max_left=44 max_left_minus=39 max_left_plus=44 max_min_left=24 max_min_left_minus=23 max_min_left_plus=24 max_min_right=23 max_min_right_minus=11 max_min_right_plus=23 max_pos_hash_score=96 max_right=47 max_right_minus=34 max_right_plus=47 neg_log10_pos_hash_p_value=0.0 new_junction_coverage=1.10 new_junction_read_count=27 polymorphism_frequency=9.168e-01 pos_hash_score=22 prediction=consensus side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=0.04 side_1_overlap=0 side_1_possible_overlap_registers=49 side_1_read_count=1 side_1_redundant=0 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=0.16 side_2_overlap=0 side_2_possible_overlap_registers=49 side_2_read_count=4 side_2_redundant=0 total_non_overlap_reads=24 unique_read_sequence=C +JC 12 . NC_001416 41600 -1 NC_001416 41604 1 0 alignment_overlap=4 coverage_minus=14 coverage_plus=8 flanking_left=50 flanking_right=50 frequency=1 junction_possible_overlap_registers=45 key=NC_001416__41600__-1__NC_001416__41600__1__4____50__50__0__0 max_left=42 max_left_minus=42 max_left_plus=38 max_min_left=22 max_min_left_minus=20 max_min_left_plus=22 max_min_right=20 max_min_right_minus=12 max_min_right_plus=20 max_pos_hash_score=90 max_right=44 max_right_minus=44 max_right_plus=37 neg_log10_pos_hash_p_value=0.0 new_junction_coverage=1.00 new_junction_read_count=23 polymorphism_frequency=1.000e+00 pos_hash_score=19 prediction=consensus side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=0.00 side_1_overlap=4 side_1_possible_overlap_registers=49 side_1_read_count=0 side_1_redundant=0 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=0.00 side_2_overlap=0 side_2_possible_overlap_registers=45 side_2_read_count=0 side_2_redundant=0 total_non_overlap_reads=22 +JC 13 . NC_001416 41711 -1 NC_001416 41712 1 -4 alignment_overlap=-4 coverage_minus=10 coverage_plus=11 flanking_left=50 flanking_right=50 frequency=1 junction_possible_overlap_registers=45 key=NC_001416__41711__-1__NC_001416__41712__1__-4__TTTT__50__50__0__0 max_left=42 max_left_minus=42 max_left_plus=30 max_min_left=19 max_min_left_minus=19 max_min_left_plus=19 max_min_right=22 max_min_right_minus=19 max_min_right_plus=22 max_pos_hash_score=80 max_right=40 max_right_minus=37 max_right_plus=40 neg_log10_pos_hash_p_value=0.0 new_junction_coverage=1.30 new_junction_read_count=30 polymorphism_frequency=1.000e+00 pos_hash_score=20 prediction=consensus side_1_annotate_key=gene side_1_continuation=5 side_1_coverage=0.00 side_1_overlap=0 side_1_possible_overlap_registers=44 side_1_read_count=0 side_1_redundant=0 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=0.00 side_2_overlap=0 side_2_possible_overlap_registers=49 side_2_read_count=0 side_2_redundant=0 total_non_overlap_reads=21 unique_read_sequence=TTTT +JC 14 . NC_001416 44074 -1 NC_001416 44079 1 0 alignment_overlap=5 coverage_minus=19 coverage_plus=5 flanking_left=50 flanking_right=50 frequency=1 junction_possible_overlap_registers=44 key=NC_001416__44074__-1__NC_001416__44074__1__5____50__50__0__0 max_left=44 max_left_minus=43 max_left_plus=44 max_min_left=21 max_min_left_minus=21 max_min_left_plus=18 max_min_right=22 max_min_right_minus=22 max_min_right_plus=12 max_pos_hash_score=88 max_right=43 max_right_minus=43 max_right_plus=27 neg_log10_pos_hash_p_value=0.0 new_junction_coverage=1.11 new_junction_read_count=25 polymorphism_frequency=1.000e+00 pos_hash_score=20 prediction=consensus side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=0.00 side_1_overlap=5 side_1_possible_overlap_registers=49 side_1_read_count=0 side_1_redundant=0 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=0.00 side_2_overlap=0 side_2_possible_overlap_registers=44 side_2_read_count=0 side_2_redundant=0 total_non_overlap_reads=24 +UN 15 . NC_001416 1 38807 +UN 16 . NC_001416 41601 41603 +UN 17 . NC_001416 44075 44078 +UN 18 . NC_001416 48488 48502 |
| b |
| diff -r 000000000000 -r f848a7f97332 test-data/gdtoolsout.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gdtoolsout.html Thu Oct 31 19:40:40 2019 -0400 |
| b |
