| Next changeset 1:15ad71e21010 (2018-10-30) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a |
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added:
glimmer2seq.py glimmer_build_icm.xml glimmer_gbk_to_orf.py glimmer_glimmer_to_gff.py glimmer_wo_icm.py macros.xml test-data/coordTest.txt test-data/extractTestOutput.fasta test-data/glimmer.gff test-data/glimmer_w_icm_trans-table-11_genomic.dout test-data/glimmer_w_icm_trans-table-11_genomic.fasta test-data/glimmer_w_icm_trans-table-11_genomic.out test-data/glimmer_wo_icm_trans-table-11_plasmid_genomic.fasta test-data/longORFSTestOutput.dat test-data/orf_aa.fa test-data/orf_nc.fa test-data/streptomyces_Tu6071_genomic.acgt test-data/streptomyces_Tu6071_genomic.fasta test-data/streptomyces_Tu6071_plasmid_genes.fasta test-data/streptomyces_Tu6071_plasmid_genes.icm test-data/streptomyces_Tue6071_plasmid_genomic.fasta test-data/test.gbk |
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| diff -r 000000000000 -r 9c195b26a5ac glimmer2seq.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/glimmer2seq.py Tue Nov 28 10:08:06 2017 -0500 |
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| @@ -0,0 +1,47 @@ +#!/usr/bin/env python +""" +Input: DNA FASTA file + Glimmer ORF file +Output: ORF sequences as FASTA file +Author: Bjoern Gruening +""" +import sys + +from Bio import SeqIO +from Bio.SeqRecord import SeqRecord + + +def glimmer2seq(glimmer_prediction=sys.argv[1], genome_sequence=sys.argv[2], outfile=sys.argv[3]): + if len(sys.argv) >= 4: + glimmerfile = open(glimmer_prediction, "r") + sequence = open(genome_sequence) + else: + print("Missing input values.") + sys.exit() + + fastafile = SeqIO.parse(sequence, "fasta") + + sequences = dict() + seq_records = list() + for entry in fastafile: + sequences[entry.description] = entry + + for line in glimmerfile: + if line.startswith('>'): + entry = sequences[line[1:].strip()] + else: + orf_start = int(line[8:17]) + orf_end = int(line[18:26]) + + orf_name = line[0:8] + if orf_start <= orf_end: + seq_records.append(SeqRecord(entry.seq[orf_start - 1:orf_end], id=orf_name, description=entry.description)) + else: + seq_records.append(SeqRecord(entry.seq[orf_end - 1:orf_start].reverse_complement(), id=orf_name, description=entry.description)) + + SeqIO.write(seq_records, outfile, "fasta") + glimmerfile.close() + sequence.close() + + +if __name__ == "__main__": + glimmer2seq() |
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| diff -r 000000000000 -r 9c195b26a5ac glimmer_build_icm.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/glimmer_build_icm.xml Tue Nov 28 10:08:06 2017 -0500 |
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| @@ -0,0 +1,122 @@ +<tool id="glimmer_build_icm" name="Glimmer ICM builder" version="@WRAPPER_VERSION@"> + <description></description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <command><![CDATA[ + build-icm + --depth $depth + $no_stops + --period $period + --width $width + + #if $stop_codon_opts.stop_codon_opts_selector == "gb": + --trans_table '${stop_codon_opts.genbank_gencode}' + #else: + --stop_codons '${stop_codon_opts.stop_codons}' + #end if + + '$outfile' < '$infile' 2>&1; +]]></command> + <inputs> + <param name="infile" type="data" format="fasta" label="Trainings Dataset" help="A set of known genes in FASTA format." /> + <param name="depth" type="integer" value="7" label="Set the depth of the ICM" help="The depth is the maximum number of positions in the context window that will be used to determine the probability of the predicted position." /> + <param name="period" type="integer" value="3" label="Set the period of the ICM" help="The period is the number of different submodels for different positions in the text in a cyclic pattern. E.g., if the period is 3, the first submodel will determine positions 1, 4, 7, ..." /> + <param name="width" type="integer" value="12" label="Set the width of the ICM" help="The width includes the predicted position." /> + <param name="no_stops" type="boolean" truevalue="--no_stops" falsevalue="" checked="false" label="Do not use any input strings with in-frame stop codons" /> + + <conditional name="stop_codon_opts"> + <param name="stop_codon_opts_selector" type="select" label="Specify start codons as"> + <option value="gb" selected="True">Genbank translation table entry</option> + <option value="free_form">Comma-separated list</option> + </param> + <when value="gb"> + <param name="genbank_gencode" type="select" label="Use Genbank translation table to specify stop codons"> + <option value="1" selected="True">1. Standard</option> + <option value="2">2. Vertebrate Mitochondrial</option> + <option value="3">3. Yeast Mitochondrial</option> + <option value="4">4. Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option> + <option value="5">5. Invertebrate Mitochondrial</option> + <option value="6">6. Ciliate, Dasycladacean and Hexamita Nuclear Code</option> + <option value="9">9. Echinoderm Mitochondrial</option> + <option value="10">10. Euplotid Nuclear</option> + <option value="11">11. Bacteria and Archaea</option> + <option value="12">12. Alternative Yeast Nuclear</option> + <option value="13">13. Ascidian Mitochondrial</option> + <option value="14">14. Flatworm Mitochondrial</option> + <option value="15">15. Blepharisma Macronuclear</option> + <option value="16">16. Chlorophycean Mitochondrial</option> + <option value="21">21. Trematode Mitochondrial</option> + <option value="22">22. Scenedesmus obliquus mitochondrial</option> + <option value="23">23. Thraustochytrium Mitochondrial</option> + <option value="24">24. Pterobranchia mitochondrial</option> + </param> + </when> + <when value="free_form"> + <param name="stop_codons" type="text" value="tag,tga,taa" label="Specify stop codons as a comma-separated list" /> + </when> + </conditional> + </inputs> + <outputs> + <data format="data" name="outfile" /> + </outputs> + <tests> + <test> + <param name="infile" value='streptomyces_Tu6071_plasmid_genes.fasta' /> + <param name="depth" value="7" /> + <param name="period" value="3" /> + <param name="width" value="12" /> + <param name="no_stops" value="" /> + <param name="genbank_gencode" value="11" /> + <!-- compare files sizes, because the output is a binary --> + <output name="outfile" file='streptomyces_Tu6071_plasmid_genes.icm' compare="sim_size" delta="1000" ftype="data" /> + </test> + </tests> + + <help> +<![CDATA[ + +**What it does** + +This program constructs an interpolated context model (ICM) from an input set of sequences. + +This model can be used by Glimmer3 to predict genes. + +**TIP** To extract CDS from a GenBank file use the tool *Extract ORF from a GenBank file*. + +----- + +**Example** + +*Input*:: + + - Genome Sequence + + >CELF22B7 C.aenorhabditis elegans (Bristol N2) cosmid F22B7 + GATCCTTGTAGATTTTGAATTTGAAGTTTTTTCTCATTCCAAAACTCTGT + GATCTGAAATAAAATGTCTCAAAAAAATAGAAGAAAACATTGCTTTATAT + TTATCAGTTATGGTTTTCAAAATTTTCTGACATACCGTTTTGCTTCTTTT + TTTCTCATCTTCTTCAAATATCAATTGTGATAATCTGACTCCTAACAATC + GAATTTCTTTTCCTTTTTCTTTTTCCAACAACTCCAGTGAGAACTTTTGA + ATATCTTCAAGTGACTTCACCACATCAGAAGGTGTCAACGATCTTGTGAG + AACATCGAATGAAGATAATTTTAATTTTAGAGTTACAGTTTTTCCTCCGA + CAATTCCTGATTTACGAACATCTTCTTCAAGCATTCTACAGATTTCTTGA + TGCTCTTCTAGGAGGATGTTGAAATCCGAAGTTGGAGAAAAAGTTCTCTC + AACTGAAATGCTTTTTCTTCGTGGATCCGATTCAGATGGACGACCTGGCA + GTCCGAGAGCCGTTCGAAGGAAAGATTCTTGTGAGAGAGGCGTGAAACAC + AAAGGGTATAGGTTCTTCTTCAGATTCATATCACCAACAGTTTGAATATC + CATTGCTTTCAGTTGAGCTTCGCATACACGACCAATTCCTCCAACCTAAA + AAATTATCTAGGTAAAACTAGAAGGTTATGCTTTAATAGTCTCACCTTAC + GAATCGGTAAATCCTTCAAAAACTCCATAATCGCGTTTTTATCATTTTCT + ..... + +*Output*:: + interpolated context model (ICM) + + + +]]> + </help> + <expand macro="citation" /> +</tool> |
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| diff -r 000000000000 -r 9c195b26a5ac glimmer_gbk_to_orf.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/glimmer_gbk_to_orf.py Tue Nov 28 10:08:06 2017 -0500 |
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| @@ -0,0 +1,63 @@ +#!/usr/bin/env python + +################################################################### +# +# gbk2orf.py by Errol Strain (estrain@gmail.com) +# +# Read a GenBank file and export fasta formatted amino acid and +# CDS files +# +################################################################### + +import sys +from optparse import OptionParser + +from Bio import SeqIO +from Bio.Seq import Seq +from Bio.SeqRecord import SeqRecord + + +# Command line usage +usage = "usage: %prog -g input.gbk -a aa.fasta -n nuc.fasta" +p = OptionParser(usage) +p.add_option("-t", "--translate", dest="transtabl", type="int", default=11, + help="Translation table used to translate coding regions (default=11)") +p.add_option("-g", "--genbank", dest="gb_file", help="GenBank input file") +p.add_option("-a", "--amino_acid", dest="aa_file", help="Fasta amino acid output") +p.add_option("-n", "--nucleotide", dest="orf_file", help="Fasta nucleotide output") +(opts, args) = p.parse_args() +# Do I need this next line? +if not opts and not args: + p.error("Use --help to see usage") +if len(sys.argv) == 1: + p.error("Use --help to see usage") + +# Lists to hold SeqRecords +aalist = [] +nuclist = [] + +# If the CDS does not have a locus tag the name will be assigned using the +# order in which it was found +feat_count = 0 + +# Iterate through genbank records in input file +for gb_record in SeqIO.parse(open(opts.gb_file, "r"), "genbank"): + for (index, feature) in enumerate(gb_record.features): + if feature.type == "CDS": + feat_count = feat_count + 1 + gene = feature.extract(gb_record.seq) + if "locus_tag" in feature.qualifiers: + value = feature.qualifiers["locus_tag"][0] + else: + value = "Index_" + str(feat_count) + nuclist.append(SeqRecord(Seq(str(gene)), id=value, name=value)) + pro = Seq(str(gene.translate(table=opts.transtabl, to_stop=True))) + aalist.append(SeqRecord(pro, id=value, name=value)) + +# Write out lists in fasta format +aa_handle = open(opts.aa_file, "w") +SeqIO.write(aalist, aa_handle, "fasta") +aa_handle.close() +orf_handle = open(opts.orf_file, "w") +SeqIO.write(nuclist, orf_handle, "fasta") +orf_handle.close() |