| @@ -0,0 +1,115 @@ +<!DOCTYPE html +PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" +"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> +<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"> +<html> +<head> +<title>Mutation Comparison</title> +<style type = "text/css"> +body {font-family: sans-serif; font-size: 11pt;} +th {background-color: rgb(0,0,0); color: rgb(255,255,255);} +table {background-color: rgb(1,0,0); color: rgb(0,0,0);} +tr {background-color: rgb(255,255,255);} +.mutation_in_codon {color:red; text-decoration : underline;} +.snp_type_synonymous{color:green;} +.snp_type_nonsynonymous{color:blue;} +.snp_type_nonsense{color:red;} +.mutation_header_row {background-color: rgb(0,130,0);} +.read_alignment_header_row {background-color: rgb(255,0,0);} +.missing_coverage_header_row {background-color: rgb(0,100,100);} +.new_junction_header_row {background-color: rgb(0,0,155);} +.copy_number_header_row {background-color: rgb(153,102,0);} +.alternate_table_row_0 {background-color: rgb(255,255,255);} +.alternate_table_row_1 {background-color: rgb(235,235,235);} +.gray_table_row {background-color: rgb(230,230,245);} +.polymorphism_table_row {background-color: rgb(160,255,160);} +.highlight_table_row {background-color: rgb(192,255,255);} +.reject_table_row {background-color: rgb(255,200,165);} +.user_defined_table_row {background-color: rgb(255,255,0);} +.information_table_row {background-color: rgb(200,255,255);} +.junction_repeat {background-color: rgb(255,165,0)} +.junction_gene {} +.hidden { display: none; } +.unhidden { display: block; } + +</style> +<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" /> +<script type="text/javascript"> + function hideTog(divID) { + var item = document.getElementById(divID); + if (item) { + item.className=(item.className=='hidden')?'unhidden':'hidden'; + } + } + function showTog(butID) { + var button = document.getElementById(butID); + if (button) { + button.value=(button.value=='Show')?'Hide':'Show'; + } + } +</script> + +</head> +<body> +<!--Output Html_Mutation_Table_String--> +<table border="0" cellspacing="1" cellpadding="3"> +<tr><th colspan="5" align="left" class="mutation_header_row">Predicted mutations</th></tr><tr> +<th>position</th> +<th>mutation</th> +<th>annotation</th> +<th>gene</th> +<th width="100%">description</th> +</tr> + +<!-- Item Lines --> + +<!-- Print The Table Row --> +<tr class="normal_table_row"> +<td align="right">41,405</td><!-- Position --> +<td align="center">(GCG)<sub>2→5</sub></td><!-- Cell Mutation --> +<td align="center">coding (325/873 nt)</td> +<td align="center"><i>NinC</i> →</td> +<td align="left">NinC protein</td> +</tr> +<!-- End Table Row --> + +<!-- Print The Table Row --> +<tr class="normal_table_row"> +<td align="right">41,601</td><!-- Position --> +<td align="center">(AAC)<sub>2→1</sub></td><!-- Cell Mutation --> +<td align="center">coding (521‑523/873 nt)</td> +<td align="center"><i>NinC</i> →</td> +<td align="left">NinC protein</td> +</tr> +<!-- End Table Row --> + +<!-- Print The Table Row --> +<tr class="normal_table_row"> +<td align="right">41,716</td><!-- Position --> +<td align="center">(T)<sub>5→9</sub></td><!-- Cell Mutation --> +<td align="center">coding (636/873 nt)</td> +<td align="center"><i>NinC</i> →</td> +<td align="left">NinC protein</td> +</tr> +<!-- End Table Row --> + +<!-- Print The Table Row --> +<tr class="normal_table_row"> +<td align="right">44,075</td><!-- Position --> +<td align="center">(CAAA)<sub>2→1</sub></td><!-- Cell Mutation --> +<td align="center">coding (190‑193/624 nt)</td> +<td align="center"><i>Q</i> →</td> +<td align="left">late gene regulator</td> +</tr> +<!-- End Table Row --> + +<!-- Print The Table Row --> +<tr class="normal_table_row"> +<td align="right">47,317</td><!-- Position --> +<td align="center">N→T</td><!-- Cell Mutation --> +<td align="center"><span style="white-space: nowrap"><font class="snp_type_nonsynonymous">?87I</font> (<font class="mutation_in_codon">N</font>TC→<font class="mutation_in_codon">A</font>TC) </span></td> +<td align="center"><i>lambdap78</i> ←</td> +<td align="left">putative envelope protein</td> +</tr> +<!-- End Table Row --> +</table></body></html> \ No newline at end of file |
| b |
| diff -r 000000000000 -r f848a7f97332 test-data/genbank_files.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genbank_files.loc Thu Oct 31 19:40:40 2019 -0400 |
| b |
| @@ -0,0 +1,3 @@ +#This configures genbank files available for specific galaxy tools (eg. breseq) +#<unique_build_id>\t<dbkey>\t<display_name>\t<file_path> +lambda1 lambda Lambda ${__HERE__}/lambda.gbk |
| b |
| diff -r 000000000000 -r f848a7f97332 test-data/lambda.gbk --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/lambda.gbk Thu Oct 31 19:40:40 2019 -0400 |
| b |
| b"@@ -0,0 +1,3280 @@\n+LOCUS NC_001416 48502 bp DNA linear PHG 21-APR-2009\n+DEFINITION Enterobacteria phage lambda, complete genome.\n+ACCESSION NC_001416\n+VERSION NC_001416.1 GI:9626243\n+DBLINK Project:14204\n+KEYWORDS .\n+SOURCE Enterobacteria phage lambda\n+ ORGANISM Enterobacteria phage lambda\n+ Viruses; dsDNA viruses, no RNA stage; Caudovirales; Siphoviridae;\n+ Lambda-like viruses.\n+REFERENCE 1 (sites)\n+ AUTHORS Chen,C.Y. and Richardson,J.P.\n+ TITLE Sequence elements essential for rho-dependent transcription\n+ termination at lambda tR1\n+ JOURNAL J. Biol. Chem. 262 (23), 11292-11299 (1987)\n+ PUBMED 3038914\n+REFERENCE 2 (sites)\n+ AUTHORS Peltz,S.W., Brown,A.L., Hasan,N., Podhajska,A.J. and Szybalski,W.\n+ TITLE Thermosensitivity of a DNA recognition site: activity of a\n+ truncated nutL antiterminator of coliphage lambda\n+ JOURNAL Science 228 (4695), 91-93 (1985)\n+ PUBMED 3156406\n+REFERENCE 3 (sites)\n+ AUTHORS Coleclough,C. and Erlitz,F.L.\n+ TITLE Use of primer-restriction-end adapters in a novel cDNA cloning\n+ strategy\n+ JOURNAL Gene 34 (2-3), 305-314 (1985)\n+ PUBMED 2408965\n+REFERENCE 4 (sites)\n+ AUTHORS Place,N., Fien,K., Mahoney,M.E., Wulff,D.L., Ho,Y.S., Debouck,C.,\n+ Rosenberg,M., Shih,M.C. and Gussin,G.N.\n+ TITLE Mutations that alter the DNA binding site for the bacteriophage\n+ lambda cII protein and affect the translation efficiency of the cII\n+ gene\n+ JOURNAL J. Mol. Biol. 180 (4), 865-880 (1984)\n+ PUBMED 6241264\n+REFERENCE 5 (sites)\n+ AUTHORS Frackman,S., Siegele,D.A. and Feiss,M.\n+ TITLE A functional domain of bacteriophage lambda terminase for prohead\n+ binding\n+ JOURNAL J. Mol. Biol. 180 (2), 283-300 (1984)\n+ PUBMED 6096564\n+REFERENCE 6 (sites)\n+ AUTHORS Craig,N.L. and Nash,H.A.\n+ TITLE E. coli integration host factor binds to specific sites in DNA\n+ JOURNAL Cell 39 (3 PT 2), 707-716 (1984)\n+ PUBMED 6096022\n+REFERENCE 7 (sites)\n+ AUTHORS Edlind,T.D., Cooley,T.E., Richards,S.H. and Ihler,G.M.\n+ TITLE Long range base-pairing in the leftward transcription unit of\n+ bacteriophage lambda. Characterization by electron microscopy and\n+ computer-aided sequence analysis\n+ JOURNAL J. Mol. Biol. 179 (3), 351-365 (1984)\n+ PUBMED 6096550\n+REFERENCE 8 (sites)\n+ AUTHORS Warren,F. and Das,A.\n+ TITLE Formation of termination-resistant transcription complex at phage\n+ lambda nut locus: effects of altered translation and a ribosomal\n+ mutation\n+ JOURNAL Proc. Natl. Acad. Sci. U.S.A. 81 (12), 3612-3616 (1984)\n+ PUBMED 6233610\n+REFERENCE 9 (sites)\n+ AUTHORS Wulff,D.L., Mahoney,M., Shatzman,A. and Rosenberg,M.\n+ TITLE Mutational analysis of a regulatory region in bacteriophage lambda\n+ that has overlapping signals for the initiation of transcription\n+ and translation\n+ JOURNAL Proc. Natl. Acad. Sci. U.S.A. 81 (2), 555-559 (1984)\n+ PUBMED 6229793\n+REFERENCE 10 (sites)\n+ AUTHORS Hohn,B.\n+ TITLE DNA sequences necessary for packaging of bacteriophage lambda DNA\n+ JOURNAL Proc. Natl. Acad. Sci. U.S.A. 80 (24), 7456-7460 (1983)\n+ PUBMED 6324174\n+REFERENCE 11 (bases 45901 to 46443)\n+ AUTHORS Taylor,A., Benedik,M. and Campbell,A.\n+ TITLE Location of the Rz gene in bacteriophage lambda\n+ JOURNAL Gene 26 (2-3), 159-163 (1983)\n+ PUBMED 6323257\n+REFERENCE 12 (bases 48469 to 48498)\n+ AUTHORS Miwa,T. and Matsubara,K.\n+ TITLE Lambda phage DNA sequences affecting the packaging process\n+ JOURNAL Gene 24 (2-3), 199-206 (1983)\n+ PUBMED 6227527\n+REFERENCE 13 (bases 29063 to 29140)\n+ AUTHORS Benedik,M., Mascarenhas,D. and Campbell,A.