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| diff -r 000000000000 -r 9c195b26a5ac glimmer_glimmer_to_gff.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/glimmer_glimmer_to_gff.py Tue Nov 28 10:08:06 2017 -0500 |
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| @@ -0,0 +1,38 @@ +#!/usr/bin/env python + +""" +Input: Glimmer3 prediction +Output: GFF3 file +Return a GFF3 file with the genes predicted by Glimmer3 +Bjoern Gruening + +Note: Its not a full-fledged GFF3 file, its a really simple one. + +""" + +import re +import sys + + +def __main__(): + input_file = open(sys.argv[1], 'r') + + print('##gff-version 3\n') + for line in input_file: + line = line.strip() + if line[0] == '>': + header = line[1:] + else: + (id, start, end, frame, score) = re.split('\s+', line) + if int(end) > int(start): + strand = '+' + else: + strand = '-' + (start, end) = (end, start) + + rest = 'frame=%s;score=%s' % (frame, score) + print('\t'.join([header, 'glimmer_prediction', 'predicted_gene', start, end, '.', strand, '.', rest])) + + +if __name__ == "__main__": + __main__() |
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| diff -r 000000000000 -r 9c195b26a5ac glimmer_wo_icm.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/glimmer_wo_icm.py Tue Nov 28 10:08:06 2017 -0500 |
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| @@ -0,0 +1,77 @@ +#!/usr/bin/env python +""" +Input: DNA Fasta File +Output: Tabular +Return Tabular File with predicted ORF's +Bjoern Gruening +""" +import os +import shutil +import subprocess +import sys +import tempfile + +from glimmer2seq import glimmer2seq + + +def main(): + genome_seq_file = sys.argv[1] + outfile_classic_glimmer = sys.argv[2] + outfile_ext_path = sys.argv[3] + oufile_genes = sys.argv[8] + + tag = 'glimmer_non_knowlegde_based_prediction' + tempdir = tempfile.gettempdir() + + trainingset = os.path.join(tempdir, tag + ".train") + icm = os.path.join(tempdir, tag + ".icm") + + longorfs = tempfile.NamedTemporaryFile() + trainingset = tempfile.NamedTemporaryFile() + icm = tempfile.NamedTemporaryFile() + + # glimmeropts = "-o0 -g110 -t30 -l" + glimmeropts = "-o%s -g%s -t%s" % (sys.argv[4], sys.argv[5], sys.argv[6]) + if sys.argv[7] == "true": + glimmeropts += " -l" + + """ + 1. Find long, non-overlapping orfs to use as a training set + """ + subprocess.Popen(["long-orfs", "-n", "-t", "1.15", + genome_seq_file, "-"], stdout=longorfs, + stderr=subprocess.PIPE).communicate() + + """ + 2. Extract the training sequences from the genome file + """ + subprocess.Popen(["extract", "-t", + genome_seq_file, longorfs.name], stdout=trainingset, + stderr=subprocess.PIPE).communicate() + + """ + 3. Build the icm from the training sequences + """ + + # the "-" parameter is used to redirect the output to stdout + subprocess.Popen(["build-icm", "-r", "-"], + stdin=open(trainingset.name), stdout=icm, + stderr=subprocess.PIPE).communicate() + + """ + Run Glimmer3 + """ + subprocess.Popen(["glimmer3", glimmeropts, + genome_seq_file, icm.name, os.path.join(tempdir, tag)], + stdout=subprocess.PIPE, stderr=subprocess.PIPE).communicate() + + if outfile_classic_glimmer.strip() != 'None': + shutil.copyfile(os.path.join(tempdir, tag + ".predict"), outfile_classic_glimmer) + if outfile_ext_path.strip() != 'None': + shutil.copyfile(os.path.join(tempdir, tag + ".detail"), outfile_ext_path) + + glimmer2seq(os.path.join(tempdir, tag + ".predict"), genome_seq_file, oufile_genes) + + +if __name__ == "__main__": + main() |
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| diff -r 000000000000 -r 9c195b26a5ac macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Nov 28 10:08:06 2017 -0500 |
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| @@ -0,0 +1,18 @@ +<?xml version="1.0"?> +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="3.02">glimmer</requirement> + <requirement type="package" version="1.70">biopython</requirement> + <yield/> + </requirements> + </xml> + + <token name="@WRAPPER_VERSION@">3.02</token> + + <xml name="citation"> + <citations> + <citation type="doi">10.1093/bioinformatics/btm009</citation> + </citations> + </xml> +</macros> |
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| diff -r 000000000000 -r 9c195b26a5ac test-data/coordTest.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/coordTest.txt Tue Nov 28 10:08:06 2017 -0500 |
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| @@ -0,0 +1,17 @@ +00001 40137 52 +2 0.892 +00002 1319 1095 -3 0.654 +00003 1555 1391 -2 0.793 +00004 1953 2066 +3 1.078 +00005 2045 2146 +2 0.919 +00006 4463 4759 +2 0.985 +00007 6785 6582 -3 1.033 +00008 6862 7020 +1 0.915 +00009 7300 7488 +1 0.900 +00010 7463 7570 +2 0.912 +00011 8399 8527 +2 1.044 +00012 10652 10545 -3 0.895 +00013 12170 12066 -3 1.108 +00014 13891 13748 -2 0.998 +00015 14157 14044 -1 1.026 +00016 15285 15410 +3 0.928 +00017 15829 15704 -2 0.949 |
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| diff -r 000000000000 -r 9c195b26a5ac test-data/extractTestOutput.fasta |
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| Binary file test-data/extractTestOutput.fasta has changed |
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| diff -r 000000000000 -r 9c195b26a5ac test-data/glimmer.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/glimmer.gff Tue Nov 28 10:08:06 2017 -0500 |
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| b'@@ -0,0 +1,62 @@\n+##gff-version 3\n+\n+gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t897\t2918\t.\t+\t.\tframe=+3;score=3.19\n+gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t144\t938\t.\t-\t.\tframe=-3;score=2.86\n+gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t7237\t7368\t.\t-\t.\tframe=-1;score=2.50\n+gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t10347\t11945\t.\t+\t.\tframe=+3;score=2.93\n+gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t12110\t12238\t.\t-\t.\tframe=-2;score=6.22\n+gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t13067\t15088\t.\t-\t.\tframe=-2;score=2.95\n+gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t15045\t16529\t.\t+\t.\tframe=+3;score=3.36\n+gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t20276\t21385\t.\t-\t.\tframe=-2;score=2.90\n+gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t21382\t23037\t.\t-\t.\tframe=-1;score=2.93\n+gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t23031\t24797\t.\t+\t.\tframe=+3;score=2.92\n+gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t27115\t27291\t.\t-\t.\tframe=-1;score=1.92\n+gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t28556\t28960\t.\t+\t.\tframe=+2;score=2.51\n+gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t29040\t30026\t.\t+\t.\tframe=+3;score=0.40\n+gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t32942\t33151\t.\t-\t.\tframe=-2;score=1.06\n+gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t34754\t38242\t.\t-\t.\tframe=-2;score=2.97\n+gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t43100\t43300\t.\t-\t.\tframe=-2;score=6.70\n+gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t43402\t43497\t.\t+\t.\tframe=+1;score=0.97\n+gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t44963\t45157\t.\t-\t.\tframe=-2;score=1.68\n+gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t46852\t47430\t.\t-\t.\tframe=-1;score=0.78\n+gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t48354\t51314\t.\t-\t.\tframe=-3;score=2.96\n+gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t55069\t55329\t.\t-\t.\tframe=-1;score=1.43\n+gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t56431\t59457\t.\t-\t.\tframe=-1;score=2.96\n+gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun seque'..b'sequence\tglimmer_prediction\tpredicted_gene\t100811\t102931\t.\t+\t.\tframe=+2;score=2.95\n+gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t103074\t105521\t.\t+\t.\tframe=+3;score=2.96\n+gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t105847\t106200\t.\t-\t.\tframe=-1;score=0.32\n+gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t108069\t108365\t.\t-\t.\tframe=-3;score=4.89\n+gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t109947\t110498\t.\t-\t.\tframe=-3;score=0.90\n+gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t110791\t110907\t.\t-\t.\tframe=-1;score=2.13\n+gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t116538\t117071\t.\t-\t.\tframe=-3;score=0.81\n+gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t117443\t117733\t.\t-\t.\tframe=-2;score=0.01\n+gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t118399\t118776\t.\t-\t.\tframe=-1;score=3.59\n+gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t119582\t119740\t.\t-\t.\tframe=-2;score=0.41\n+gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t123152\t123484\t.\t+\t.\tframe=+2;score=2.86\n+gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t123767\t123925\t.\t+\t.\tframe=+2;score=0.89\n+gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t124906\t126459\t.\t-\t.\tframe=-1;score=2.93\n+gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t126704\t128992\t.\t-\t.\tframe=-2;score=2.95\n+gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t129011\t129178\t.\t-\t.\tframe=-2;score=1.85\n+gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t130337\t132172\t.\t-\t.\tframe=-2;score=2.94\n+gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t134993\t136987\t.\t+\t.\tframe=+2;score=2.94\n+gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t137245\t137523\t.\t-\t.\tframe=-1;score=1.14\n+gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t137825\t140512\t.\t-\t.\tframe=-2;score=2.96\n+gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t140766\t142487\t.\t-\t.\tframe=-3;score=2.94\n+gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t142484\t143056\t.\t-\t.\tframe=-2;score=0.89\n+gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t143099\t143578\t.\t-\t.\tframe=-2;score=0.42\n+gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\tglimmer_prediction\tpredicted_gene\t144230\t147016\t.\t-\t.\tframe=-2;score=2.96\n' |