\n+ TITLE The integrase promoter and T'I terminator in bacteriophages lambda\n+ and 434\n+ "..b'atctcgc ttatataacg agcgtgttta\n+ 45421 tcggctacat cggtactgac tcgattggtt cgcttatcaa acgcttcgct gctaaaaaag\n+ 45481 ccggagtaga agatggtaga aatcaataat caacgtaagg cgttcctcga tatgctggcg\n+ 45541 tggtcggagg gaactgataa cggacgtcag aaaaccagaa atcatggtta tgacgtcatt\n+ 45601 gtaggcggag agctatttac tgattactcc gatcaccctc gcaaacttgt cacgctaaac\n+ 45661 ccaaaactca aatcaacagg cgccggacgc taccagcttc tttcccgttg gtgggatgcc\n+ 45721 taccgcaagc agcttggcct gaaagacttc tctccgaaaa gtcaggacgc tgtggcattg\n+ 45781 cagcagatta aggagcgtgg cgctttacct atgattgatc gtggtgatat ccgtcaggca\n+ 45841 atcgaccgtt gcagcaatat ctgggcttca ctgccgggcg ctggttatgg tcagttcgag\n+ 45901 cataaggctg acagcctgat tgcaaaattc aaagaagcgg gcggaacggt cagagagatt\n+ 45961 gatgtatgag cagagtcacc gcgattatct ccgctctggt tatctgcatc atcgtctgcc\n+ 46021 tgtcatgggc tgttaatcat taccgtgata acgccattac ctacaaagcc cagcgcgaca\n+ 46081 aaaatgccag agaactgaag ctggcgaacg cggcaattac tgacatgcag atgcgtcagc\n+ 46141 gtgatgttgc tgcgctcgat gcaaaataca cgaaggagtt agctgatgct aaagctgaaa\n+ 46201 atgatgctct gcgtgatgat gttgccgctg gtcgtcgtcg gttgcacatc aaagcagtct\n+ 46261 gtcagtcagt gcgtgaagcc accaccgcct ccggcgtgga taatgcagcc tccccccgac\n+ 46321 tggcagacac cgctgaacgg gattatttca ccctcagaga gaggctgatc actatgcaaa\n+ 46381 aacaactgga aggaacccag aagtatatta atgagcagtg cagatagagt tgcccatatc\n+ 46441 gatgggcaac tcatgcaatt attgtgagca atacacacgc gcttccagcg gagtataaat\n+ 46501 gcctaaagta ataaaaccga gcaatccatt tacgaatgtt tgctgggttt ctgttttaac\n+ 46561 aacattttct gcgccgccac aaattttggc tgcatcgaca gttttcttct gcccaattcc\n+ 46621 agaaacgaag aaatgatggg tgatggtttc ctttggtgct actgctgccg gtttgttttg\n+ 46681 aacagtaaac gtctgttgag cacatcctgt aataagcagg gccagcgcag tagcgagtag\n+ 46741 catttttttc atggtgttat tcccgatgct ttttgaagtt cgcagaatcg tatgtgtaga\n+ 46801 aaattaaaca aaccctaaac aatgagttga aatttcatat tgttaatatt tattaatgta\n+ 46861 tgtcaggtgc gatgaatcgt cattgtattc ccggattaac tatgtccaca gccctgacgg\n+ 46921 ggaacttctc tgcgggagtg tccgggaata attaaaacga tgcacacagg gtttagcgcg\n+ 46981 tacacgtatt gcattatgcc aacgccccgg tgctgacacg gaagaaaccg gacgttatga\n+ 47041 tttagcgtgg aaagatttgt gtagtgttct gaatgctctc agtaaatagt aatgaattat\n+ 47101 caaaggtata gtaatatctt ttatgttcat ggatatttgt aacccatcgg aaaactcctg\n+ 47161 ctttagcaag attttccctg tattgctgaa atgtgatttc tcttgatttc aacctatcat\n+ 47221 aggacgtttc tataagatgc gtgtttcttg agaatttaac atttacaacc tttttaagtc\n+ 47281 cttttattaa cacggtgtta tcgttttcta acacgangtg aatattatct gtggctagat\n+ 47341 agtaaatata atgtgagacg ttgtgacgtt ttagttcaga ataaaacaat tcacagtcta\n+ 47401 aatcttttcg cacttgatcg aatatttctt taaaaatggc aacctgagcc attggtaaaa\n+ 47461 ccttccatgt gatacgaggg cgcgtagttt gcattatcgt ttttatcgtt tcaatctggt\n+ 47521 ctgacctcct tgtgttttgt tgatgattta tgtcaaatat taggaatgtt ttcacttaat\n+ 47581 agtattggtt gcgtaacaaa gtgcggtcct gctggcattc tggagggaaa tacaaccgac\n+ 47641 agatgtatgt aaggccaacg tgctcaaatc ttcatacaga aagatttgaa gtaatatttt\n+ 47701 aaccgctaga tgaagagcaa gcgcatggag cgacaaaatg aataaagaac aatctgctga\n+ 47761 tgatccctcc gtggatctga ttcgtgtaaa aaatatgctt aatagcacca tttctatgag\n+ 47821 ttaccctgat gttgtaattg catgtataga acataaggtg tctctggaag cattcagagc\n+ 47881 aattgaggca gcgttggtga agcacgataa taatatgaag gattattccc tggtggttga\n+ 47941 ctgatcacca taactgctaa tcattcaaac tatttagtct gtgacagagc caacacgcag\n+ 48001 tctgtcactg tcaggaaagt ggtaaaactg caactcaatt actgcaatgc cctcgtaatt\n+ 48061 aagtgaattt acaatatcgt cctgttcgga gggaagaacg cgggatgttc attcttcatc\n+ 48121 acttttaatt gatgtatatg ctctcttttc tgacgttagt ctccgacggc aggcttcaat\n+ 48181 gacccaggct gagaaattcc cggacccttt ttgctcaaga gcgatgttaa tttgttcaat\n+ 48241 catttggtta ggaaagcgga tgttgcgggt tgttgttctg cgggttctgt tcttcgttga\n+ 48301 catgaggttg ccccgtattc agtgtcgctg atttgtattg tctgaagttg tttttacgtt\n+ 48361 aagttgatgc agatcaatta atacgatacc tgcgtcataa ttgattattt gacgtggttt\n+ 48421 gatggcctcc acgcacgttg tgatatgtag atgataatca ttatcacttt acgggtcctt\n+ 48481 tccggtgatc cgacaggtta cg\n+//\n+\n' |
| b |
| diff -r 000000000000 -r f848a7f97332 test-data/lambda.short_sequence_repeats.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/lambda.short_sequence_repeats.fastq Thu Oct 31 19:40:40 2019 -0400 |
| b |
| b'@@ -0,0 +1,20000 @@\n+@../data/lambda/lambda.short_sequence_repeats.fastq.000000000\n+TTCGGGAAAACGGGATCACCACGATGGAACAGGTTAACGCAGGAATGCGC\n++\n+HHIHHHHIHHIIIHGIFEIIFIGCGIGHIIDFAFII@EFHHGIII<IIGI\n+@../data/lambda/lambda.short_sequence_repeats.fastq.000000001\n+TCTGCGGGAGTGTCCGGGAATAATTAAAACGATGCACACAGGGTTTAGCG\n++\n+IHIIHIGHHIIIIGFEGIGIIIEIGIHIDCIDI?FIIIIH@<IIIDIBH=\n+@../data/lambda/lambda.short_sequence_repeats.fastq.000000002\n+AACGTGACGGACGTAACCACCGCGACATGTGTGTGCTGTTCCGCTGGGCA\n++\n+IIIHHIHIHHFIGIIIEIEIHHIGEDIGIDIBGHIDGIGEIIICGIHGII\n+@../data/lambda/lambda.short_sequence_repeats.fastq.000000003\n+GGCAACTCATGCAATTATTGTGAGCAATACACACGCGCTTCCAGCGGAGT\n++\n+IIIHIHIIHIIFHIHFGEIGFHHIHIDIDACIIIGIDDICIIEBDAIICI\n+@../data/lambda/lambda.short_sequence_repeats.fastq.000000004\n+TTTTTTAATGAGGTCATCACGGGATCCCATGTGCGTGACGGACATCGGGA\n++\n+HIIHIGHIIIIIIHHIIHGIICDHIHIIIICIDCFHIIIIIIIIEGII;I\n+@../data/lambda/lambda.short_sequence_repeats.fastq.000000005\n+AATTTAACATTTACAACCTTTTTAAGTCCTTTTATTAACACGGTGTTATC\n++\n+IHIHHHGIHIIIDFEFEGHGIIFIFICHGIHICI@EIIFCFIBHEI?ICI\n+@../data/lambda/lambda.short_sequence_repeats.fastq.000000006\n+TGAAAACGTAATGCACGTCTTTACCTGCCCGTCGCTTTTGCTCCATTAGC\n++\n+IIHIIHIIGIHIIHIIIGHHFEIIGIFIIICDIBIIG?IDIICDDI=GID\n+@../data/lambda/lambda.short_sequence_repeats.fastq.000000007\n+AGAATGTCGCTGGACGGTATCGCGAAAATGTATTCAGAAAATGATTATCA\n++\n+IHIHIIIHIGHFHIIIIFGGIFFIEIGDGDFIGHEGIIIBI@:IID=<9I\n+@../data/lambda/lambda.short_sequence_repeats.fastq.000000008\n+GGTAAGGTCTGGCGAACGGTGTATTACCGGTTTGCTACCAGGGAAGAACG\n++\n+IHIHIIIHHIIIIIFFIHEHFAIIGHIGIIIFIIHIIIIBI9GDIFIIEI\n+@../data/lambda/lambda.short_sequence_repeats.fastq.000000009\n+TGAGCAAATGATGATTGATGGCTTATCAGAGCGTGGAAACGTTAATCACT\n++\n+IIHHIIHHIGGIHIIDIIGIHGHHHGIIIIEAIFIIHIIBEIII:H?DIH\n+@../data/lambda/lambda.short_sequence_repeats.fastq.000000010\n+TTCAGTTCTCTGGCATTTTTGTCGCGCTGGGCTTTGTAGGTAATGGCGTT\n++\n+IHIIIHIIIGIHIEHIIIIIGECIDGIHIEIIIFFIFFFHIIHIIHII@C\n+@../data/lambda/lambda.short_sequence_repeats.fastq.000000011\n+CTACACAAATCTTTCCACGCTAAATCATAACGTCCGGTTTCTTCCGTGTC\n++\n+IHHIIFHGIGFIIHFIGEIGIFEIEIFHIAGAGCBIIGGIF>II<GBI5?\n+@../data/lambda/lambda.short_sequence_repeats.fastq.000000012\n+ATTACAAAGTTACCTGTCAAACGGTGCAATGAAGCCAAGTTAGAACTCGT\n++\n+HHHHIIIHIIHHIGIIIHGCIIDCEIHIIFIIIICIIIFIFIIICIGDI;\n+@../data/lambda/lambda.short_sequence_repeats.fastq.000000013\n+AGTAATTGACGCGTTCGCCAGCTTCAGTTCTCTGGCATTTTTGTCGCGCT\n++\n+HHHIHIHIFGIHIIIFHGIIHHHIIIIGIFGFEFFIII@IIHB@ICIE@G\n+@../data/lambda/lambda.short_sequence_repeats.fastq.000000014\n+CGACTCAATGCTCTTACCTGTTGTGCAGATATAAAAAATCCCGAAACCGT\n++\n+IIIIHHHGHIIIGIGIIIIHGIIGIEICFGIIIIII?IDHII>GGHI<II\n+@../data/lambda/lambda.short_sequence_repeats.fastq.000000015\n+TCAGGCTGTCAGCCTTATGCTCGAACTGACCATAACCAGCGCCCGGCAGT\n++\n+IHHIIIIIGHIHHIHFEIEIGHDGDIDCFHICGAEIIIHIBIIDHIFIII\n+@../data/lambda/lambda.short_sequence_repeats.fastq.000000016\n+CTGCCGTTTTGCCCGTGCATATCGGTCACGAACAAATCTGATTACTTAAA\n++\n+IIHHHHIIIIIIFGIGHHIIDGGIFIIEEIBIIIIIIGGC@C?IEIBA;I\n+@../data/lambda/lambda.short_sequence_repeats.fastq.000000017\n+ACTGTCGATGCAGCCAAAATTTGTGGCGGCGCAGAAAATGTTGTTAAAAC\n++\n+IHHHIHHIHIIIHHHGIIICGGIHFIIIHIIIEIFI@FIFIHGIIIIII@\n+@../data/lambda/lambda.short_sequence_repeats.fastq.000000018\n+GAAATCAAAGGCGCGGACACGTTCATCTTTGGTCATACGCCAGCAGTGAA\n++\n+IHHIHHHIFGHFIHIIFIIIIIIGHBHIAIIIIFHIIIIGIIIEI>IIDH\n+@../data/lambda/lambda.short_sequence_repeats.fastq.000000019\n+GCCGTGTAGTTGAAGGTTTTTCCGTCAGATTCTTTTGGGATTGGCTTGGG\n++\n+IHIHHHIIHIGHHIIHEFFIF?IIBIIIEGDEIIIIIHIIHID=GIFEGI\n+@../data/lambda/lambda.short_sequence_repeats.fastq.000000020\n+CTGCCGCTCTGAATTGCAGCATCCGGTTTCACCACAGAAAGGTCGTTTTC\n++\n+IHIIHIHHIGIGIFFIIFGFGFGIIHDIGGFGGHCDIIDIBIAFI=IAII\n+@../data/lambda/lambda.short_sequence_repeats.fastq.000000021\n+TGTCCCCCTGTTTTGAGGGATAGCAATCCCCCAATTTGAGGGAGTGTTTT\n++\n+IIHGIHGHFHIIHHGGIHIHIEIIIBIHIGFDIIHIIHIIIFI(BIIHI=\n+@../data/lambda/lambda.short_sequence_repeats.fastq.000000022\n+TTTGAAGTAATATTTTAACCGCTAGATGAAGAGCAAGCGCATGGAGCCAC\n++\n+HHHIIHIIIIEIFGIFIGHIIIIICDEIEHICIIIIIIGDIIIIIHI5FB\n+@../data/lambda/lambda.short_sequence_repeats.fastq.000000023\n+CGCTG'..b'GTAGCCGATAAACACGCTCGTTATATAAGCGAG\n++\n+IIHIHIIIIIIIIIGFGHIHIFBIIEIFIIDIIFGDIIAEA?BIIAE@I=\n+@../data/lambda/lambda.short_sequence_repeats.fastq.000004977\n+GTACAGGCCGTGCGGTTGATATTGCCAAAACAGAGCTGTGGGGGAGAGTT\n++\n+IHHIIIHHHIHIHGHCHGIFEE=GHGCIIFIFFHIEGBIIHHCHI@HHGI\n+@../data/lambda/lambda.short_sequence_repeats.fastq.000004978\n+GAGTGTCCGGGAATAATTAAAACGATGCACACAGGGTTTAGCGCGTACGC\n++\n+IHHIIIIGGHHGHIHIHIIFIIEHIGIFDBEDFIIIII<BIHH=EIGI<I\n+@../data/lambda/lambda.short_sequence_repeats.fastq.000004979\n+ATGTGAGACGTTGTGACGTTTTAGTTCAGAATAAAACAATTCACAGTCTA\n++\n+HIIHGGIIGGIIIFIEIIIIHIIIHIIHIIDAEGIIHIEIEIIIIIBIBA\n+@../data/lambda/lambda.short_sequence_repeats.fastq.000004980\n+CAGGGGAATGTGATTAATTCCAGGCATTAAACGTTCTCTGCACCACGATC\n++\n+IIHHHHIIHGHGGEGIEIIGGHIIFHIG>IGIFHHFIHFHHI?IGHIGIH\n+@../data/lambda/lambda.short_sequence_repeats.fastq.000004981\n+ACGCCGGGGGCAAGATGCAGAGATTGCCATGGTACAGGCCGTGCGGTTGA\n++\n+HIHIIHIHIIIIIGIIIFIIH@IIGHGIIIIFAIGIIBFIIGABHI>HIG\n+@../data/lambda/lambda.short_sequence_repeats.fastq.000004982\n+ACCGTTCCGCCCGCTTCTTTGAATTTTGCAATCAGGCTGTCAGCCTTATG\n++\n+IHIHHHIHGHHIIIGIHFEGHHHICIBEIDHHIBIFIHIIDIIII9HIII\n+@../data/lambda/lambda.short_sequence_repeats.fastq.000004983\n+ACAGGCGCCGGACGCTACCAGCTTCTTTCCCGTTGGTGGGATGCCTACCG\n++\n+IIIHHHHIIIHIIHIGHIIIGGGDHGIIICFGIIIE@DGIBI8IICGIBI\n+@../data/lambda/lambda.short_sequence_repeats.fastq.000004984\n+TTTACACGAATCAGATCCACGGAGGGATCATCAGCAGATTGTTCTTTATT\n++\n+HIIHHHHHHGHHHIIHIIIEHFIFGHIHEGHHGIGCIIHII9DIIIIBG:\n+@../data/lambda/lambda.short_sequence_repeats.fastq.000004985\n+CATGCAGCTTCTGACCGCAGTTAGCGCACGTTAAAGCTCGCTCGACGCTT\n++\n+HHHHIHIIHHGGIGICIIIGIGIG@DIICIIIICID7GIID@IHIIHI?F\n+@../data/lambda/lambda.short_sequence_repeats.fastq.000004986\n+ATCTTCTACTCCGGCTTTTTTAGCAGCGAAGCGTTTGATAAGCGAACCAA\n++\n+IIHHGHIIIIIIGIGGIIIIIEIHDIIIIIGBIIIIIDIGGICDIIIIID\n+@../data/lambda/lambda.short_sequence_repeats.fastq.000004987\n+CTTGCCCCCGGCGTCGCGGCACTACGGCAATAATCCGCATAAGCGAATGT\n++\n+IIHIHIHHIHGIIHHHFIHHFIDEIGIHFIIDIIIFIIIIIIII@GAI=I\n+@../data/lambda/lambda.short_sequence_repeats.fastq.000004988\n+ATGCGCTATTACGAAAAAATTGATGGCAGCAAATACCGAAATATTTGGGT\n++\n+IIIIIIHIIIHIGIIIIHHGIIEEIIGIFIIIAIIHAIHGHGIGADIIID\n+@../data/lambda/lambda.short_sequence_repeats.fastq.000004989\n+CCGGACATTACCGGACAACTGCTGCGGCACCTCAACTCCGATTTAATGTA\n++\n+HHHHHGIIFIIGFEIHIIIGHHGFIEIFGIHEICICG@EGIAIII?IF1D\n+@../data/lambda/lambda.short_sequence_repeats.fastq.000004990\n+GAATAGCGTTTTGCTGATGTGCTGGAGATCGAATTACAAAGGTTAGTTTT\n++\n+IHIIHIHIIIIGIIIIIIIIIIIIGEIGFFIIIIE<DHIGIEIIEIIFBG\n+@../data/lambda/lambda.short_sequence_repeats.fastq.000004991\n+TAACTTCGATTTTGGTCAATCACCTTGTTTTCCTCGCACGACGTCTTAGC\n++\n+IIHIIIHIHIHIIIIHHIHDHGIIFGGHIIIIHGEFIIGIIACIIFHCII\n+@../data/lambda/lambda.short_sequence_repeats.fastq.000004992\n+GGATATTCAGACGCGAATGCCTGTTCTGAAGCCATTTATCGATATGGTAA\n++\n+IHIIHIHIHIHIIHIHHFEIIIIFFIIIHEDIEF@FIDIHF?DH@ABI?>\n+@../data/lambda/lambda.short_sequence_repeats.fastq.000004993\n+TTTGTTGAGATTTATGTCAAATATTAGGAATGTTTTCACTTAATAGTATT\n++\n+HIHIIHHHIIIGHGIIFIIIIIIIIFIIIFFIIIIFIIIIIHIIIIIEI9\n+@../data/lambda/lambda.short_sequence_repeats.fastq.000004994\n+CCCGCTTTCACGAAGGTCATGTGTAAAAGGCCGCAGCGTGACTATTACTA\n++\n+IIHIIGIGIHGGHEHIIIIIHIGFIIIGIBEGIIGIIFI>IADHDIHIIG\n+@../data/lambda/lambda.short_sequence_repeats.fastq.000004995\n+GGTGCAATGCCACAAAGAAGAGTCAATCGCAGACAACATTTTGAATGCGG\n++\n+HIHHHHGHHHHHGGGHGIHFIGEDFIHEIGF@GDIGHEIFGIIIDFIIDB\n+@../data/lambda/lambda.short_sequence_repeats.fastq.000004996\n+ATCATTACCGTGATAACGCCATTACCTACAAAGCCCAGCGCGACAAAAAT\n++\n+HIHHIIHGGHIHIIGEHIIIGEFGDIHGIIFFHGCGIIHIBDIIAIIFBD\n+@../data/lambda/lambda.short_sequence_repeats.fastq.000004997\n+AAATATTTGGGTAGTTGGCGATCTGCACGGATGCTACACGAACCTGATGA\n++\n+IIIIIIHHHGHGHIHHIHCIHDIEFIIEICIIAIIA@IICGIFII>CCIC\n+@../data/lambda/lambda.short_sequence_repeats.fastq.000004998\n+CGTCACCTAAGCAGGCCCATAGCTTCCTGTTTTGGTCTAAGCTGCGGTTG\n++\n+HIHHHIHGHHGGGIGHIFIHHIIIHIIIIHDIIHFBIIHDIIGI>IFDIG\n+@../data/lambda/lambda.short_sequence_repeats.fastq.000004999\n+ATAATATTCACATCGTGTTAGAAAACGATAACACCGTGTTAATAAAAGGA\n++\n+IHIHIHIGIGIIGGIFHDHHFIFHDFBCGCCEDIIIIIIFIFIICIIDHI\n' |
| b |
| diff -r 000000000000 -r f848a7f97332 test-data/log.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/log.txt Thu Oct 31 19:40:40 2019 -0400 |
| b |
| @@ -0,0 +1,4 @@ +Thu Oct 17 16:09:32 2019 + +breseq --num-processors 1 -o results --reference /private/var/folders/8d/z84mms353qb2n0r3n2jhww0m0000gq/T/tmpYSLdP2/files/000/dataset_3.dat /private/var/folders/8d/z84mms353qb2n0r3n2jhww0m0000gq/T/tmpYSLdP2/files/000/dataset_1.dat --name smallest + |