| b |
| diff -r 000000000000 -r 9c195b26a5ac test-data/glimmer_w_icm_trans-table-11_genomic.dout --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/glimmer_w_icm_trans-table-11_genomic.dout Tue Nov 28 10:08:06 2017 -0500 |
| b |
| b'@@ -0,0 +1,1391 @@\n+Command: glimmer3 -o 50 -g 90 -t 30 -z 11 -A atg,gtg,ttg -l /tmp/tmpubrxoL/files/000/dataset_1.dat /tmp/tmpubrxoL/files/000/dataset_2.dat glimmer_output\n+\n+Sequence file = /tmp/tmpubrxoL/files/000/dataset_1.dat\n+Number of sequences = 1\n+ICM model file = /tmp/tmpubrxoL/files/000/dataset_2.dat\n+Excluded regions file = none\n+List of orfs file = none\n+Input is NOT separate orfs\n+Independent (non-coding) scores are used\n+Circular genome = false\n+Truncated orfs = false\n+Minimum gene length = 90 bp\n+Maximum overlap bases = 50\n+Threshold score = 30\n+Use first start codon = false\n+Translation table = 11\n+Start codons = atg,gtg,ttg\n+Start probs = 0.333,0.333,0.333\n+Stop codons = taa,tag,tga\n+GC percentage = 70.9%\n+Ignore score on orfs longer than 1738\n+\n+\n+>gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\n+Sequence length = 147347\n+\n+ ----- Start ----- --- Length ---- ------------- Scores -------------\n+ ID Frame of Orf of Gene Stop of Orf of Gene Raw InFrm F1 F2 F3 R1 R2 R3 NC\n+ +1 289 316 417 126 99 -12.44 0 0 0 0 - 0 0 99\n+ +1 418 706 894 474 186 -12.50 0 0 0 72 - 0 0 26\n+ +2 203 755 907 702 150 -7.78 0 - 0 4 - 0 5 89\n+ -2 934 478 245 687 231 -16.05 0 - 0 0 - 0 0 99\n+ -1 1005 960 808 195 150 -10.87 0 - - 0 0 - 0 99\n+ +1 895 904 1029 132 123 -21.92 0 0 - 0 - - 0 99\n+ +2 1211 1316 1450 237 132 -9.27 0 0 0 0 0 0 99 0\n+ -2 1513 1462 1295 216 165 -13.99 0 0 - 0 0 0 99 0\n+ -1 1587 1506 1006 579 498 -11.27 0 - - 0 0 - 1 98\n+ +1 1132 1774 2016 882 240 -10.77 0 0 0 0 0 0 99 0\n+ -2 2221 1633 1514 705 117 -17.27 0 0 0 0 - 0 0 99\n+ +2 1451 2192 2287 834 93 -3.86 2 0 2 11 0 - 5 80\n+ +2 2288 2414 2524 234 108 -14.85 0 0 0 0 0 0 98 0\n+ +1 2386 2521 2676 288 153 -10.44 0 0 0 0 - 0 99 0\n+ -2 2704 2332 2222 480 108 -8.27 0 - - 83 0 0 7 9\n+ +1 2677 2713 2865 186 150 -16.16 0 0 0 42 - 0 4 53\n+0001 +3 174 183 2918 2742 2733 -2.60 0 - - 0 - - 99 0\n+ +2 2525 2828 2947 420 117 -8.18 0 - 0 - - 0 0 99\n+0002 -3 3062 2777 144 2916 2631 -1.16 0 0 - - 0 - 0 99\n+ -2 3301 2845 2705 594 138 -6.29 0 0 0 62 - 0 0 37\n+ +2 2948 3149 3352 402 201 -10.20 0 0 0 0 0 - - 99\n+ +1 2866 3262 3363 495 99 -8.25 0 0 - 13 0 - 3 83\n+ -1 3396 3171 2995 399 174 -6.74 0 0 0 - 0 0 - 99\n+ -2 3403 3400 3302 99 96 -10.07 0 - - 95 0 0 1 2\n+ -3 3419 3407 3195 222 210 -5.41 0 - - 1 - - 0 98\n+ -1 3810 3810 3553 255 255 -10.41 0 - 0 0 0 - 99 0\n+ +3 3102 3750 3866 762 114 0.43 0 0 0 0 - 0 98 0\n+ +3 3867 4098 4313 444 213 -6.66 0 0 0 0 - 38 0 60\n+ -3 4343 3824 3420 921 402 -0.79 4 - 0 0 - - 4 95\n+ +2 3353 3869 4357 1002 486 1.19 5 0 5 - - 94 - 0\n+ +1 3754 4183 4413 657 228 -5.38 0 0 - - 0 0 - 99\n+ -1 4416 4254 4105 309 1'..b' 150 -7.28 0 0 0 2 - 0 0 97\n+ -1 141903 141825 141724 177 99 -7.85 0 - 0 0 0 0 0 99\n+ -2 141958 141406 141242 714 162 -12.78 0 0 0 0 0 0 94 5\n+ +1 141736 141769 142011 273 240 -5.49 0 0 0 0 - - 9 90\n+ -1 142218 142149 141982 234 165 -12.14 0 - 0 0 0 0 0 99\n+ +2 141086 142130 142381 1293 249 -10.31 0 - 0 0 - 0 0 99\n+ +3 141180 142323 142421 1239 96 -3.68 2 - - 2 0 0 8 88\n+ -2 142483 142222 141959 522 261 -10.97 0 - 0 0 - 0 0 99\n+0093 -3 142526 142487 140766 1758 1719 -5.32 0 0 - - - - 0 99\n+ -1 142713 142491 142321 390 168 -10.76 0 - - - 0 - 0 99\n+ +1 142357 142720 142821 462 99 -4.75 1 1 0 0 - 0 - 98\n+ +3 142539 142764 143033 492 267 -10.35 0 - 0 0 - 94 - 5\n+ -1 143058 142938 142801 255 135 -9.38 0 - 0 0 0 69 - 30\n+0094 -2 143098 143056 142484 612 570 1.09 99 - 0 - - 99 - 0\n+ -1 143415 143403 143248 165 153 -4.05 0 58 0 - 0 33 - 8\n+ -1 143571 143571 143458 111 111 -7.95 0 0 0 0 0 99 - 0\n+ +2 142460 143489 143683 1221 192 -4.68 0 0 0 0 - 99 - 0\n+ -3 143888 143819 143655 231 162 -14.45 0 0 - - - 0 0 99\n+ +1 143197 143746 143892 693 144 -17.23 0 0 0 - - 0 0 99\n+0095 -2 143938 143578 143099 837 477 0.65 95 - 0 - - 95 - 4\n+ +2 143750 143822 143944 192 120 -13.31 0 - 0 - - - - 99\n+ -1 143985 143970 143857 126 111 -14.74 0 - - - 0 - - 99\n+ +1 143893 143971 144120 225 147 -5.00 0 0 88 - - - 0 11\n+ -2 144229 144130 143981 246 147 -3.60 0 - 14 - - 0 0 84\n+ -1 144303 144111 143986 315 123 -5.94 0 0 81 - 0 13 0 5\n+ -3 144344 143981 143889 453 90 -20.25 0 0 - 0 0 - 0 99\n+ -1 144762 144504 144358 402 144 -10.51 0 0 34 0 0 6 0 58\n+ -3 144860 144584 144345 513 237 -5.22 0 - 92 0 - 3 0 3\n+ +3 144102 144816 144926 822 108 -10.12 0 0 9 0 - 84 - 6\n+ +3 144927 145053 145172 243 117 -8.72 0 0 78 0 0 0 3 18\n+ -3 145283 144956 144861 420 93 -5.48 0 0 19 - 0 11 0 68\n+ -1 145479 145422 144835 642 585 -11.68 0 - 99 - 0 0 - 0\n+ +3 145173 145734 145922 747 186 -11.77 0 0 99 0 0 0 0 0\n+ -1 145959 145836 145480 477 354 -16.86 0 - 99 0 0 0 0 0\n+0096 +2 143945 144212 145963 2016 1749 2.07 99 - 99 - - - - 0\n+ -3 145985 145880 145305 678 573 -3.74 0 - 74 0 - 0 0 25\n+ +3 146058 146082 146261 201 177 -21.64 0 - 0 0 - 0 - 99\n+ +3 146397 146721 146954 555 231 -17.15 0 - 0 0 - 0 0 99\n+ -3 146996 146627 146202 792 423 -8.83 0 - 3 - - 0 0 96\n+0097 -2 147025 147016 144230 2793 2784 -2.16 0 - 99 0 - 0 - 0\n+ -1 147072 147000 146782 288 216 -16.68 0 - 0 - 0 0 0 99\n+ +2 145964 146987 147097 1131 108 -13.39 0 - 0 0 - - - 99\n+ +3 146991 147033 147131 138 96 -12.90 0 - - 0 - - - 99\n+ -2 147346 147343 147062 282 279 -8.69 0 0 - - - 0 - 99\n' |
| b |
| diff -r 000000000000 -r 9c195b26a5ac test-data/glimmer_w_icm_trans-table-11_genomic.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/glimmer_w_icm_trans-table-11_genomic.fasta Tue Nov 28 10:08:06 2017 -0500 |
| b |
| b'@@ -0,0 +1,1140 @@\n+>orf00001 gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\n+ATGGCGAATGATCCGGCGGGCGAGTACGGGGCGTGGATTCACGAACTCGGTTTGTCCGAG\n+GCAATCGCGCGAAAAATCGTCGCGCCTTTTGAGATTGACGTTTTGGAGATTACTGATCCT\n+GAGCCGGAATTGATGGAGGGATTGGATCGGGAGGCGCGGCGTGGGCGGCGGCTTGCGTTG\n+CTTCAGACCGGGCTTTTGGAGCACGCGGCCGAGCATAATATTTGCACCATGATGACGCTT\n+CATCAGCAGGTTGAGGAGGCGGCGGCTTTCGCGGAGAAAATGCCGGAGACGGCGGCGGAG\n+CTTTACCGGAATGAGGTGTCGGCGGAGGATTTTGCCCTGGCCGAGGAGCTCCCGGCCTCC\n+GAGGTGGGTGGGGGGTTCTACGAGCTGGAGCCGGGGCGTCATGTGCCGCCGTCGCGGGTG\n+TGGTCGCGGTGGCTGTATGGGGAGCATCCTGTGGCCGAACGGCGTTCTGTGCTGCGGGAG\n+TTCGCGAACGGGATGGACGCGGAGGGGCGGCGGGTGCACCGGGCGTTCCTCGCTTCCGTA\n+CGGGTCCTGGGTGAGGGCGTCGACATCGTCGGGGAGCGCGGGGTCGAGGCGATCTGCTTT\n+GCCGACGCACGCGGGTCTCAGGTGGAGATCGTGCAGAACATCGGGCGCGCGTTGCGCCAG\n+AACCCGGATGGGCGGGCGAAGACGGCGCGGATCATCGTGCCGGTCTTCCTGCGGCCGGAC\n+GAGGACGGGGAGGGCATGGTGGCGTCGGAGGCGTACCGGCCGCTCGTCGCCGTACTCCAG\n+GGCCTGCGCTCGCACGACGAGCACCTGGTCGAGAAACTCATGCTGCGGGCGCGCGTACGG\n+GCCGAGAGCGCGAGCGCGCGCAGCGCGGAGGAGGGCGGTGCGGGGCCCTCGCGGCTCCTG\n+TCGGACTCCGGGACGGCGGCTGCGGCCTCCGAGGGCGTCGAGGGCCAGGAGCAGGGCGAG\n+GACGGCGCCGAGGCGGAGTCGGTGCTGCTGCGGTTCTCCTCGCCGCGCGCGGCGTCGACG\n+GTCGCGGCGTTCCTGCGGACGCGGGTGTACCAGCCCGAGTCGCTGGTGTGGCTGGAGGGG\n+TACGAGGCCCTGCGCGCCTGGCGGGCCGAGCAAGGGGTGAGCGGGGTGTGCGCGGTCCCG\n+TACGACGCCGAGGTCGCCGCGGGGGCCTCGCGGCGGTACCCGGTCGGGCGGTGGACCGCC\n+GCGCAACGCCGCGCCCGCCGCGAGGGCACCCTCAGCGCACACCGCGTCGAGCTCCTCGAC\n+GCGGAGGGCATGGTGTGGGAGCCGCGCGAGGAGGAATGGGAGCGCACGCTCGCGGGGCTT\n+CGCTCCTACCGGACGGCGTACGGGCACCTCGCCCCCCACAGGCGCGAAACCTGGGGCGAA\n+GACGAGGGTGAGGACGTCGTACGCGTCGGGGACCTGATGGCGAACCTCCGCCGCAAGGAC\n+GGACTCGGGAAGGACGCGAAGCGGGCCGCCGCGCGCGCCGCGCAGCTGAGGGCCGTCGAT\n+GCGGACTGGGACTGCCCGTGGCCGCTGGACTGGCAGCGCTGCTGCCGGAAACTCGTGCTC\n+CTGGCCGCGGACGAGCCCGGCGGGCGCCTGCCGGAGATCGCGCCCGGGGTCTGCCTGGAC\n+GGGGATGACCTCGGGGTGTGGGTCGCGCGGCAGCAGGAGCCGCGGGTGTGGGCGCGGCTC\n+AGCACCGAGCAGCGGGCGCGGCTCGAAGCGCTCGGGCTGCGGCCCACCGAAGCGGCCCCG\n+GGGCGGGGTGTGGAGGGCACGGGGGCGGCGGGGAGCATGAAGCGGACGGCGACGGCGCGA\n+ACGGCTTTTCAGCGGGGTGTGGCGGCGCTCGCGCAGTGGGTCGAGCGGGAAGGCGCGGGG\n+AAACCCGTACCCCGCAAACACGTCGAGACCGTCAGCGTCGACGGCGAGGACGTCGACGTA\n+CGCCTCGGCGTATGGATCTCGAACACCAAGAGCCGGTACGACGGGCTGAGCGAGGACGAA\n+CGCGCGCAGCTCACCGCACTCGGAATGCCCTGGGCAGGATGA\n+>orf00002 gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\n+GTGAATCCACGCCCCGTACTCGCCCGCCGGATCATTCGCCATCGTCACGAGTGCCGGCGC\n+CTCCCCGCGTCCCTCCTCGCCCTCGTGCCTGGCGGGACGGGCCGGGGCCAGGACGCGCGG\n+GGTCGCGGTGAGGTACAGCCGGTGCGCCGCCGGAAAACGGGCGTTGTCGTGGATCGCCGC\n+CCACGCCTTCTCCGCGCTGCCCGCCGTGCGGTGCGCCTCGTCCACGACCGCAAGGTCGAA\n+GCCATCCATCCGCTGCCCGTACAAGCCAGCCCCGGCGAGAGCGGCCTCCAAGGGTCCGCC\n+CTGCCCGTCCTCGCCCACGAGCGAGGAGTACGTCGCCAGCACGACCACCGGCCCCGATCC\n+GGCCCAAAGCGCGAGCCGGATCGGGTGGGTCGTCGTCCGCACCCGCAGCTCCTCCAGGAG\n+CAGATCCCTGGGCAGCGAGCACACCCCGACCATCGGCGCCGTGTGCCCCACCGCCCGCCA\n+CGACTGCGCCGTCTGCACCAGCAGATCCAGCGTCGGCACCATCACGAGAACCCGCCCCGA\n+AGGGAACAACTCCAACGCCGCAGCAGCCGCGCTGATCGTCTTTCCCGTACCCGTAGCGGA\n+CACCACCGTGGCCCGCGCCCCACGCTCCGTGCGGGCGCTTTCCCGGGCGGCTACCCGGAC\n+CCATTTCCTGAGGTCCGACATAAGCTCTACCTGATGTTTCCGCAGCGGAACCCGGGAAAC\n+AGACATTTGAATCTCCTCACGAGGCAGACGAGCCAAATCCCCAACTCAACATATGCATCA\n+ATTGGGCTGCGTTGA\n+>orf00003 gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\n+GTGCCTTCACGGCGCATTCTTCGACAGTCCGGTGAGGAATCTCCACGGCGTCCAGGTCAC\n+CAACAGGGGCTGGATGAGCATCTTCGTCAGCAGTATCTCCTACACCGCGACAGTCAAAGC\n+GTCAAGCGGTAG\n+>orf00006 gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\n+GTGGCGCCGTCAGCCTATGGCGGGCCACATGCTGCGGCGGGTGCCGAGCCCGCCCTTACC\n+GTCTCCGGGGTAGAGGTAGAGGTGGTCGACGCTGTTGAGAACAACGATGTCGGCGTTGCC\n+GTCACCGTTGAAATCGCCGCTCAGCAGGGCGTGGAAGCCGCCCCAGCTCGCGTCGTCCCA\n+CATCAGTTTGGCGTTGGCGAATGTACCGTCCGTCTTCCCCGGGTAGAGGGCCAGTTCGCC\n+CTTCTGGGAGATCGCGGCGATGTCGTTGAGGCCGTCCCCGTTGAAGTCGGCGCTGGTGAG\n+GAACTTCTTGTCCCAGGTGGCGTCGTGCCACACCTCGGTGCGACTGTCGGTGAGGATGCC\n+GTTGGCCCCGGTCGCGTACGCGTAGAGGCGGCCGGTGGGCGCGATGGCAACGAGGCCGTC\n+GCGCGTCCAGCCCTTGGCACGGTACGTCGTCGGCAGGT'..b'GACGGTACTCGGCCAGCCGTGGGTGAGCACGATCGGCAGGGCGTCAGG\n+GTGTTCGGCCTCGTAACGCAGGTAGTGCACTCGTGTGCCGGCGATGTCGGCAAAATGGGA\n+GGGCAGTGCGTTGACGGCGGCTTCGTGGGTGCGCCACGTGTAGTCGGTGGCCCAGTACAT\n+GACGAGGCGGCGGAGTTCGGCTGCGTCGGTACCCGCCTGCCAGCCGTCGACCGGCCAGGG\n+CTCGGGCCAGCGAGTGGCGCGCAGCCGGGTGCGGAGGTCTTCCAGGTCGGCGTCGGCGAC\n+CTGGATGACGGGTGTGCTGGTCGGCACGGTGTGCTCCTTCATGTGCGTGATGTGCAGGGG\n+GACGGCGGCGGTGCGGTTCGTTCTCGTGCGTGA\n+>orf00095 gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\n+GTGGTAGGTGCGCTCGGCCCAGCTCCGGGGCGGTTGGGCGAGGTCTGCGGGGAACAGGGC\n+GAGGGCGGTGGGGACGTCGACCCGCCGCACGCGCCGGGTGAGCTGGTGCGCGTACTCGTA\n+GTACGGGCGGAAGGACGTGGAGATCGTGCCGGTGAACCAGTAGAGCGATGCCTGGGTGAG\n+GAGGAAGTCGTCGCCGAAGCGGGTGGACAGGTCGCCGCCGCAGTCGGTCCACGCGCGGTA\n+CTTCTCGAGGATCCAGGAGAGCAGTCCGGCGGGCGAGTCGTTCAGTGCGGGCGCGAGGGT\n+GAGGGGACGGGTGTTCTGCTGGTGCATGTAGGCGCCCTCCTCTGCCTGCCAGGCCGCGGC\n+GGACAACAGGTGGGTCTTCTCCTCAGGGGTGAGCGAGGCCGGATCGTACTCTGCCGGGGC\n+CGCGGCAGCGAGCAGATGAATGCCGACGACGGCCTCGGGGTGGGCCTCGGCGAGCCGTGA\n+>orf00097 gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\n+TTGGCTTGTCTGCCTCGTGAGGAGTTTCAAATTTCTGTTTCTCGGGTTCCGTTGCGGAAA\n+CATCAGGTGGAGCTTATGTCGGACCTCAGGAAATGGGTTCGGGTGGCTGCCCGGGAAAGC\n+GCCCGTTCGGGGCGGGGGGCGCGGGCGACGGTGGTGTCCGCTACGGGTACGGGGAAGACG\n+ATCAGCGCGGCTGTTGCGGCGTTGGAGTTGTTCCCTTCGGGGCGGGTTCTCGTGATGGTG\n+CCGACGCTGGATCTGCTGGTGCAGACGGCGCAGTCGTGGCGGGCGGTGGGGCACACGGCG\n+CCGATGGTCGGGGTGTGCTCGCTGCCCGGGGATCTGCTCCTGGAGGAGTTGCGGGTGCGG\n+ACGACGACGCACCCGATCCGGCTCGCGCTGTGGGCCGGGCAGGGGCCTGTGGTCGTGCTG\n+GCGACGTACTCCTCGCTCGTGGGCGGGGACGGGCAGGGCGGGCCCCTGGAGGCCGCCCTG\n+GCGGGCTCGGGGTTGTACGGGCAGCGGATGGACGGCTTCGACCTCGCGGTCGTGGACGAG\n+GCGCACCGTACGGCGGGCAGCGCGGCGAAGCCCTGGGCCGCGATCCACGACAACGCCCGT\n+ATCCCGGCGGCGCACCGGCTCTACCTCACCGCCACCCCGCGCGTCCTCGCGCCCGCCCGC\n+CCCGACAGGGACGAGGACCAGGAGGAGGGCGGCGGGGAGGCGCCGGCACTCGTGACGATG\n+GCGAACGACCCGGAAGGCGAGTACGGGGCGTGGATTCACGAACTCGGGTTGTCCGAGGCG\n+ATCGAGCGGAAAATTCTTGCGCCTTTCGAGATTGATGTTTTGGAGATTACCGATCCTGAG\n+CCGGAATTGATGGAAGGAATGGACCGGGAGGCGCGGCGTGGGCGGCGGCTCGCCCTGCTC\n+CAGACTGCGTTGCTGGAGCACGCGGCCGAGCACAATCTGCGCACCGTGATGACGTTCCAT\n+CAGCGGGTGGAGGAGGCGGCGGCTTTCGCGGAGAAAATGCCGGAGACAGCGGCGGAGCTT\n+TACCGGAATGAGGTGTCGGCGGAGGATCTTGCCCTAGCCGAGGAGCTCCCGGCCTCCGAG\n+GTGGGCGGGGGCTTCTACGAGCTGGAGCCGGGGCGGCATGTGCGGCCGGAGCGGGTGTGG\n+TCGCGGTGGCTGTACGGAGAGCACCCGGTGGCCGAACGCCGTGCGGTGCTGCGGGAGTTC\n+GCGAACGGGATGGACTCGGCAGGGGTGCGGGTGCACCGCGCGTTCCTCGCCTCCGTCCGC\n+GTGCTCGGCGAGGGCGTCGACATCGTCGGGGAGCGCGGGGTCGAGGCGATCTGCTTCGCC\n+GACGCGCGCGGGTCCCAGGTCGAGATCGTGCAGAACATCGGCAGGGCGCTGCGCCCGAAC\n+CCGGACGGGCAGACGAAGACGGCGCGGATCATCGTGCCCGTCTTCTTGGAGGCCGACGAG\n+GACGGGGAGGGGATGGTCGCGAGCGAGGCGTACCGGCCGCTCGTGGCCGTGCTCCAGGGG\n+CTGCGCTCGCACTCCGAGCACCTGGTCGAGAAGCTGATGCTCCGGGCCCGGGTGCGGGCC\n+GAGAGCGCGAGCGCGCGCAGCGCGGAGGAGGCCGGTGCGGGGCCCGCGCGGGTCCTGTCC\n+GACTCCGGGACCTCTTCCCCCGCCTCCCAGGCCTCCGGGGACGTCGAAGGCGAGAACGAG\n+GACGACGTCGAGGCGGGCGCGGACGGCGCTGAGGCGGGCGCGGACGGCGCTGAGGAGTCG\n+GAGTCGGTGTTGTTGCGGTTCTCGACGCCGCGCTCGGCGTCGACCATCGCGGCCTTCCTG\n+CGGACGCGGGTGTACCAGCCGGAGTCGACGGTGTGGCTGGAGGGCTACGAGGCGCTGCGC\n+GCCTGGCGGGCCGAGCAAGGGGTGCGCGGCTTGTGCGCGGTCCCGTACGACGCCGAGGTC\n+GCCGCGGGGGCCTCGCGGCGGTACCCGGTCGGGCGGTGGACCACCGCGCAACGCCGCGCC\n+CGCCGCGAGGGCACCCTCAGCGCACACCGCATCGACCTGCTCGACGCGGAGGGCATGGTG\n+TGGGAGCCGCGCGAAGAGGAGTGGGAGCGCACGCTCGCCGGGCTTCGCTCCTACCGGGCC\n+GCGTACGGGCACCTCGCCCCCCGCCGGCGCGAAACCTGGGGCGAAGACGAGGGTGAGGAC\n+GTCGTACGCGTCGGGGACCTGATGGCGAACCTCCGCCGCAAGGACGGACTCGGGCGGGAC\n+GCGGAGCGGGCCGCCGCGCGCGCGGCCCAGCTGAGGGCCGTCGATGCGGACTGGGACTGC\n+CCCTGGCCGCTGGACTGGCAGCGCTGCTGTCGGCAGCTCGCGCTCCTGGCCGCCGACGAA\n+CCCGACGGACGCGCGCCCCGGATCGCGCGCGGGGTGCGCATCGACGGGGACGACCTCGGC\n+GCGTGGGTCGCGCGGCAGCAGGAACCGCGGGTGTGGGCGAAGCTCAGCACCGAGCAGCGG\n+GCGCGACTCGAAGCGCTCGGGCTCCGGCCTACCGAGACGGCCCCACGGCGGGGTGTGGAG\n+GGCACGGGGGCGGCGGGGAGCGGGAAGCGGACGGCGGCGGCGCGAACGGCCTTCCAGCGC\n+GGCCTCGCGGCGCTCGCGCAGTGGGTCGAGCGGGAAGGCGCGGAGAAACCCGTACCCCGC\n+AAACACACCGAGACCGTGAGCGTGGACGGTGAGGACGTCGACGTACGCCTCGGCGTGTGG\n+GTCTCGAACGTGAAGAGCCGCTTCGACGGGATGGGCGAGGACGAGCGCGGCCAGCTCACC\n+GCGCTCGGAGTGCCCTGGGCGGTGTAG\n' |
| b |
| diff -r 000000000000 -r 9c195b26a5ac test-data/glimmer_w_icm_trans-table-11_genomic.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/glimmer_w_icm_trans-table-11_genomic.out Tue Nov 28 10:08:06 2017 -0500 |
| b |
| @@ -0,0 +1,61 @@ +>gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence +orf00001 897 2918 +3 3.19 +orf00002 938 144 -3 2.86 +orf00003 7368 7237 -1 2.50 +orf00006 10347 11945 +3 2.93 +orf00007 12238 12110 -2 6.22 +orf00008 15088 13067 -2 2.95 +orf00009 15045 16529 +3 3.36 +orf00014 21385 20276 -2 2.90 +orf00016 23037 21382 -1 2.93 +orf00017 23031 24797 +3 2.92 +orf00020 27291 27115 -1 1.92 +orf00021 28556 28960 +2 2.51 +orf00022 29040 30026 +3 0.40 +orf00025 33151 32942 -2 1.06 +orf00028 38242 34754 -2 2.97 +orf00031 43300 43100 -2 6.70 +orf00032 43402 43497 +1 0.97 +orf00033 45157 44963 -2 1.68 +orf00034 47430 46852 -1 0.78 +orf00036 51314 48354 -3 2.96 +orf00037 55329 55069 -1 1.43 +orf00040 59457 56431 -1 2.96 +orf00041 59669 60169 +2 2.15 +orf00042 60516 60881 +3 0.34 +orf00043 62032 60959 -2 2.90 +orf00044 61997 62821 +2 3.73 +orf00046 66395 62922 -3 2.97 +orf00047 70996 71166 +1 0.90 +orf00049 81960 81835 -1 1.90 +orf00050 87355 89982 +1 2.96 +orf00051 90028 90390 +1 1.66 +orf00053 91917 92009 +3 0.65 +orf00054 93540 93307 -1 1.81 +orf00055 96379 94568 -2 2.94 +orf00056 96523 96383 -2 0.37 +orf00057 99628 100467 +1 3.23 +orf00058 99645 98455 -1 2.91 +orf00062 100811 102931 +2 2.95 +orf00065 103074 105521 +3 2.96 +orf00066 106200 105847 -1 0.32 +orf00067 108365 108069 -3 4.89 +orf00068 110498 109947 -3 0.90 +orf00069 110907 110791 -1 2.13 +orf00074 117071 116538 -3 0.81 +orf00075 117733 117443 -2 0.01 +orf00076 118776 118399 -1 3.59 +orf00077 119740 119582 -2 0.41 +orf00078 123152 123484 +2 2.86 +orf00079 123767 123925 +2 0.89 +orf00080 126459 124906 -1 2.93 +orf00084 128992 126704 -2 2.95 +orf00085 129178 129011 -2 1.85 +orf00086 132172 130337 -2 2.94 +orf00088 134993 136987 +2 2.94 +orf00089 137523 137245 -1 1.14 +orf00092 140512 137825 -2 2.96 +orf00093 142487 140766 -3 2.94 +orf00094 143056 142484 -2 0.89 +orf00095 143578 143099 -2 0.42 +orf00097 147016 144230 -2 2.96 |
| b |
| diff -r 000000000000 -r 9c195b26a5ac test-data/glimmer_wo_icm_trans-table-11_plasmid_genomic.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/glimmer_wo_icm_trans-table-11_plasmid_genomic.fasta Tue Nov 28 10:08:06 2017 -0500 |
| b |
| b'@@ -0,0 +1,2213 @@\n+>orf00001 gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\n+TTGGCTCGTCTGCCTCGTGAGGAGATTCAAATGTCTGTTTCCCGGGTTCCGCTGCGGAAA\n+CATCAGGTAGAGCTTATGTCGGACCTCAGGAAATGGGTCCGGGTAGCCGCCCGGGAAAGC\n+GCCCGCACGGAGCGTGGGGCGCGGGCCACGGTGGTGTCCGCTACGGGTACGGGAAAGACG\n+ATCAGCGCGGCTGCTGCGGCGTTGGAGTTGTTCCCTTCGGGGCGGGTTCTCGTGATGGTG\n+CCGACGCTGGATCTGCTGGTGCAGACGGCGCAGTCGTGGCGGGCGGTGGGGCACACGGCG\n+CCGATGGTCGGGGTGTGCTCGCTGCCCAGGGATCTGCTCCTGGAGGAGCTGCGGGTGCGG\n+ACGACGACCCACCCGATCCGGCTCGCGCTTTGGGCCGGATCGGGGCCGGTGGTCGTGCTG\n+GCGACGTACTCCTCGCTCGTGGGCGAGGACGGGCAGGGCGGACCCTTGGAGGCCGCTCTC\n+GCCGGGGCTGGCTTGTACGGGCAGCGGATGGATGGCTTCGACCTTGCGGTCGTGGACGAG\n+GCGCACCGCACGGCGGGCAGCGCGGAGAAGGCGTGGGCGGCGATCCACGACAACGCCCGT\n+TTTCCGGCGGCGCACCGGCTGTACCTCACCGCGACCCCGCGCGTCCTGGCCCCGGCCCGT\n+CCCGCCAGGCACGAGGGCGAGGAGGGACGCGGGGAGGCGCCGGCACTCGTGACGATGGCG\n+AATGATCCGGCGGGCGAGTACGGGGCGTGGATTCACGAACTCGGTTTGTCCGAGGCAATC\n+GCGCGAAAAATCGTCGCGCCTTTTGAGATTGACGTTTTGGAGATTACTGATCCTGAGCCG\n+GAATTGATGGAGGGATTGGATCGGGAGGCGCGGCGTGGGCGGCGGCTTGCGTTGCTTCAG\n+ACCGGGCTTTTGGAGCACGCGGCCGAGCATAATATTTGCACCATGATGACGCTTCATCAG\n+CAGGTTGAGGAGGCGGCGGCTTTCGCGGAGAAAATGCCGGAGACGGCGGCGGAGCTTTAC\n+CGGAATGAGGTGTCGGCGGAGGATTTTGCCCTGGCCGAGGAGCTCCCGGCCTCCGAGGTG\n+GGTGGGGGGTTCTACGAGCTGGAGCCGGGGCGTCATGTGCCGCCGTCGCGGGTGTGGTCG\n+CGGTGGCTGTATGGGGAGCATCCTGTGGCCGAACGGCGTTCTGTGCTGCGGGAGTTCGCG\n+AACGGGATGGACGCGGAGGGGCGGCGGGTGCACCGGGCGTTCCTCGCTTCCGTACGGGTC\n+CTGGGTGAGGGCGTCGACATCGTCGGGGAGCGCGGGGTCGAGGCGATCTGCTTTGCCGAC\n+GCACGCGGGTCTCAGGTGGAGATCGTGCAGAACATCGGGCGCGCGTTGCGCCAGAACCCG\n+GATGGGCGGGCGAAGACGGCGCGGATCATCGTGCCGGTCTTCCTGCGGCCGGACGAGGAC\n+GGGGAGGGCATGGTGGCGTCGGAGGCGTACCGGCCGCTCGTCGCCGTACTCCAGGGCCTG\n+CGCTCGCACGACGAGCACCTGGTCGAGAAACTCATGCTGCGGGCGCGCGTACGGGCCGAG\n+AGCGCGAGCGCGCGCAGCGCGGAGGAGGGCGGTGCGGGGCCCTCGCGGCTCCTGTCGGAC\n+TCCGGGACGGCGGCTGCGGCCTCCGAGGGCGTCGAGGGCCAGGAGCAGGGCGAGGACGGC\n+GCCGAGGCGGAGTCGGTGCTGCTGCGGTTCTCCTCGCCGCGCGCGGCGTCGACGGTCGCG\n+GCGTTCCTGCGGACGCGGGTGTACCAGCCCGAGTCGCTGGTGTGGCTGGAGGGGTACGAG\n+GCCCTGCGCGCCTGGCGGGCCGAGCAAGGGGTGAGCGGGGTGTGCGCGGTCCCGTACGAC\n+GCCGAGGTCGCCGCGGGGGCCTCGCGGCGGTACCCGGTCGGGCGGTGGACCGCCGCGCAA\n+CGCCGCGCCCGCCGCGAGGGCACCCTCAGCGCACACCGCGTCGAGCTCCTCGACGCGGAG\n+GGCATGGTGTGGGAGCCGCGCGAGGAGGAATGGGAGCGCACGCTCGCGGGGCTTCGCTCC\n+TACCGGACGGCGTACGGGCACCTCGCCCCCCACAGGCGCGAAACCTGGGGCGAAGACGAG\n+GGTGAGGACGTCGTACGCGTCGGGGACCTGATGGCGAACCTCCGCCGCAAGGACGGACTC\n+GGGAAGGACGCGAAGCGGGCCGCCGCGCGCGCCGCGCAGCTGAGGGCCGTCGATGCGGAC\n+TGGGACTGCCCGTGGCCGCTGGACTGGCAGCGCTGCTGCCGGAAACTCGTGCTCCTGGCC\n+GCGGACGAGCCCGGCGGGCGCCTGCCGGAGATCGCGCCCGGGGTCTGCCTGGACGGGGAT\n+GACCTCGGGGTGTGGGTCGCGCGGCAGCAGGAGCCGCGGGTGTGGGCGCGGCTCAGCACC\n+GAGCAGCGGGCGCGGCTCGAAGCGCTCGGGCTGCGGCCCACCGAAGCGGCCCCGGGGCGG\n+GGTGTGGAGGGCACGGGGGCGGCGGGGAGCATGAAGCGGACGGCGACGGCGCGAACGGCT\n+TTTCAGCGGGGTGTGGCGGCGCTCGCGCAGTGGGTCGAGCGGGAAGGCGCGGGGAAACCC\n+GTACCCCGCAAACACGTCGAGACCGTCAGCGTCGACGGCGAGGACGTCGACGTACGCCTC\n+GGCGTATGGATCTCGAACACCAAGAGCCGGTACGACGGGCTGAGCGAGGACGAACGCGCG\n+CAGCTCACCGCACTCGGAATGCCCTGGGCAGGATGA\n+>orf00005 gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\n+GTGCTCGCCGCCGTACGGGACACGATCGCCGAGACCGGCCAGGGACCGTCCGTACGGCAG\n+ATCCAGCGCGTCACCGGGCTCGCGCTCGGCACCATCGCCCACCACCTGAAGGCGCTGGAG\n+GAGAGCGGCCCCCTCGTCCGTACGGGCCTGCACTGGCGCACCTGCCGCCTGGGCTGA\n+>orf00006 gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\n+GTGACCGATGAACTGCTCCGCCTCGCCCAGGAGAGGCGTGCGACCTACCGCGACCTCACC\n+CTCGGCGGCCCCGCCCGCCCCCCGACACCTCTGCGCCGGGCACTGATCCGGCAGTCCGCC\n+CGCCTGCTCGACGGCCCGCCCACCACGGCCCGCCGGGCTCTGCTGTGCCGCCCGCCCACG\n+CCCGCGTCCCCGCCCTCGCGGGGGACCAGGTGA\n+>orf00007 gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\n+GTGACCGATTTCCCCGACGATCTCCTCGCGGCTCAGCGCGACCTCACCGCCGTACGCGCC\n+ACCCTTTCCGCCCGCCTCGCGGCGCTGCCGCCCTCGGCCGAGCCGATGCCCGCGTGGGAG\n+CGGCCCGACGGCTACTGGGCGGGCGCCCGTACGCACCCGGCCTCCCCGGGGTGGAGCGAG\n+GAGGAGCGCGAGGAGGTCGCCGCGCTCCGCGAGCGGGAGCGGGATCTGGCCGGGGTGATC\n+GTGACGCACGAGCTGTGGGCGAGCGTGCCGGCCGGGGAGCGGA'..b'CCTGGCAGGCAGAGGAGGGCGCCTACATG\n+CACCAGCAGAACACCCGTCCCCTCACCCTCGCGCCCGCACTGAACGACTCGCCCGCCGGA\n+CTGCTCTCCTGGATCCTCGAGAAGTACCGCGCGTGGACCGACTGCGGCGGCGACCTGTCC\n+ACCCGCTTCGGCGACGACTTCCTCCTCACCCAGGCATCGCTCTACTGGTTCACCGGCACG\n+ATCTCCACGTCCTTCCGCCCGTACTACGAGTACGCGCACCAGCTCACCCGGCGCGTGCGG\n+CGGGTCGACGTCCCCACCGCCCTCGCCCTGTTCCCCGCAGACCTCGCCCAACCGCCCCGG\n+AGCTGGGCCGAGCGCACCTACCACCTCACGCGTTACACCCGTATGCCTCGCGGCGGCCAC\n+TTCGCCGCGCACGAGGAACCGGCCTTGCTTGCCGACGACATCACCGCGTTCTTCGGCGAC\n+CTCCGTTAG\n+>orf00336 gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\n+GTGGATGGACTGCATGGGAGCCCACTTCATAAGAGGCTCGACGAACACTGCGCTGGCCGA\n+TTCGGGATCGCACCACCGCTAACCGGGGAAATCACCACGAAGATCAACCACTGA\n+>orf00337 gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\n+ATGCCCACCGAGACCCTGCCGCCCGAGGTGCGGAATTTCATCGACGATGCGCGGCGTCAC\n+CTGGCTTTCTGCGCCGGGCTGCGCGCGGGCGAGGACCCGGCGTACGCGACCGTGCTCCTG\n+GCCGCCGCCGAGCAGGGAGAAGAAGTCCTCGCCCGGTACGAAGGCCGCGTAGCTTAG\n+>orf00339 gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\n+TTGGCTTGTCTGCCTCGTGAGGAGTTTCAAATTTCTGTTTCTCGGGTTCCGTTGCGGAAA\n+CATCAGGTGGAGCTTATGTCGGACCTCAGGAAATGGGTTCGGGTGGCTGCCCGGGAAAGC\n+GCCCGTTCGGGGCGGGGGGCGCGGGCGACGGTGGTGTCCGCTACGGGTACGGGGAAGACG\n+ATCAGCGCGGCTGTTGCGGCGTTGGAGTTGTTCCCTTCGGGGCGGGTTCTCGTGATGGTG\n+CCGACGCTGGATCTGCTGGTGCAGACGGCGCAGTCGTGGCGGGCGGTGGGGCACACGGCG\n+CCGATGGTCGGGGTGTGCTCGCTGCCCGGGGATCTGCTCCTGGAGGAGTTGCGGGTGCGG\n+ACGACGACGCACCCGATCCGGCTCGCGCTGTGGGCCGGGCAGGGGCCTGTGGTCGTGCTG\n+GCGACGTACTCCTCGCTCGTGGGCGGGGACGGGCAGGGCGGGCCCCTGGAGGCCGCCCTG\n+GCGGGCTCGGGGTTGTACGGGCAGCGGATGGACGGCTTCGACCTCGCGGTCGTGGACGAG\n+GCGCACCGTACGGCGGGCAGCGCGGCGAAGCCCTGGGCCGCGATCCACGACAACGCCCGT\n+ATCCCGGCGGCGCACCGGCTCTACCTCACCGCCACCCCGCGCGTCCTCGCGCCCGCCCGC\n+CCCGACAGGGACGAGGACCAGGAGGAGGGCGGCGGGGAGGCGCCGGCACTCGTGACGATG\n+GCGAACGACCCGGAAGGCGAGTACGGGGCGTGGATTCACGAACTCGGGTTGTCCGAGGCG\n+ATCGAGCGGAAAATTCTTGCGCCTTTCGAGATTGATGTTTTGGAGATTACCGATCCTGAG\n+CCGGAATTGATGGAAGGAATGGACCGGGAGGCGCGGCGTGGGCGGCGGCTCGCCCTGCTC\n+CAGACTGCGTTGCTGGAGCACGCGGCCGAGCACAATCTGCGCACCGTGATGACGTTCCAT\n+CAGCGGGTGGAGGAGGCGGCGGCTTTCGCGGAGAAAATGCCGGAGACAGCGGCGGAGCTT\n+TACCGGAATGAGGTGTCGGCGGAGGATCTTGCCCTAGCCGAGGAGCTCCCGGCCTCCGAG\n+GTGGGCGGGGGCTTCTACGAGCTGGAGCCGGGGCGGCATGTGCGGCCGGAGCGGGTGTGG\n+TCGCGGTGGCTGTACGGAGAGCACCCGGTGGCCGAACGCCGTGCGGTGCTGCGGGAGTTC\n+GCGAACGGGATGGACTCGGCAGGGGTGCGGGTGCACCGCGCGTTCCTCGCCTCCGTCCGC\n+GTGCTCGGCGAGGGCGTCGACATCGTCGGGGAGCGCGGGGTCGAGGCGATCTGCTTCGCC\n+GACGCGCGCGGGTCCCAGGTCGAGATCGTGCAGAACATCGGCAGGGCGCTGCGCCCGAAC\n+CCGGACGGGCAGACGAAGACGGCGCGGATCATCGTGCCCGTCTTCTTGGAGGCCGACGAG\n+GACGGGGAGGGGATGGTCGCGAGCGAGGCGTACCGGCCGCTCGTGGCCGTGCTCCAGGGG\n+CTGCGCTCGCACTCCGAGCACCTGGTCGAGAAGCTGATGCTCCGGGCCCGGGTGCGGGCC\n+GAGAGCGCGAGCGCGCGCAGCGCGGAGGAGGCCGGTGCGGGGCCCGCGCGGGTCCTGTCC\n+GACTCCGGGACCTCTTCCCCCGCCTCCCAGGCCTCCGGGGACGTCGAAGGCGAGAACGAG\n+GACGACGTCGAGGCGGGCGCGGACGGCGCTGAGGCGGGCGCGGACGGCGCTGAGGAGTCG\n+GAGTCGGTGTTGTTGCGGTTCTCGACGCCGCGCTCGGCGTCGACCATCGCGGCCTTCCTG\n+CGGACGCGGGTGTACCAGCCGGAGTCGACGGTGTGGCTGGAGGGCTACGAGGCGCTGCGC\n+GCCTGGCGGGCCGAGCAAGGGGTGCGCGGCTTGTGCGCGGTCCCGTACGACGCCGAGGTC\n+GCCGCGGGGGCCTCGCGGCGGTACCCGGTCGGGCGGTGGACCACCGCGCAACGCCGCGCC\n+CGCCGCGAGGGCACCCTCAGCGCACACCGCATCGACCTGCTCGACGCGGAGGGCATGGTG\n+TGGGAGCCGCGCGAAGAGGAGTGGGAGCGCACGCTCGCCGGGCTTCGCTCCTACCGGGCC\n+GCGTACGGGCACCTCGCCCCCCGCCGGCGCGAAACCTGGGGCGAAGACGAGGGTGAGGAC\n+GTCGTACGCGTCGGGGACCTGATGGCGAACCTCCGCCGCAAGGACGGACTCGGGCGGGAC\n+GCGGAGCGGGCCGCCGCGCGCGCGGCCCAGCTGAGGGCCGTCGATGCGGACTGGGACTGC\n+CCCTGGCCGCTGGACTGGCAGCGCTGCTGTCGGCAGCTCGCGCTCCTGGCCGCCGACGAA\n+CCCGACGGACGCGCGCCCCGGATCGCGCGCGGGGTGCGCATCGACGGGGACGACCTCGGC\n+GCGTGGGTCGCGCGGCAGCAGGAACCGCGGGTGTGGGCGAAGCTCAGCACCGAGCAGCGG\n+GCGCGACTCGAAGCGCTCGGGCTCCGGCCTACCGAGACGGCCCCACGGCGGGGTGTGGAG\n+GGCACGGGGGCGGCGGGGAGCGGGAAGCGGACGGCGGCGGCGCGAACGGCCTTCCAGCGC\n+GGCCTCGCGGCGCTCGCGCAGTGGGTCGAGCGGGAAGGCGCGGAGAAACCCGTACCCCGC\n+AAACACACCGAGACCGTGAGCGTGGACGGTGAGGACGTCGACGTACGCCTCGGCGTGTGG\n+GTCTCGAACGTGAAGAGCCGCTTCGACGGGATGGGCGAGGACGAGCGCGGCCAGCTCACC\n+GCGCTCGGAGTGCCCTGGGCGGTGTAG\n' |
| b |
| diff -r 000000000000 -r 9c195b26a5ac test-data/longORFSTestOutput.dat --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/longORFSTestOutput.dat Tue Nov 28 10:08:06 2017 -0500 |
| b |
| @@ -0,0 +1,1 @@ +00001 173 182 -2 1.026 |
| b |
| diff -r 000000000000 -r 9c195b26a5ac test-data/orf_aa.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/orf_aa.fa Tue Nov 28 10:08:06 2017 -0500 |
| b |
| @@ -0,0 +1,20 @@ +>PROKKA_00001 <unknown description> +MSQVTEQSVRFQTALASIKLIQASAVLDLTEDDFDFLTSNKVWIATDRSRARRCVEACVY +GTLDFVGYPRFPAPVEFIAAVIAYYVHPVNIQTACLIMEGAEFTENIINGVERPVKAAEL +FAFTLRVRAGNTDVLTDAEENVRQKLRAEGVM +>PROKKA_00002 <unknown description> +MSKGKKRSGARPGRPQPLRGTKGKRKGARLWYVGGQQF +>PROKKA_00003 <unknown description> +MPDRTEANPNELNQDDARYGFRCCHLKNIWTAPLPPETELSRQMTTSTTSIDIMGLQAAY +ANLHTDQERDYFMQRYHDVISSFGGKTSYDADNRPLLVMRSNLWASGYDVDGTDQTSLGQ +FSGRVQQTYKHSVPRFFVPEHGTMFTLALVRFPPTATKEIQYLNAKGALTYTDIAGDPVL +YGNLPPREISMKDVFRSGDSSKKFKIAEGQWYRYAPSYVSPAYHLLEGFPFIQEPPSGDL +QERVLIRHHDYDQCFQSVQLLQWNSQVKFNVTVYRNLPTTRDSIMTS +>PROKKA_00004 <unknown description> +LVLLLAVLLLLLLVAPCLNCLEAVKKPPPVAFKVMCLLPITIL +>PROKKA_00005 <unknown description> +MAKAGKGLLEGTLQAGTSAVSDKLLDLVGLGGKSAADKGKDTRDYLAAAFPELNAWERAG +ADASSAGMVDAGFENQKELTKMQLDNQKEIAEMQNETQKEIAGIQSATSRQNTKDQVYAQ +NEMLAYQQKESTARVASIMENTNLSKQQQVSEIMRQMLTQAQTAGQYFTNDQIKEMTRKV +SAEVDLVHQQTQNQRYGSSHIGATAKDISNVVTDAASGVVDIFHGIDKAVADTWNNFWKD +GKADGIGSNLSRK |
| b |
| diff -r 000000000000 -r 9c195b26a5ac test-data/orf_nc.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/orf_nc.fa Tue Nov 28 10:08:06 2017 -0500 |
| b |
| @@ -0,0 +1,46 @@ +>PROKKA_00001 <unknown description> +ATGAGTCAAGTTACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTC +ATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTGACGAGTAAC +AAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTAT +GGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCC +GTCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGC +GCTGAATTTACGGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTG +TTCGCGTTTACCTTGCGTGTACGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAA +AACGTGCGTCAAAAATTACGTGCGGAAGGAGTGATGTAA +>PROKKA_00002 <unknown description> +ATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGT +ACTAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAA +>PROKKA_00003 <unknown description> +ATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGCTCGTTATGGT +TTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTT +TCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTAT +GCTAATTTGCATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCATGATGTTATT +TCTTCATTTGGAGGTAAAACCTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGC +TCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAACGTCGTTAGGCCAG +TTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCCGCGTTTCTTTGTTCCTGAG +CATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATT +CAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTG +TATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCG +TCTAAGAAGTTTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCT +CCTGCTTATCACCTTCTTGAAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTG +CAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGTGTTTCCAGTCCGTTCAGTTG +TTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCTGCCGACCACT +CGCGATTCAATCATGACTTCGTGA +>PROKKA_00004 <unknown description> +TTGGTGCTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGT +TTGGAGGCGGTCAAAAAGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATA +ACAATACTGTAG +>PROKKA_00005 <unknown description> +ATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTT +TCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAG +GATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGT +GCTGATGCTTCCTCTGCTGGTATGGTTGACGCCGGATTTGAGAATCAAAAAGAGCTTACT +AAAATGCAACTGGACAATCAGAAAGAGATTGCCGAGATGCAAAATGAGACTCAAAAAGAG +ATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGACCAGGTATATGCACAA +AATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTATGGAA +AACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAA +GCTCAAACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTT +AGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCAT +ATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTT +GATATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCTGGAAAGAC +GGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAA |
| b |
| diff -r 000000000000 -r 9c195b26a5ac test-data/streptomyces_Tu6071_genomic.acgt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/streptomyces_Tu6071_genomic.acgt Tue Nov 28 10:08:06 2017 -0500 |
| b |