| b |
| diff -r 000000000000 -r f848a7f97332 test-data/out.tar.gz |
| b |
| Binary file test-data/out.tar.gz has changed |
| b |
| diff -r 000000000000 -r f848a7f97332 test-data/report.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/report.html Thu Oct 31 19:40:40 2019 -0400 |
| [ |
| @@ -0,0 +1,176 @@ +<!DOCTYPE html +PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" +"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> +<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"> +<html> +<head> +<title>smallest :: BRESEQ :: Mutation Predictions</title> +<style type = "text/css"> +body {font-family: sans-serif; font-size: 11pt;} +th {background-color: rgb(0,0,0); color: rgb(255,255,255);} +table {background-color: rgb(1,0,0); color: rgb(0,0,0);} +tr {background-color: rgb(255,255,255);} +.mutation_in_codon {color:red; text-decoration : underline;} +.snp_type_synonymous{color:green;} +.snp_type_nonsynonymous{color:blue;} +.snp_type_nonsense{color:red;} +.mutation_header_row {background-color: rgb(0,130,0);} +.read_alignment_header_row {background-color: rgb(255,0,0);} +.missing_coverage_header_row {background-color: rgb(0,100,100);} +.new_junction_header_row {background-color: rgb(0,0,155);} +.copy_number_header_row {background-color: rgb(153,102,0);} +.alternate_table_row_0 {background-color: rgb(255,255,255);} +.alternate_table_row_1 {background-color: rgb(235,235,235);} +.gray_table_row {background-color: rgb(230,230,245);} +.polymorphism_table_row {background-color: rgb(160,255,160);} +.highlight_table_row {background-color: rgb(192,255,255);} +.reject_table_row {background-color: rgb(255,200,165);} +.user_defined_table_row {background-color: rgb(255,255,0);} +.information_table_row {background-color: rgb(200,255,255);} +.junction_repeat {background-color: rgb(255,165,0)} +.junction_gene {} +.hidden { display: none; } +.unhidden { display: block; } + +</style> +<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" /> +<script type="text/javascript"> + function hideTog(divID) { + var item = document.getElementById(divID); + if (item) { + item.className=(item.className=='hidden')?'unhidden':'hidden'; + } + } + function showTog(butID) { + var button = document.getElementById(butID); + if (button) { + button.value=(button.value=='Show')?'Hide':'Show'; + } + } +</script> + +</head> +<body> +<table width="100%" border="0" cellspacing="0" cellpadding="3"> +<tr> +<td><a href="http://barricklab.org/breseq"><img src="evidence/breseq_small.png" /></a></td> +<td width="100%"> +<b><i>breseq</i></b> version 0.34.0 +<br><a href="index.html">mutation predictions</a> | +<a href="marginal.html">marginal predictions</a> | +<a href="summary.html">summary statistics</a> | +<a href="output.gd">genome diff</a> | +<a href="log.txt">command line log</a> +</td></tr></table> + +<p> +<!--Mutation Predictions --> +<p> +<!--Output Html_Mutation_Table_String--> +<table border="0" cellspacing="1" cellpadding="3"> +<tr><th colspan="6" align="left" class="mutation_header_row">Predicted mutations</th></tr><tr> +<th>evidence</th> +<th>position</th> +<th>mutation</th> +<th>annotation</th> +<th>gene</th> +<th width="100%">description</th> +</tr> + +<!-- Item Lines --> + +<!-- Print The Table Row --> +<tr class="normal_table_row"> +<td align="center"><a href="evidence/JC_11.html">JC</a></td><!-- Evidence --> +<td align="right">41,405</td><!-- Position --> +<td align="center">(GCG)<sub>2→5</sub></td><!-- Cell Mutation --> +<td align="center">coding (325/873 nt)</td> +<td align="center"><i>NinC</i> →</td> +<td align="left">NinC protein</td> +</tr> +<!-- End Table Row --> + +<!-- Print The Table Row --> +<tr class="normal_table_row"> +<td align="center"><a href="evidence/MC_PLOT_8.html">MC</a> <a href="evidence/JC_12.html">JC</a></td><!-- Evidence --> +<td align="right">41,601</td><!-- Position --> +<td align="center">(AAC)<sub>2→1</sub></td><!-- Cell Mutation --> +<td align="center">coding (521‑523/873 nt)</td> +<td align="center"><i>NinC</i> →</td> +<td align="left">NinC protein</td> +</tr> +<!-- End Table Row --> + +<!-- Print The Table Row --> +<tr class="normal_table_row"> +<td align="center"><a href="evidence/JC_13.html">JC</a></td><!-- Evidence --> +<td align="right">41,716</td><!-- Position --> +<td align="center">(T)<sub>5→9</sub></td><!-- Cell Mutation --> +<td align="center">coding (636/873 nt)</td> +<td align="center"><i>NinC</i> →</td> +<td align="left">NinC protein</td> +</tr> +<!-- End Table Row --> + +<!-- Print The Table Row --> +<tr class="normal_table_row"> +<td align="center"><a href="evidence/MC_PLOT_9.html">MC</a> <a href="evidence/JC_14.html">JC</a></td><!-- Evidence --> +<td align="right">44,075</td><!-- Position --> +<td align="center">(CAAA)<sub>2→1</sub></td><!-- Cell Mutation --> +<td align="center">coding (190‑193/624 nt)</td> +<td align="center"><i>Q</i> →</td> +<td align="left">late gene regulator</td> +</tr> +<!-- End Table Row --> + +<!-- Print The Table Row --> +<tr class="normal_table_row"> +<td align="center"><a href="evidence/SNP_5.html">RA</a></td><!-- Evidence --> +<td align="right">47,317</td><!-- Position --> +<td align="center">N→T</td><!-- Cell Mutation --> +<td align="center"><span style="white-space: nowrap"><font class="snp_type_nonsynonymous">?87I</font> (<font class="mutation_in_codon">N</font>TC→<font class="mutation_in_codon">A</font>TC) </span></td> +<td align="center"><i>lambdap78</i> ←</td> +<td align="left">putative envelope protein</td> +</tr> +<!-- End Table Row --> +</table> +<p> +<table border="0" cellspacing="1" cellpadding="3" width="100%"> +<tr><th colspan="11" align="left" class="missing_coverage_header_row">Unassigned missing coverage evidence</th></tr> +<tr><th> </th><th> </th><th> </th><th>seq id</th> +<th>start</th> +<th>end</th> +<th>size</th> +<th>←reads</th> +<th>reads→</th> +<th>gene</th> +<th width="100%">description</th> +</tr> +<tr> +<td><a href="evidence/MC_SIDE_1_7.html">*</a></td> +<td><a href="evidence/MC_SIDE_2_7.html">*</a></td> +<td><a href="evidence/MC_PLOT_7.html">÷</a></td> +<td>NC_001416</td> +<td align="right">1</td> +<td align="right">38810</td> +<td align="right">38810</td> +<td align="center">NA [0]</td> +<td align="center">[10] 13</td> +<td align="center"><i>nu1–[O]</i></td> +<td align="left">nu1,A,W,B,C,nu3,D,E,Fi,Fii,Z,U,V,G,T,H,M,L,K,I,J,lom,orf‑401,orf206b,orf‑314,orf‑194,ea47,ea31,ea59,int,xis,lambdap35,ea8.5,ea22,orf61,orf63,orf60a,exo,bet,gam,kil,cIII,ea10,ral,orf28,lambdap48,N,rexb,rexa,cI,cro,cII,[O]</td> +</tr> +<tr> +<td><a href="evidence/MC_SIDE_1_10.html">*</a></td> +<td><a href="evidence/MC_SIDE_2_10.html">*</a></td> +<td><a href="evidence/MC_PLOT_10.html">÷</a></td> +<td>NC_001416</td> +<td align="right">48475</td> +<td align="right">48502</td> +<td align="right">28</td> +<td align="center">12 [10]</td> +<td align="center">[0] NA</td> +<td align="center"><i>lambdap79/–</i></td> +<td align="left">hypothetical protein/–</td> +</tr> +</table> +</body></html> \ No newline at end of file |
| b |
| diff -r 000000000000 -r f848a7f97332 tool-data/genbank_files.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/genbank_files.loc.sample Thu Oct 31 19:40:40 2019 -0400 |
| b |
| @@ -0,0 +1,4 @@ +#This configures genbank files available for specific galaxy tools (eg. breseq) +#<unique_build_id>\t<dbkey>\t<display_name>\t<file_path> +#ecoliMC4100 ecoliMC4100 E. coli MC4100 /afs/igc.gulbenkian.pt/folders/UBI/PROJECTS/GALAXY/genomes/genbank/NC_012759.1_BW2952.gb +#ecoliMG1655 ecoliMG1655 E. coli MG1655 /afs/igc.gulbenkian.pt/folders/UBI/PROJECTS/GALAXY/genomes/genbank/NC_012759.1_BW2952.gb |
| b |
| diff -r 000000000000 -r f848a7f97332 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Thu Oct 31 19:40:40 2019 -0400 |
| b |
| @@ -0,0 +1,6 @@ +<tables> + <table name="genbank_files" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/genbank_files.loc" /> + </table> +</tables> |
| b |
| diff -r 000000000000 -r f848a7f97332 tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Thu Oct 31 19:40:40 2019 -0400 |
| b |
| @@ -0,0 +1,6 @@ +<tables> + <table name="genbank_files" comment_char="#" allow_duplicate_entries="False"> + <columns>value, dbkey, name, path</columns> + <file path="${__HERE__}/test-data/genbank_files.loc" /> + </table> +</tables> |