| @@ -0,0 +1,123 @@ +>gi|333022496:2500-3701 Streptomyces sp. Tu6071 chromosome, whole genome shotgun sequence +Position Length As Cs Gs Ts Other %GC + 1 10 20.0 30.0 50.0 0.0 0.0 80.0 + 11 10 30.0 30.0 40.0 0.0 0.0 70.0 + 21 10 0.0 50.0 50.0 0.0 0.0 100.0 + 31 10 10.0 30.0 40.0 20.0 0.0 70.0 + 41 10 20.0 30.0 30.0 20.0 0.0 60.0 + 51 10 10.0 50.0 30.0 10.0 0.0 80.0 + 61 10 30.0 30.0 40.0 0.0 0.0 70.0 + 71 10 10.0 50.0 20.0 20.0 0.0 70.0 + 81 10 0.0 50.0 30.0 20.0 0.0 80.0 + 91 10 20.0 20.0 60.0 0.0 0.0 80.0 + 101 10 10.0 60.0 20.0 10.0 0.0 80.0 + 111 10 0.0 30.0 60.0 10.0 0.0 90.0 + 121 10 20.0 10.0 50.0 20.0 0.0 60.0 + 131 10 10.0 40.0 20.0 30.0 0.0 60.0 + 141 10 10.0 40.0 40.0 10.0 0.0 80.0 + 151 10 10.0 30.0 40.0 20.0 0.0 70.0 + 161 10 0.0 30.0 60.0 10.0 0.0 90.0 + 171 10 10.0 30.0 30.0 30.0 0.0 60.0 + 181 10 10.0 10.0 30.0 50.0 0.0 40.0 + 191 10 10.0 30.0 40.0 20.0 0.0 70.0 + 201 10 0.0 10.0 60.0 30.0 0.0 70.0 + 211 10 10.0 40.0 30.0 20.0 0.0 70.0 + 221 10 20.0 30.0 50.0 0.0 0.0 80.0 + 231 10 0.0 50.0 30.0 20.0 0.0 80.0 + 241 10 10.0 30.0 30.0 30.0 0.0 60.0 + 251 10 0.0 30.0 60.0 10.0 0.0 90.0 + 261 10 20.0 20.0 50.0 10.0 0.0 70.0 + 271 10 30.0 30.0 40.0 0.0 0.0 70.0 + 281 10 0.0 10.0 60.0 30.0 0.0 70.0 + 291 10 0.0 20.0 60.0 20.0 0.0 80.0 + 301 10 0.0 30.0 70.0 0.0 0.0 100.0 + 311 10 10.0 20.0 50.0 20.0 0.0 70.0 + 321 10 20.0 20.0 40.0 20.0 0.0 60.0 + 331 10 0.0 40.0 40.0 20.0 0.0 80.0 + 341 10 20.0 20.0 40.0 20.0 0.0 60.0 + 351 10 10.0 30.0 30.0 30.0 0.0 60.0 + 361 10 30.0 20.0 40.0 10.0 0.0 60.0 + 371 10 20.0 20.0 60.0 0.0 0.0 80.0 + 381 10 20.0 40.0 40.0 0.0 0.0 80.0 + 391 10 20.0 0.0 60.0 20.0 0.0 60.0 + 401 10 0.0 30.0 40.0 30.0 0.0 70.0 + 411 10 10.0 30.0 30.0 30.0 0.0 60.0 + 421 10 20.0 40.0 40.0 0.0 0.0 80.0 + 431 10 0.0 20.0 40.0 40.0 0.0 60.0 + 441 10 20.0 40.0 40.0 0.0 0.0 80.0 + 451 10 20.0 30.0 30.0 20.0 0.0 60.0 + 461 10 10.0 30.0 40.0 20.0 0.0 70.0 + 471 10 20.0 20.0 40.0 20.0 0.0 60.0 + 481 10 20.0 50.0 20.0 10.0 0.0 70.0 + 491 10 10.0 40.0 30.0 20.0 0.0 70.0 + 501 10 10.0 30.0 30.0 30.0 0.0 60.0 + 511 10 0.0 30.0 60.0 10.0 0.0 90.0 + 521 10 0.0 40.0 30.0 30.0 0.0 70.0 + 531 10 30.0 20.0 40.0 10.0 0.0 60.0 + 541 10 20.0 10.0 60.0 10.0 0.0 70.0 + 551 10 10.0 20.0 40.0 30.0 0.0 60.0 + 561 10 0.0 60.0 10.0 30.0 0.0 70.0 + 571 10 30.0 0.0 60.0 10.0 0.0 60.0 + 581 10 20.0 20.0 40.0 20.0 0.0 60.0 + 591 10 0.0 20.0 50.0 30.0 0.0 70.0 + 601 10 30.0 20.0 40.0 10.0 0.0 60.0 + 611 10 20.0 30.0 50.0 0.0 0.0 80.0 + 621 10 20.0 20.0 30.0 30.0 0.0 50.0 + 631 10 0.0 30.0 40.0 30.0 0.0 70.0 + 641 10 0.0 30.0 60.0 10.0 0.0 90.0 + 651 10 20.0 20.0 50.0 10.0 0.0 70.0 + 661 10 20.0 20.0 40.0 20.0 0.0 60.0 + 671 10 10.0 40.0 50.0 0.0 0.0 90.0 + 681 10 0.0 0.0 70.0 30.0 0.0 70.0 + 691 10 20.0 40.0 30.0 10.0 0.0 70.0 + 701 10 20.0 30.0 50.0 0.0 0.0 80.0 + 711 10 20.0 10.0 30.0 40.0 0.0 40.0 + 721 10 20.0 30.0 50.0 0.0 0.0 80.0 + 731 10 10.0 40.0 20.0 30.0 0.0 60.0 + 741 10 30.0 20.0 50.0 0.0 0.0 70.0 + 751 10 20.0 50.0 30.0 0.0 0.0 80.0 + 761 10 0.0 30.0 50.0 20.0 0.0 80.0 + 771 10 10.0 30.0 60.0 0.0 0.0 90.0 + 781 10 0.0 30.0 50.0 20.0 0.0 80.0 + 791 10 10.0 20.0 60.0 10.0 0.0 80.0 + 801 10 0.0 30.0 60.0 10.0 0.0 90.0 + 811 10 0.0 30.0 70.0 0.0 0.0 100.0 + 821 10 10.0 30.0 60.0 0.0 0.0 90.0 + 831 10 20.0 20.0 30.0 30.0 0.0 50.0 + 841 10 10.0 30.0 40.0 20.0 0.0 70.0 + 851 10 0.0 30.0 50.0 20.0 0.0 80.0 + 861 10 30.0 10.0 50.0 10.0 0.0 60.0 + 871 10 10.0 30.0 40.0 20.0 0.0 70.0 + 881 10 20.0 30.0 40.0 10.0 0.0 70.0 + 891 10 10.0 30.0 20.0 40.0 0.0 50.0 + 901 10 10.0 40.0 40.0 10.0 0.0 80.0 + 911 10 10.0 20.0 60.0 10.0 0.0 80.0 + 921 10 10.0 50.0 30.0 10.0 0.0 80.0 + 931 10 30.0 10.0 40.0 20.0 0.0 50.0 + 941 10 10.0 20.0 40.0 30.0 0.0 60.0 + 951 10 20.0 40.0 40.0 0.0 0.0 80.0 + 961 10 20.0 30.0 50.0 0.0 0.0 80.0 + 971 10 0.0 40.0 30.0 30.0 0.0 70.0 + 981 10 10.0 40.0 50.0 0.0 0.0 90.0 + 991 10 10.0 50.0 40.0 0.0 0.0 90.0 + 1001 10 0.0 40.0 40.0 20.0 0.0 80.0 + 1011 10 20.0 20.0 50.0 10.0 0.0 70.0 + 1021 10 0.0 50.0 40.0 10.0 0.0 90.0 + 1031 10 0.0 20.0 60.0 20.0 0.0 80.0 + 1041 10 10.0 40.0 30.0 20.0 0.0 70.0 + 1051 10 10.0 30.0 60.0 0.0 0.0 90.0 + 1061 10 40.0 10.0 30.0 20.0 0.0 40.0 + 1071 10 10.0 30.0 40.0 20.0 0.0 70.0 + 1081 10 10.0 30.0 30.0 30.0 0.0 60.0 + 1091 10 10.0 50.0 10.0 30.0 0.0 60.0 + 1101 10 30.0 40.0 20.0 10.0 0.0 60.0 + 1111 10 20.0 30.0 50.0 0.0 0.0 80.0 + 1121 10 10.0 10.0 70.0 10.0 0.0 80.0 + 1131 10 10.0 30.0 40.0 20.0 0.0 70.0 + 1141 10 30.0 30.0 10.0 30.0 0.0 40.0 + 1151 10 30.0 40.0 20.0 10.0 0.0 60.0 + 1161 10 0.0 50.0 0.0 50.0 0.0 50.0 + 1171 10 10.0 30.0 30.0 30.0 0.0 60.0 + 1181 10 0.0 30.0 20.0 50.0 0.0 50.0 + 1191 10 30.0 20.0 40.0 10.0 0.0 60.0 + 1201 2 0.0 100.0 0.0 0.0 0.0 100.0 |
| b |
| diff -r 000000000000 -r 9c195b26a5ac test-data/streptomyces_Tu6071_genomic.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/streptomyces_Tu6071_genomic.fasta Tue Nov 28 10:08:06 2017 -0500 |
| b |
| @@ -0,0 +1,20 @@ +>gi|333022496:2500-3701 Streptomyces sp. Tu6071 chromosome, whole genome shotgun sequence +CCGAGGAGGCGAAGACCGGCGCGCGCGCCGTGGCACCGTGATCCGCATGGGCGGCACCTCGACCAGAGCG +CCCGCATCGTGGTCCTCGCCAGGCGGCAGGCGCCTGACCCGGGCGGTCGCACGTGGAGGTCGCTCAGCTT +CCCGAGTGCGCGCGGATGCTTGGCGGCGGCCATCGGCGTTTTTAGTGGCTGCCCGATGTGGTGTCGGTGG +ACGGCTTGCCAGGGAGCCCGTCTGCGCCCGTAGCGTGCTCGGTGGCGGCCCAGGTGGCGAGAAGCCGCAG +GGTGTCGTGGTCGGGGGTGCCGGGGGCGGCGCTGTAGGCGGTCAGGGTCAGTCCCGGCTGAGCCGGTAGT +TCCATGGCGTCGAAGTCGAGGGCGAGGACGCCGACAGCGGGGTGGTGGAACGCTTTGCGGCCCGTGTGAT +GCAGGCGCACGTTGTGCCTGGCCCAAGCGGTGCGGAACTCATCGCTGCGGGTGACGAGCTCCCCGATCAG +TCCGGTCAGCCCGGTGTCATGCGGGGCTCGTCCGGCTTCGGTACGCAGGAGGGAGACGGTGGTGTTCACG +GCTTCCTCCCAGTGGGGGAAGAATTCGCGGCCTGTGGGGTCGAGGAACTGGAAGCGCGCGATGTTGACCG +GTTCGCGTGCGCCGGTGGCGTAGAGCGGGCTGTACAGGGCGCGGCCCAGGGGGTTGGTGGCCAGGACGTC +AAGGCGGCCGTTTCGGATGAAGGCCGGGCATTCGCCCATGGAGCGCAGGACGCGCAGCACGCTGTCGGGC +AGGGGGCCGCGGGCGCGCTTGGTGCGACGGGCGGGCCGGTGGGCGGCGGCGCGGGCCAGGTCGTACAGGT +GAGCGCGTTCGGCGTCGTCGAGCTGGAGAGCGTTCGCGAGCGCGTCAAGGACTTCTTCGGAGGCTCCGGC +GAGGTGGCCGCGCTCCAGGCGGACGTAGTAGTCGATGCTGACGCCGGCGAGCAGGGCGACTTCCTCGCGG +CGCAGGCCGGGCACGCGCCGGTTGCCGCCGTAGGCGGGCAGCCCGGCCTGCTGCGGGGTGATCCTGGCGC +GGCGGGAGCCAAGGAATTCGCGGATGTCGCTCGCGGTACTCATGCCTTCCACGCTAAGCCGGACGGCGCA +GACGTGGGGGGGCCTGTCAGTACCTGTAACAGCAAGCCCTTCTTCCCCTTCTTGACCTGGTGTTTCCTCG +AAGTCGCAGGCC + |
| b |
| diff -r 000000000000 -r 9c195b26a5ac test-data/streptomyces_Tu6071_plasmid_genes.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/streptomyces_Tu6071_plasmid_genes.fasta Tue Nov 28 10:08:06 2017 -0500 |
| [ |
| b'@@ -0,0 +1,1937 @@\n+>lcl|NZ_CM001166.1_gene_1 [locus_tag=STTU_p0001] [location=183..2918]\n+TTGGCTCGTCTGCCTCGTGAGGAGATTCAAATGTCTGTTTCCCGGGTTCCGCTGCGGAAACATCAGGTAG\n+AGCTTATGTCGGACCTCAGGAAATGGGTCCGGGTAGCCGCCCGGGAAAGCGCCCGCACGGAGCGTGGGGC\n+GCGGGCCACGGTGGTGTCCGCTACGGGTACGGGAAAGACGATCAGCGCGGCTGCTGCGGCGTTGGAGTTG\n+TTCCCTTCGGGGCGGGTTCTCGTGATGGTGCCGACGCTGGATCTGCTGGTGCAGACGGCGCAGTCGTGGC\n+GGGCGGTGGGGCACACGGCGCCGATGGTCGGGGTGTGCTCGCTGCCCAGGGATCTGCTCCTGGAGGAGCT\n+GCGGGTGCGGACGACGACCCACCCGATCCGGCTCGCGCTTTGGGCCGGATCGGGGCCGGTGGTCGTGCTG\n+GCGACGTACTCCTCGCTCGTGGGCGAGGACGGGCAGGGCGGACCCTTGGAGGCCGCTCTCGCCGGGGCTG\n+GCTTGTACGGGCAGCGGATGGATGGCTTCGACCTTGCGGTCGTGGACGAGGCGCACCGCACGGCGGGCAG\n+CGCGGAGAAGGCGTGGGCGGCGATCCACGACAACGCCCGTTTTCCGGCGGCGCACCGGCTGTACCTCACC\n+GCGACCCCGCGCGTCCTGGCCCCGGCCCGTCCCGCCAGGCACGAGGGCGAGGAGGGACGCGGGGAGGCGC\n+CGGCACTCGTGACGATGGCGAATGATCCGGCGGGCGAGTACGGGGCGTGGATTCACGAACTCGGTTTGTC\n+CGAGGCAATCGCGCGAAAAATCGTCGCGCCTTTTGAGATTGACGTTTTGGAGATTACTGATCCTGAGCCG\n+GAATTGATGGAGGGATTGGATCGGGAGGCGCGGCGTGGGCGGCGGCTTGCGTTGCTTCAGACCGGGCTTT\n+TGGAGCACGCGGCCGAGCATAATATTTGCACCATGATGACGCTTCATCAGCAGGTTGAGGAGGCGGCGGC\n+TTTCGCGGAGAAAATGCCGGAGACGGCGGCGGAGCTTTACCGGAATGAGGTGTCGGCGGAGGATTTTGCC\n+CTGGCCGAGGAGCTCCCGGCCTCCGAGGTGGGTGGGGGGTTCTACGAGCTGGAGCCGGGGCGTCATGTGC\n+CGCCGTCGCGGGTGTGGTCGCGGTGGCTGTATGGGGAGCATCCTGTGGCCGAACGGCGTTCTGTGCTGCG\n+GGAGTTCGCGAACGGGATGGACGCGGAGGGGCGGCGGGTGCACCGGGCGTTCCTCGCTTCCGTACGGGTC\n+CTGGGTGAGGGCGTCGACATCGTCGGGGAGCGCGGGGTCGAGGCGATCTGCTTTGCCGACGCACGCGGGT\n+CTCAGGTGGAGATCGTGCAGAACATCGGGCGCGCGTTGCGCCAGAACCCGGATGGGCGGGCGAAGACGGC\n+GCGGATCATCGTGCCGGTCTTCCTGCGGCCGGACGAGGACGGGGAGGGCATGGTGGCGTCGGAGGCGTAC\n+CGGCCGCTCGTCGCCGTACTCCAGGGCCTGCGCTCGCACGACGAGCACCTGGTCGAGAAACTCATGCTGC\n+GGGCGCGCGTACGGGCCGAGAGCGCGAGCGCGCGCAGCGCGGAGGAGGGCGGTGCGGGGCCCTCGCGGCT\n+CCTGTCGGACTCCGGGACGGCGGCTGCGGCCTCCGAGGGCGTCGAGGGCCAGGAGCAGGGCGAGGACGGC\n+GCCGAGGCGGAGTCGGTGCTGCTGCGGTTCTCCTCGCCGCGCGCGGCGTCGACGGTCGCGGCGTTCCTGC\n+GGACGCGGGTGTACCAGCCCGAGTCGCTGGTGTGGCTGGAGGGGTACGAGGCCCTGCGCGCCTGGCGGGC\n+CGAGCAAGGGGTGAGCGGGGTGTGCGCGGTCCCGTACGACGCCGAGGTCGCCGCGGGGGCCTCGCGGCGG\n+TACCCGGTCGGGCGGTGGACCGCCGCGCAACGCCGCGCCCGCCGCGAGGGCACCCTCAGCGCACACCGCG\n+TCGAGCTCCTCGACGCGGAGGGCATGGTGTGGGAGCCGCGCGAGGAGGAATGGGAGCGCACGCTCGCGGG\n+GCTTCGCTCCTACCGGACGGCGTACGGGCACCTCGCCCCCCACAGGCGCGAAACCTGGGGCGAAGACGAG\n+GGTGAGGACGTCGTACGCGTCGGGGACCTGATGGCGAACCTCCGCCGCAAGGACGGACTCGGGAAGGACG\n+CGAAGCGGGCCGCCGCGCGCGCCGCGCAGCTGAGGGCCGTCGATGCGGACTGGGACTGCCCGTGGCCGCT\n+GGACTGGCAGCGCTGCTGCCGGAAACTCGTGCTCCTGGCCGCGGACGAGCCCGGCGGGCGCCTGCCGGAG\n+ATCGCGCCCGGGGTCTGCCTGGACGGGGATGACCTCGGGGTGTGGGTCGCGCGGCAGCAGGAGCCGCGGG\n+TGTGGGCGCGGCTCAGCACCGAGCAGCGGGCGCGGCTCGAAGCGCTCGGGCTGCGGCCCACCGAAGCGGC\n+CCCGGGGCGGGGTGTGGAGGGCACGGGGGCGGCGGGGAGCATGAAGCGGACGGCGACGGCGCGAACGGCT\n+TTTCAGCGGGGTGTGGCGGCGCTCGCGCAGTGGGTCGAGCGGGAAGGCGCGGGGAAACCCGTACCCCGCA\n+AACACGTCGAGACCGTCAGCGTCGACGGCGAGGACGTCGACGTACGCCTCGGCGTATGGATCTCGAACAC\n+CAAGAGCCGGTACGACGGGCTGAGCGAGGACGAACGCGCGCAGCTCACCGCACTCGGAATGCCCTGGGCA\n+GGATGA\n+>lcl|NZ_CM001166.1_gene_2 [locus_tag=STTU_p0002] [location=complement(2995..3171)]\n+GTGCTCGCCGCCGTACGGGACACGATCGCCGAGACCGGCCAGGGACCGTCCGTACGGCAGATCCAGCGCG\n+TCACCGGGCTCGCGCTCGGCACCATCGCCCACCACCTGAAGGCGCTGGAGGAGAGCGGCCCCCTCGTCCG\n+TACGGGCCTGCACTGGCGCACCTGCCGCCTGGGCTGA\n+>lcl|NZ_CM001166.1_gene_3 [locus_tag=STTU_p0003] [location=complement(3195..3407)]\n+GTGACCGATGAACTGCTCCGCCTCGCCCAGGAGAGGCGTGCGACCTACCGCGACCTCACCCTCGGCGGCC\n+CCGCCCGCCCCCCGACACCTCTGCGCCGGGCACTGATCCGGCAGTCCGCCCGCCTGCTCGACGGCCCGCC\n+CACCACGGCCCGCCGGGCTCTGCTGTGCCGCCCGCCCACGCCCGCGTCCCCGCCCTCGCGGGGGACCAGG\n+TGA\n+>lcl|NZ_CM001166.1_gene_4 [locus_tag=STTU_p0004] [location=3510..3866]\n+GTGACCGATTTCCCCGACGATCTCCTCGCGGCTCAGCGCGACCTCACCGCCGTACGCGCCACCCTTTCCG\n+CCCGCCTCGCGGCGCTGCCGCCCTCGGCCGAGCCGATGCCCGCGTGGGAGCGGCCCGACGGCTACTGGGC\n+GGGCGCCCGTACGCACCCGGCCTCCCCGGGGTGGAGCGAGGAGGAGCGCGAGGAGGTCGCCGCGCTCCGC\n+GAGCGGGAGCGGGATCTGGCCGGGGTGATCGTGACGCACGAGCTGTGGGCGAGCGTGCCGGCCGGGGAGC\n+GGATGCGGGCCCGCGACGCACTCAAGCACGCCCACGAGGCCCCGGCCGCAGCCGGGGCGGCGGGGGCGCG\n+GGGCTGA\n+>lcl|NZ_CM001166.1_gene_5 [locus_tag=STTU_p0005] [location=complement(4344..560'..b'ATCTGCTCGCTGCCGCGGCCCCG\n+GCAGAGTACGATCCGGCCTCGCTCACCCCTGAGGAGAAGACCCACCTGTTGTCCGCCGCGGCCTGGCAGG\n+CAGAGGAGGGCGCCTACATGCACCAGCAGAACACCCGTCCCCTCACCCTCGCGCCCGCACTGAACGACTC\n+GCCCGCCGGACTGCTCTCCTGGATCCTCGAGAAGTACCGCGCGTGGACCGACTGCGGCGGCGACCTGTCC\n+ACCCGCTTCGGCGACGACTTCCTCCTCACCCAGGCATCGCTCTACTGGTTCACCGGCACGATCTCCACGT\n+CCTTCCGCCCGTACTACGAGTACGCGCACCAGCTCACCCGGCGCGTGCGGCGGGTCGACGTCCCCACCGC\n+CCTCGCCCTGTTCCCCGCAGACCTCGCCCAACCGCCCCGGAGCTGGGCCGAGCGCACCTACCACCTCACG\n+CGTTACACCCGTATGCCTCGCGGCGGCCACTTCGCCGCGCACGAGGAACCGGCCTTGCTTGCCGACGACA\n+TCACCGCGTTCTTCGGCGACCTCCGTTAG\n+>lcl|NZ_CM001166.1_gene_174 [locus_tag=STTU_p0174] [location=complement(143857..143970)]\n+GTGGATGGACTGCATGGGAGCCCACTTCATAAGAGGCTCGACGAACACTGCGCTGGCCGATTCGGGATCG\n+CACCACCGCTAACCGGGGAAATCACCACGAAGATCAACCACTGA\n+>lcl|NZ_CM001166.1_gene_175 [locus_tag=STTU_p0175] [location=complement(143981..144157)]\n+ATGCCCACCGAGACCCTGCCGCCCGAGGTGCGGAATTTCATCGACGATGCGCGGCGTCACCTGGCTTTCT\n+GCGCCGGGCTGCGCGCGGGCGAGGACCCGGCGTACGCGACCGTGCTCCTGGCCGCCGCCGAGCAGGGAGA\n+AGAAGTCCTCGCCCGGTACGAAGGCCGCGTAGCTTAG\n+>lcl|NZ_CM001166.1_gene_176 [locus_tag=STTU_p0176] [location=complement(144230..147016)]\n+TTGGCTTGTCTGCCTCGTGAGGAGTTTCAAATTTCTGTTTCTCGGGTTCCGTTGCGGAAACATCAGGTGG\n+AGCTTATGTCGGACCTCAGGAAATGGGTTCGGGTGGCTGCCCGGGAAAGCGCCCGTTCGGGGCGGGGGGC\n+GCGGGCGACGGTGGTGTCCGCTACGGGTACGGGGAAGACGATCAGCGCGGCTGTTGCGGCGTTGGAGTTG\n+TTCCCTTCGGGGCGGGTTCTCGTGATGGTGCCGACGCTGGATCTGCTGGTGCAGACGGCGCAGTCGTGGC\n+GGGCGGTGGGGCACACGGCGCCGATGGTCGGGGTGTGCTCGCTGCCCGGGGATCTGCTCCTGGAGGAGTT\n+GCGGGTGCGGACGACGACGCACCCGATCCGGCTCGCGCTGTGGGCCGGGCAGGGGCCTGTGGTCGTGCTG\n+GCGACGTACTCCTCGCTCGTGGGCGGGGACGGGCAGGGCGGGCCCCTGGAGGCCGCCCTGGCGGGCTCGG\n+GGTTGTACGGGCAGCGGATGGACGGCTTCGACCTCGCGGTCGTGGACGAGGCGCACCGTACGGCGGGCAG\n+CGCGGCGAAGCCCTGGGCCGCGATCCACGACAACGCCCGTATCCCGGCGGCGCACCGGCTCTACCTCACC\n+GCCACCCCGCGCGTCCTCGCGCCCGCCCGCCCCGACAGGGACGAGGACCAGGAGGAGGGCGGCGGGGAGG\n+CGCCGGCACTCGTGACGATGGCGAACGACCCGGAAGGCGAGTACGGGGCGTGGATTCACGAACTCGGGTT\n+GTCCGAGGCGATCGAGCGGAAAATTCTTGCGCCTTTCGAGATTGATGTTTTGGAGATTACCGATCCTGAG\n+CCGGAATTGATGGAAGGAATGGACCGGGAGGCGCGGCGTGGGCGGCGGCTCGCCCTGCTCCAGACTGCGT\n+TGCTGGAGCACGCGGCCGAGCACAATCTGCGCACCGTGATGACGTTCCATCAGCGGGTGGAGGAGGCGGC\n+GGCTTTCGCGGAGAAAATGCCGGAGACAGCGGCGGAGCTTTACCGGAATGAGGTGTCGGCGGAGGATCTT\n+GCCCTAGCCGAGGAGCTCCCGGCCTCCGAGGTGGGCGGGGGCTTCTACGAGCTGGAGCCGGGGCGGCATG\n+TGCGGCCGGAGCGGGTGTGGTCGCGGTGGCTGTACGGAGAGCACCCGGTGGCCGAACGCCGTGCGGTGCT\n+GCGGGAGTTCGCGAACGGGATGGACTCGGCAGGGGTGCGGGTGCACCGCGCGTTCCTCGCCTCCGTCCGC\n+GTGCTCGGCGAGGGCGTCGACATCGTCGGGGAGCGCGGGGTCGAGGCGATCTGCTTCGCCGACGCGCGCG\n+GGTCCCAGGTCGAGATCGTGCAGAACATCGGCAGGGCGCTGCGCCCGAACCCGGACGGGCAGACGAAGAC\n+GGCGCGGATCATCGTGCCCGTCTTCTTGGAGGCCGACGAGGACGGGGAGGGGATGGTCGCGAGCGAGGCG\n+TACCGGCCGCTCGTGGCCGTGCTCCAGGGGCTGCGCTCGCACTCCGAGCACCTGGTCGAGAAGCTGATGC\n+TCCGGGCCCGGGTGCGGGCCGAGAGCGCGAGCGCGCGCAGCGCGGAGGAGGCCGGTGCGGGGCCCGCGCG\n+GGTCCTGTCCGACTCCGGGACCTCTTCCCCCGCCTCCCAGGCCTCCGGGGACGTCGAAGGCGAGAACGAG\n+GACGACGTCGAGGCGGGCGCGGACGGCGCTGAGGCGGGCGCGGACGGCGCTGAGGAGTCGGAGTCGGTGT\n+TGTTGCGGTTCTCGACGCCGCGCTCGGCGTCGACCATCGCGGCCTTCCTGCGGACGCGGGTGTACCAGCC\n+GGAGTCGACGGTGTGGCTGGAGGGCTACGAGGCGCTGCGCGCCTGGCGGGCCGAGCAAGGGGTGCGCGGC\n+TTGTGCGCGGTCCCGTACGACGCCGAGGTCGCCGCGGGGGCCTCGCGGCGGTACCCGGTCGGGCGGTGGA\n+CCACCGCGCAACGCCGCGCCCGCCGCGAGGGCACCCTCAGCGCACACCGCATCGACCTGCTCGACGCGGA\n+GGGCATGGTGTGGGAGCCGCGCGAAGAGGAGTGGGAGCGCACGCTCGCCGGGCTTCGCTCCTACCGGGCC\n+GCGTACGGGCACCTCGCCCCCCGCCGGCGCGAAACCTGGGGCGAAGACGAGGGTGAGGACGTCGTACGCG\n+TCGGGGACCTGATGGCGAACCTCCGCCGCAAGGACGGACTCGGGCGGGACGCGGAGCGGGCCGCCGCGCG\n+CGCGGCCCAGCTGAGGGCCGTCGATGCGGACTGGGACTGCCCCTGGCCGCTGGACTGGCAGCGCTGCTGT\n+CGGCAGCTCGCGCTCCTGGCCGCCGACGAACCCGACGGACGCGCGCCCCGGATCGCGCGCGGGGTGCGCA\n+TCGACGGGGACGACCTCGGCGCGTGGGTCGCGCGGCAGCAGGAACCGCGGGTGTGGGCGAAGCTCAGCAC\n+CGAGCAGCGGGCGCGACTCGAAGCGCTCGGGCTCCGGCCTACCGAGACGGCCCCACGGCGGGGTGTGGAG\n+GGCACGGGGGCGGCGGGGAGCGGGAAGCGGACGGCGGCGGCGCGAACGGCCTTCCAGCGCGGCCTCGCGG\n+CGCTCGCGCAGTGGGTCGAGCGGGAAGGCGCGGAGAAACCCGTACCCCGCAAACACACCGAGACCGTGAG\n+CGTGGACGGTGAGGACGTCGACGTACGCCTCGGCGTGTGGGTCTCGAACGTGAAGAGCCGCTTCGACGGG\n+ATGGGCGAGGACGAGCGCGGCCAGCTCACCGCGCTCGGAGTGCCCTGGGCGGTGTAG\n+\n' |
| b |
| diff -r 000000000000 -r 9c195b26a5ac test-data/streptomyces_Tu6071_plasmid_genes.icm |
| b |
| Binary file test-data/streptomyces_Tu6071_plasmid_genes.icm has changed |
| b |
| diff -r 000000000000 -r 9c195b26a5ac test-data/streptomyces_Tue6071_plasmid_genomic.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/streptomyces_Tue6071_plasmid_genomic.fasta Tue Nov 28 10:08:06 2017 -0500 |
| b |
| b'@@ -0,0 +1,2107 @@\n+>gi|333028963|ref|NZ_CM001166.1| Streptomyces sp. Tu6071 plasmid pTu6071, whole genome shotgun sequence\n+GGCCCCGTACGAGGGGCGCGGCCCCGTACGAGGGGCGCGGCGGCGCGGGTTTCATCATACGCTGCATCAG\n+GTGCTGATGCACTGTGTAGACTTGGGGGAATTCGGTGACACCCTGCCGCGTGTAGCTCTTCCCTGATTCG\n+CCCTCAACGCAGCCCAATTGATGCATATGTTGAGTTGGGGATTTGGCTCGTCTGCCTCGTGAGGAGATTC\n+AAATGTCTGTTTCCCGGGTTCCGCTGCGGAAACATCAGGTAGAGCTTATGTCGGACCTCAGGAAATGGGT\n+CCGGGTAGCCGCCCGGGAAAGCGCCCGCACGGAGCGTGGGGCGCGGGCCACGGTGGTGTCCGCTACGGGT\n+ACGGGAAAGACGATCAGCGCGGCTGCTGCGGCGTTGGAGTTGTTCCCTTCGGGGCGGGTTCTCGTGATGG\n+TGCCGACGCTGGATCTGCTGGTGCAGACGGCGCAGTCGTGGCGGGCGGTGGGGCACACGGCGCCGATGGT\n+CGGGGTGTGCTCGCTGCCCAGGGATCTGCTCCTGGAGGAGCTGCGGGTGCGGACGACGACCCACCCGATC\n+CGGCTCGCGCTTTGGGCCGGATCGGGGCCGGTGGTCGTGCTGGCGACGTACTCCTCGCTCGTGGGCGAGG\n+ACGGGCAGGGCGGACCCTTGGAGGCCGCTCTCGCCGGGGCTGGCTTGTACGGGCAGCGGATGGATGGCTT\n+CGACCTTGCGGTCGTGGACGAGGCGCACCGCACGGCGGGCAGCGCGGAGAAGGCGTGGGCGGCGATCCAC\n+GACAACGCCCGTTTTCCGGCGGCGCACCGGCTGTACCTCACCGCGACCCCGCGCGTCCTGGCCCCGGCCC\n+GTCCCGCCAGGCACGAGGGCGAGGAGGGACGCGGGGAGGCGCCGGCACTCGTGACGATGGCGAATGATCC\n+GGCGGGCGAGTACGGGGCGTGGATTCACGAACTCGGTTTGTCCGAGGCAATCGCGCGAAAAATCGTCGCG\n+CCTTTTGAGATTGACGTTTTGGAGATTACTGATCCTGAGCCGGAATTGATGGAGGGATTGGATCGGGAGG\n+CGCGGCGTGGGCGGCGGCTTGCGTTGCTTCAGACCGGGCTTTTGGAGCACGCGGCCGAGCATAATATTTG\n+CACCATGATGACGCTTCATCAGCAGGTTGAGGAGGCGGCGGCTTTCGCGGAGAAAATGCCGGAGACGGCG\n+GCGGAGCTTTACCGGAATGAGGTGTCGGCGGAGGATTTTGCCCTGGCCGAGGAGCTCCCGGCCTCCGAGG\n+TGGGTGGGGGGTTCTACGAGCTGGAGCCGGGGCGTCATGTGCCGCCGTCGCGGGTGTGGTCGCGGTGGCT\n+GTATGGGGAGCATCCTGTGGCCGAACGGCGTTCTGTGCTGCGGGAGTTCGCGAACGGGATGGACGCGGAG\n+GGGCGGCGGGTGCACCGGGCGTTCCTCGCTTCCGTACGGGTCCTGGGTGAGGGCGTCGACATCGTCGGGG\n+AGCGCGGGGTCGAGGCGATCTGCTTTGCCGACGCACGCGGGTCTCAGGTGGAGATCGTGCAGAACATCGG\n+GCGCGCGTTGCGCCAGAACCCGGATGGGCGGGCGAAGACGGCGCGGATCATCGTGCCGGTCTTCCTGCGG\n+CCGGACGAGGACGGGGAGGGCATGGTGGCGTCGGAGGCGTACCGGCCGCTCGTCGCCGTACTCCAGGGCC\n+TGCGCTCGCACGACGAGCACCTGGTCGAGAAACTCATGCTGCGGGCGCGCGTACGGGCCGAGAGCGCGAG\n+CGCGCGCAGCGCGGAGGAGGGCGGTGCGGGGCCCTCGCGGCTCCTGTCGGACTCCGGGACGGCGGCTGCG\n+GCCTCCGAGGGCGTCGAGGGCCAGGAGCAGGGCGAGGACGGCGCCGAGGCGGAGTCGGTGCTGCTGCGGT\n+TCTCCTCGCCGCGCGCGGCGTCGACGGTCGCGGCGTTCCTGCGGACGCGGGTGTACCAGCCCGAGTCGCT\n+GGTGTGGCTGGAGGGGTACGAGGCCCTGCGCGCCTGGCGGGCCGAGCAAGGGGTGAGCGGGGTGTGCGCG\n+GTCCCGTACGACGCCGAGGTCGCCGCGGGGGCCTCGCGGCGGTACCCGGTCGGGCGGTGGACCGCCGCGC\n+AACGCCGCGCCCGCCGCGAGGGCACCCTCAGCGCACACCGCGTCGAGCTCCTCGACGCGGAGGGCATGGT\n+GTGGGAGCCGCGCGAGGAGGAATGGGAGCGCACGCTCGCGGGGCTTCGCTCCTACCGGACGGCGTACGGG\n+CACCTCGCCCCCCACAGGCGCGAAACCTGGGGCGAAGACGAGGGTGAGGACGTCGTACGCGTCGGGGACC\n+TGATGGCGAACCTCCGCCGCAAGGACGGACTCGGGAAGGACGCGAAGCGGGCCGCCGCGCGCGCCGCGCA\n+GCTGAGGGCCGTCGATGCGGACTGGGACTGCCCGTGGCCGCTGGACTGGCAGCGCTGCTGCCGGAAACTC\n+GTGCTCCTGGCCGCGGACGAGCCCGGCGGGCGCCTGCCGGAGATCGCGCCCGGGGTCTGCCTGGACGGGG\n+ATGACCTCGGGGTGTGGGTCGCGCGGCAGCAGGAGCCGCGGGTGTGGGCGCGGCTCAGCACCGAGCAGCG\n+GGCGCGGCTCGAAGCGCTCGGGCTGCGGCCCACCGAAGCGGCCCCGGGGCGGGGTGTGGAGGGCACGGGG\n+GCGGCGGGGAGCATGAAGCGGACGGCGACGGCGCGAACGGCTTTTCAGCGGGGTGTGGCGGCGCTCGCGC\n+AGTGGGTCGAGCGGGAAGGCGCGGGGAAACCCGTACCCCGCAAACACGTCGAGACCGTCAGCGTCGACGG\n+CGAGGACGTCGACGTACGCCTCGGCGTATGGATCTCGAACACCAAGAGCCGGTACGACGGGCTGAGCGAG\n+GACGAACGCGCGCAGCTCACCGCACTCGGAATGCCCTGGGCAGGATGACGAGCAGGCGGCGGATGCGACC\n+AGCGTAGGAGGGGCGGGGAGCGGCGGCAGCCGGACCGGGCCCGGCTGCCGCCGGTCAGCCCAGGCGGCAG\n+GTGCGCCAGTGCAGGCCCGTACGGACGAGGGGGCCGCTCTCCTCCAGCGCCTTCAGGTGGTGGGCGATGG\n+TGCCGAGCGCGAGCCCGGTGACGCGCTGGATCTGCCGTACGGACGGTCCCTGGCCGGTCTCGGCGATCGT\n+GTCCCGTACGGCGGCGAGCACGCGGTGGCGCCCGTCCCCCGCCGTCACCTGGTCCCCCGCGAGGGCGGGG\n+ACGCGGGCGTGGGCGGGCGGCACAGCAGAGCCCGGCGGGCCGTGGTGGGCGGGCCGTCGAGCAGGCGGGC\n+GGACTGCCGGATCAGTGCCCGGCGCAGAGGTGTCGGGGGGCGGGCGGGGCCGCCGAGGGTGAGGTCGCGG\n+TAGGTCGCACGCCTCTCCTGGGCGAGGCGGAGCAGTTCATCGGTCACCCCCACACTGGATCACGTGTTCG\n+ATTTTCTGGGCAACCGAACCCTCACAAAACGCCACATCACCACCGTGCGCGCGCTCTGGCCGGTCGTACT\n+CTCGCTGGTGTGACCGATTTCCCCGACGATCTCCTCGCGGCTCAGCGCGACCTCACCGCCGTACGCGCCA\n+CCCTTTCCGCCCGCCTCGCGGCGCTGCCGCCCTCGGCCGAGCCGATGCCCGCGTGGGAGCGGCCCGACGG\n+CTACTGGGCGGGCGCCCGTACGCACCCGGCCTCCCCGGGGTGGAGCGAGGAGGAGCGCGAGGAGGTCGCC\n+GCGCTCCGCGAGCGGGAGCGGGATCTGGCCGGGGTGATCGTGACGCACGAGCTGTGGG'..b'GAGTACGCGCACCAGCTCACCCGGCGCGTGCGGCGGGTC\n+GACGTCCCCACCGCCCTCGCCCTGTTCCCCGCAGACCTCGCCCAACCGCCCCGGAGCTGGGCCGAGCGCA\n+CCTACCACCTCACGCGTTACACCCGTATGCCTCGCGGCGGCCACTTCGCCGCGCACGAGGAACCGGCCTT\n+GCTTGCCGACGACATCACCGCGTTCTTCGGCGACCTCCGTTAGACCGCAGGCCCATGCGTGACTCTGTCG\n+GTGACGTCGGGAATGTCCGACGGGCGGCGGACCCGATGACCCTGGGGCCATTCCAGCCCCTGTGGGGTTC\n+GGGGAAGAGGCCCCCGAGATGTTCGGGTTTCCCCACCACTGATGCTGACTCATGTTTGCCCTGGCCAGTC\n+GACGTTTCAGTGGTTGATCTTCGTGGTGATTTCCCCGGTTAGCGGTGGTGCGATCCCGAATCGGCCAGCG\n+CAGTGTTCGTCGAGCCTCTTATGAAGTGGGCTCCCATGCAGTCCATCCACGTGGCAATCACTAAGCTACG\n+CGGCCTTCGTACCGGGCGAGGACTTCTTCTCCCTGCTCGGCGGCGGCCAGGAGCACGGTCGCGTACGCCG\n+GGTCCTCGCCCGCGCGCAGCCCGGCGCAGAAAGCCAGGTGACGCCGCGCATCGTCGATGAAATTCCGCAC\n+CTCGGGCGGCAGGGTCTCGGTGGGCATCGGCGTACGCGCCACCCCAGGCGGAGACGTCCCGCCGGGGGCG\n+GCGCGTACGGCGTGGACATCGACCACCACCTACACCGCCCAGGGCACTCCGAGCGCGGTGAGCTGGCCGC\n+GCTCGTCCTCGCCCATCCCGTCGAAGCGGCTCTTCACGTTCGAGACCCACACGCCGAGGCGTACGTCGAC\n+GTCCTCACCGTCCACGCTCACGGTCTCGGTGTGTTTGCGGGGTACGGGTTTCTCCGCGCCTTCCCGCTCG\n+ACCCACTGCGCGAGCGCCGCGAGGCCGCGCTGGAAGGCCGTTCGCGCCGCCGCCGTCCGCTTCCCGCTCC\n+CCGCCGCCCCCGTGCCCTCCACACCCCGCCGTGGGGCCGTCTCGGTAGGCCGGAGCCCGAGCGCTTCGAG\n+TCGCGCCCGCTGCTCGGTGCTGAGCTTCGCCCACACCCGCGGTTCCTGCTGCCGCGCGACCCACGCGCCG\n+AGGTCGTCCCCGTCGATGCGCACCCCGCGCGCGATCCGGGGCGCGCGTCCGTCGGGTTCGTCGGCGGCCA\n+GGAGCGCGAGCTGCCGACAGCAGCGCTGCCAGTCCAGCGGCCAGGGGCAGTCCCAGTCCGCATCGACGGC\n+CCTCAGCTGGGCCGCGCGCGCGGCGGCCCGCTCCGCGTCCCGCCCGAGTCCGTCCTTGCGGCGGAGGTTC\n+GCCATCAGGTCCCCGACGCGTACGACGTCCTCACCCTCGTCTTCGCCCCAGGTTTCGCGCCGGCGGGGGG\n+CGAGGTGCCCGTACGCGGCCCGGTAGGAGCGAAGCCCGGCGAGCGTGCGCTCCCACTCCTCTTCGCGCGG\n+CTCCCACACCATGCCCTCCGCGTCGAGCAGGTCGATGCGGTGTGCGCTGAGGGTGCCCTCGCGGCGGGCG\n+CGGCGTTGCGCGGTGGTCCACCGCCCGACCGGGTACCGCCGCGAGGCCCCCGCGGCGACCTCGGCGTCGT\n+ACGGGACCGCGCACAAGCCGCGCACCCCTTGCTCGGCCCGCCAGGCGCGCAGCGCCTCGTAGCCCTCCAG\n+CCACACCGTCGACTCCGGCTGGTACACCCGCGTCCGCAGGAAGGCCGCGATGGTCGACGCCGAGCGCGGC\n+GTCGAGAACCGCAACAACACCGACTCCGACTCCTCAGCGCCGTCCGCGCCCGCCTCAGCGCCGTCCGCGC\n+CCGCCTCGACGTCGTCCTCGTTCTCGCCTTCGACGTCCCCGGAGGCCTGGGAGGCGGGGGAAGAGGTCCC\n+GGAGTCGGACAGGACCCGCGCGGGCCCCGCACCGGCCTCCTCCGCGCTGCGCGCGCTCGCGCTCTCGGCC\n+CGCACCCGGGCCCGGAGCATCAGCTTCTCGACCAGGTGCTCGGAGTGCGAGCGCAGCCCCTGGAGCACGG\n+CCACGAGCGGCCGGTACGCCTCGCTCGCGACCATCCCCTCCCCGTCCTCGTCGGCCTCCAAGAAGACGGG\n+CACGATGATCCGCGCCGTCTTCGTCTGCCCGTCCGGGTTCGGGCGCAGCGCCCTGCCGATGTTCTGCACG\n+ATCTCGACCTGGGACCCGCGCGCGTCGGCGAAGCAGATCGCCTCGACCCCGCGCTCCCCGACGATGTCGA\n+CGCCCTCGCCGAGCACGCGGACGGAGGCGAGGAACGCGCGGTGCACCCGCACCCCTGCCGAGTCCATCCC\n+GTTCGCGAACTCCCGCAGCACCGCACGGCGTTCGGCCACCGGGTGCTCTCCGTACAGCCACCGCGACCAC\n+ACCCGCTCCGGCCGCACATGCCGCCCCGGCTCCAGCTCGTAGAAGCCCCCGCCCACCTCGGAGGCCGGGA\n+GCTCCTCGGCTAGGGCAAGATCCTCCGCCGACACCTCATTCCGGTAAAGCTCCGCCGCTGTCTCCGGCAT\n+TTTCTCCGCGAAAGCCGCCGCCTCCTCCACCCGCTGATGGAACGTCATCACGGTGCGCAGATTGTGCTCG\n+GCCGCGTGCTCCAGCAACGCAGTCTGGAGCAGGGCGAGCCGCCGCCCACGCCGCGCCTCCCGGTCCATTC\n+CTTCCATCAATTCCGGCTCAGGATCGGTAATCTCCAAAACATCAATCTCGAAAGGCGCAAGAATTTTCCG\n+CTCGATCGCCTCGGACAACCCGAGTTCGTGAATCCACGCCCCGTACTCGCCTTCCGGGTCGTTCGCCATC\n+GTCACGAGTGCCGGCGCCTCCCCGCCGCCCTCCTCCTGGTCCTCGTCCCTGTCGGGGCGGGCGGGCGCGA\n+GGACGCGCGGGGTGGCGGTGAGGTAGAGCCGGTGCGCCGCCGGGATACGGGCGTTGTCGTGGATCGCGGC\n+CCAGGGCTTCGCCGCGCTGCCCGCCGTACGGTGCGCCTCGTCCACGACCGCGAGGTCGAAGCCGTCCATC\n+CGCTGCCCGTACAACCCCGAGCCCGCCAGGGCGGCCTCCAGGGGCCCGCCCTGCCCGTCCCCGCCCACGA\n+GCGAGGAGTACGTCGCCAGCACGACCACAGGCCCCTGCCCGGCCCACAGCGCGAGCCGGATCGGGTGCGT\n+CGTCGTCCGCACCCGCAACTCCTCCAGGAGCAGATCCCCGGGCAGCGAGCACACCCCGACCATCGGCGCC\n+GTGTGCCCCACCGCCCGCCACGACTGCGCCGTCTGCACCAGCAGATCCAGCGTCGGCACCATCACGAGAA\n+CCCGCCCCGAAGGGAACAACTCCAACGCCGCAACAGCCGCGCTGATCGTCTTCCCCGTACCCGTAGCGGA\n+CACCACCGTCGCCCGCGCCCCCCGCCCCGAACGGGCGCTTTCCCGGGCAGCCACCCGAACCCATTTCCTG\n+AGGTCCGACATAAGCTCCACCTGATGTTTCCGCAACGGAACCCGAGAAACAGAAATTTGAAACTCCTCAC\n+GAGGCAGACAAGCCAAATCCCCAACTCAACATATGCATCAGTCACCCGCGTTGAGGGCAAGTCAGGGAAG\n+AGCTACACGCGACAGGGTGTTACCTAATTCCCCCAAGTCTACACAGTGCATCAGCACCTGATGCGGCGTA\n+TGATGAAACCCGCGCTCGTCGTACGGGGCCGCGCTCGTCGTACGGGGCCGCGCTCGTCGTACGGGGCCGC\n+GCTCGTCGTACGGGGCCGCGCTCGTCGTACGGGGCCGCGCTCGTCGTACGGGGCCGCGCTCGTCGTACGG\n+GGCCGCGCTCGTCGTACGGGGCCGCGCTCGTCGTACGGGGCCGCGCTCGTCGTACGGGGCCACGCTC\n+\n' |
| b |
| diff -r 000000000000 -r 9c195b26a5ac test-data/test.gbk --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.gbk Tue Nov 28 10:08:06 2017 -0500 |
| b |
| b'@@ -0,0 +1,257 @@\n+LOCUS contig1 350 bp DNA linear 21-MAR-2017\n+DEFINITION Genus species strain strain.\n+ACCESSION \n+VERSION\n+KEYWORDS .\n+SOURCE Genus species\n+ ORGANISM Genus species\n+ Unclassified.\n+COMMENT Annotated using prokka 1.12 from\n+ https://github.com/tseemann/prokka.\n+FEATURES Location/Qualifiers\n+ source 1..350\n+ /organism="Genus species"\n+ /mol_type="genomic DNA"\n+ /strain="strain"\n+ORIGIN \n+ 1 gagttttatc gcttccatga cgcagaagtt aacactttcg gatatttctg atgagtcgaa\n+ 61 aaattatctt gataaagcag gaattactac tgcttgttta cgaattaaat cgaagtggac\n+ 121 tgctggcgga aaatgagaaa attcgaccta tccttgcgca gctcgagaag ctcttacttt\n+ 181 gcgacctttc gccatcaact aacgattctg tcaaaaactg acgcgttgga tgaggagaag\n+ 241 tggcttaata tgcttggcac gttcgtcaag gactggttta gatatgagtc acattttgtt\n+ 301 catggtagag attctcttgt tgacatttta aaagagcgtg gattactatc\n+//\n+LOCUS contig2 840 bp DNA linear 21-MAR-2017\n+DEFINITION Genus species strain strain.\n+ACCESSION \n+VERSION\n+KEYWORDS .\n+SOURCE Genus species\n+ ORGANISM Genus species\n+ Unclassified.\n+COMMENT Annotated using prokka 1.12 from\n+ https://github.com/tseemann/prokka.\n+FEATURES Location/Qualifiers\n+ source 1..840\n+ /organism="Genus species"\n+ /mol_type="genomic DNA"\n+ /strain="strain"\n+ CDS 40..498\n+ /locus_tag="PROKKA_00001"\n+ /inference="ab initio prediction:Prodigal:2.6"\n+ /codon_start=1\n+ /transl_table=11\n+ /product="hypothetical protein"\n+ /translation="MSQVTEQSVRFQTALASIKLIQASAVLDLTEDDFDFLTSNKVWI\n+ ATDRSRARRCVEACVYGTLDFVGYPRFPAPVEFIAAVIAYYVHPVNIQTACLIMEGAE\n+ FTENIINGVERPVKAAELFAFTLRVRAGNTDVLTDAEENVRQKLRAEGVM"\n+ CDS 498..614\n+ /locus_tag="PROKKA_00002"\n+ /inference="ab initio prediction:Prodigal:2.6"\n+ /codon_start=1\n+ /transl_table=11\n+ /product="hypothetical protein"\n+ /translation="MSKGKKRSGARPGRPQPLRGTKGKRKGARLWYVGGQQF"\n+ORIGIN \n+ 1 tgagtccgat gctgttcaac cactaatagg taagaaatca tgagtcaagt tactgaacaa\n+ 61 tccgtacgtt tccagaccgc tttggcctct attaagctca ttcaggcttc tgccgttttg\n+ 121 gatttaaccg aagatgattt cgattttctg acgagtaaca aagtttggat tgctactgac\n+ 181 cgctctcgtg ctcgtcgctg cgttgaggct tgcgtttatg gtacgctgga ctttgtggga\n+ 241 taccctcgct ttcctgctcc tgttgagttt attgctgccg tcattgctta ttatgttcat\n+ 301 cccgtcaaca ttcaaacggc ctgtctcatc atggaaggcg ctgaatttac ggaaaacatt\n+ 361 attaatggcg tcgagcgtcc ggttaaagcc gctgaattgt tcgcgtttac cttgcgtgta\n+ 421 cgcgcaggaa acactgacgt tcttactgac gcagaagaaa acgtgcgtca aaaattacgt\n+ 481 gcggaaggag tgatgtaatg tctaaaggta aaaaacgttc tggcgctcgc cctggtcgtc\n+ 541 cgcagccgtt gcgaggtact aaaggcaagc gtaaaggcgc tcgtctttgg tatgtaggtg\n+ 601 gtcaacaatt ttaattgcag gggcttcggc cccttacttg aggataaatt atgtctaata\n+ 661 ttcaaactgg cgccgagcgt atgccgcatg acctttccca tcttggcttc cttgctggtc\n+ 721 agattggtcg tcttattacc atttcaacta ctccggttat cgctggcgac tccttcgaga\n+ 781 tggacgccgt tggcgctctc cgtctttctc cattgcgtcg tggccttgct attgactcta\n+//\n+LOCUS contig3 210 bp DNA linear 21-MAR-2017\n+DEFINITION Genus species strain strain.\n+ACCESSION \n+VERSION\n+KEYWORDS .\n+SOURCE Genus species\n+ ORGANISM Genus species\n+ Unclassified.\n+COMMENT Annotated using prokka 1.12 from\n+ https://github.com/tseemann/prokka.\n+FEATURES Location/Qualifiers\n+ source 1..210\n+ /organism="Genus species"\n+ '..b'nitio prediction:Prodigal:2.6"\n+ /codon_start=1\n+ /transl_table=11\n+ /product="hypothetical protein"\n+ /translation="MAKAGKGLLEGTLQAGTSAVSDKLLDLVGLGGKSAADKGKDTRD\n+ YLAAAFPELNAWERAGADASSAGMVDAGFENQKELTKMQLDNQKEIAEMQNETQKEIA\n+ GIQSATSRQNTKDQVYAQNEMLAYQQKESTARVASIMENTNLSKQQQVSEIMRQMLTQ\n+ AQTAGQYFTNDQIKEMTRKVSAEVDLVHQQTQNQRYGSSHIGATAKDISNVVTDAASG\n+ VVDIFHGIDKAVADTWNNFWKDGKADGIGSNLSRK"\n+ORIGIN \n+ 1 gtgctatggc taaagctggt aaaggacttc ttgaaggtac gttgcaggct ggcacttctg\n+ 61 ccgtttctga taagttgctt gatttggttg gacttggtgg caagtctgcc gctgataaag\n+ 121 gaaaggatac tcgtgattat cttgctgctg catttcctga gcttaatgct tgggagcgtg\n+ 181 ctggtgctga tgcttcctct gctggtatgg ttgacgccgg atttgagaat caaaaagagc\n+ 241 ttactaaaat gcaactggac aatcagaaag agattgccga gatgcaaaat gagactcaaa\n+ 301 aagagattgc tggcattcag tcggcgactt cacgccagaa tacgaaagac caggtatatg\n+ 361 cacaaaatga gatgcttgct tatcaacaga aggagtctac tgctcgcgtt gcgtctatta\n+ 421 tggaaaacac caatctttcc aagcaacagc aggtttccga gattatgcgc caaatgctta\n+ 481 ctcaagctca aacggctggt cagtatttta ccaatgacca aatcaaagaa atgactcgca\n+ 541 aggttagtgc tgaggttgac ttagttcatc agcaaacgca gaatcagcgg tatggctctt\n+ 601 ctcatattgg cgctactgca aaggatattt ctaatgtcgt cactgatgct gcttctggtg\n+ 661 tggttgatat ttttcatggt attgataaag ctgttgccga tacttggaac aatttctgga\n+ 721 aagacggtaa agctgatggt attggctcta atttgtctag gaaataaccg tcaggattga\n+ 781 caccctccca attgtatgtt ttcatgcctc caaatcttgg aggctttttt atggttcgtt\n+ 841 cttattaccc ttctgaatgt cacgctgatt attttgactt tgagcgtatc gaggctctta\n+ 901 aacctgctat tgaggcttgt ggcatttcta ctctttctca atccccaatg cttggcttcc\n+ 961 ataagcagat ggataaccgc atcaagctct tggaagagat tctgtctttt cgtatgcagg\n+ 1021 gcgttgagtt cgataatggt gatatgtatg ttgacggcca taaggctgct tctgacgttc\n+ 1081 gtgatgagtt tgtatctgtt actgagaagt taatggatga attggcacaa tgctacaatg\n+ 1141 tgctccccca acttgatatt aataacacta tagaccaccg ccccgaaggg gacgaaaaat\n+ 1201 ggtttttaga gaacgagaag acggttacgc agttttgccg caagctggct gctgaacgcc\n+ 1261 ctcttaagga tattcgcgat gagtataatt accccaaaaa gaaaggtatt aaggatgagt\n+ 1321 gttcaagatt gctggaggcc tccactatga aatcgcgtag aggctttgct attcagcgtt\n+ 1381 tgatgaatgc aatgcgacag gctcatgctg atggttggtt tatcgttttt gacactctca\n+ 1441 cgttggctga cgaccgatta gaggcgtttt atgataatcc caatgctttg cgtgactatt\n+ 1501 ttcgtgatat tggtcgtatg gttcttgctg ccgagggtcg caaggctaat gattcacacg\n+ 1561 ccgactgcta tcagtatttt tgtgtgcctg agtatggtac agctaatggc cgtcttcatt\n+ 1621 tccatgcggt gcactttatg cggacacttc ctacaggtag cgttgaccct aattttggtc\n+ 1681 gtcgggtacg caatcgccgc cagttaaata gcttgcaaaa tacgtggcct tatggttaca\n+ 1741 gtatgcccat cgcagttcgc tacacgcagg acgctttttc acgttctggt tggttgtggc\n+ 1801 ctgttgatgc taaaggtgag ccgcttaaag ctaccagtta tatggctgtt ggtttctatg\n+ 1861 tggctaaata cgttaacaaa aagtcagata tggaccttgc tgctaaaggt ctaggagcta\n+ 1921 aagaatggaa caactcacta aaaaccaagc tgtcgctact\n+//\n+LOCUS contig7 276 bp DNA linear 21-MAR-2017\n+DEFINITION Genus species strain strain.\n+ACCESSION \n+VERSION\n+KEYWORDS .\n+SOURCE Genus species\n+ ORGANISM Genus species\n+ Unclassified.\n+COMMENT Annotated using prokka 1.12 from\n+ https://github.com/tseemann/prokka.\n+FEATURES Location/Qualifiers\n+ source 1..276\n+ /organism="Genus species"\n+ /mol_type="genomic DNA"\n+ /strain="strain"\n+ORIGIN \n+ 1 tcccaagaag ctgttcagaa tcagaatgag ccgcaacttc gggatgaaaa tgctcacaat\n+ 61 gacaaatctg tccacggagt gcttaatcca acttaccaag ctgggttacg acgcgacgcc\n+ 121 gttcaaccag atattgaagc agaacgcaaa aagagagatg agattgaggc tgggaaaagt\n+ 181 tactgtagcc gacgttttgg cggcgcaacc tgtgacgaca aatctgctca aatttatgcg\n+ 241 cgcttcgata aaaatgattg gcgtatccaa cctgca\n+//\n' |