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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty |
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ConcatPhyl.xml README.rst macros.xml scripts/S01_concatenate.py static/images/adaptsearch_picture_helps.png test-data/Phylogeny_RAxML_BootStrap.txt test-data/Phylogeny_concatenation_fasta_nuc.fasta test-data/RAxML_bestTree.nwk test-data/RAxML_bestTree_test3.nwk test-data/RAxML_bipartitions.nwk test-data/RAxML_bipartitions_test3.nwk test-data/RAxML_bootstrap test-data/input_filter_assemblies/AcAcaud_trinity.fasta test-data/input_filter_assemblies/AmAmphi_trinity.fasta test-data/input_filter_assemblies/ApApomp_trinity.fasta test-data/input_filter_assemblies/PgPgras_trinity.fasta test-data/input_filter_assemblies/PhPhess_trinity.fasta test-data/input_filter_assemblies/ThThelep_trinity.fasta test-data/input_from_CDS_Search/orthogroup_147_sp3_sp3.fasta test-data/input_from_CDS_Search/orthogroup_17_sp3_sp3.fasta test-data/input_from_CDS_Search/orthogroup_183_sp3_sp3.fasta test-data/input_from_CDS_Search/orthogroup_334_sp3_sp3.fasta |
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| diff -r 000000000000 -r b186cae246bd ConcatPhyl.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ConcatPhyl.xml Fri Feb 01 10:27:42 2019 -0500 |
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| b'@@ -0,0 +1,408 @@\n+<tool name="ConcatPhyl" id="concatphyl" version="2.0.2">\n+\n+\t<description>\n+\t\tConcatenation and phylogeny\n+\t</description>\n+\n+\t<macros>\n+\t\t<import>macros.xml</import>\n+\t</macros>\n+\n+\t<requirements>\n+\t\t<expand macro="python_required" />\n+\t\t<requirement type="package" version="8.2.9">raxml</requirement>\n+\t</requirements>\n+\n+ \t<command><![CDATA[\n+ #set $infiles_filter_assemblies = ""\n+ #for $input_filter_assemblie in $input_filter_assemblies\n+ ln -s \'$input_filter_assemblie\' \'$input_filter_assemblie.element_identifier\';\n+ #set $infiles_filter_assemblies = $infiles_filter_assemblies + $input_filter_assemblie.element_identifier + ","\n+ #end for\n+ #set $infiles_filter_assemblies = $infiles_filter_assemblies[:-1]\n+ \n+ #for $input_alignment in $input_alignments\n+ ln -s \'$input_alignment\' \'$input_alignment.element_identifier\';\n+ echo \'$input_alignment.element_identifier\' >> list_files; \n+ #end for \n+\n+ python $__tool_directory__/scripts/S01_concatenate.py \n+\n+ $infiles_filter_assemblies\n+\n+ #if $format.format_run == "nucleic" :\n+ nucleic\n+ #elif $format.format_run == "proteic" :\n+ proteic\n+ #end if\n+\n+ list_files\n+ \n+ > ${output};\n+\n+ raxmlHPC -n galaxy_run\n+ #if $format.format_run == "nucleic" :\n+ ##-q 05_partitions_gene_NUC\n+ -s "03_Concatenation_nuc.phy"\n+ -m $format.base_model\n+ #elif $format.format_run == "proteic" :\n+ ##-q 06_partitions_gene_AA\n+ -s 02_Concatenation_aa.phy\n+ -m $format.base_model$format.aa_search_matrix\n+ #end if\n+\n+ -p $random_seed\n+ \n+ #if $number_of_runs !="" and $number_of_runs_bootstop =="":\n+ -N $number_of_runs\n+ -x $rapid_bootstrap_random_seed\n+ #elif ($number_of_runs !="" and $number_of_runs_bootstop !="") or ($number_of_runs =="" and $number_of_runs_bootstop !=""):\n+ -N $number_of_runs_bootstop\n+ -x $rapid_bootstrap_random_seed\n+ #end if\n+\n+ -f $search_algorithm\n+\n+ >> ${output};\n+ ]]>\n+ \t</command>\n+\n+ \t<inputs>\n+\n+\t\t<param name="input_filter_assemblies" type="data" format="fasta" multiple="true" label="Files from Filter assemblies" />\n+ <param name="input_alignments" type="data" format="fasta" multiple="true" label="Aligned files without indels" help="nucleic or proteic format according to the analysis you want to do below"/>\n+\n+\t\t<conditional name="format">\n+\t\t\t<param name="format_run" type="select" label="Which format do you want to use for this tool (concatenation and RAxML run) ? ">\n+\t\t\t\t<option value="nucleic">Nucleic format</option>\n+\t\t\t\t<option value="proteic">Proteic format</option>\n+\t\t\t</param>\n+\n+\t\t\t<when value="nucleic">\t\t\t\t\n+\t\t \t<param name="base_model" type="select" label="Substitution Model">\n+\t\t \t<option value="GTRCAT">GTRCAT</option>\n+\t\t \t<option value="GTRCATI">GTRCATI</option>\n+\t\t \t<option value="GTRGAMMA" selected="true">GTRGAMMA</option>\n+\t\t \t<option value="GTRGAMMAI">GTRGAMMAI</option>\n+\t\t \t\t</param>\n+\t\t\t</when>\n+\n+\t\t\t<when value="proteic">\t\t\t\n+\t\t \t<param name="base_model" type="select" label="Substitution Model (-m)">\n+\t\t\t\t\t<option value="PROTCAT" selected="true">PROTCAT</option>\n+\t\t\t\t\t<option value="PROTCATI">PROTCATI</option>\n+\t\t\t\t\t<option value="PROTGAMMA">PROTGAMMA</option>\n+\t\t\t \t<option value="PROTGAMMAI">PROTGAMMAI</option>\n+\t\t \t</param>\n+\t\t \t<param name="aa_search_matrix" type="select" label="Matrix">\n+\t\t\t\t\t<option value="DAYHOFF" selected="true">DAYHOFF</option>\n+\t\t\t\t\t<option value="JTT">JTT</option>\n+\t\t\t\t\t<option value="WAG">WAG</option>\n+\t\t\t\t\t<option value="BLOSUM62">BLOSUM62</option>\n+\t\t\t </param>\n+\t\t\t</when>\n+\t\t</conditional>\n+\n+\t\t<param name="random_seed" type="integer" value="1234567890" size="12" label="Random seed use'..b'ML that require some sort of randomization, this option must be specified. Make sure to pass different random number seeds to RAxML and not only 12345.\n+ \n+ - Number of runs (-N) : Specifies the number of alternative runs. \n+ By default it\'s an integer of value 100.\n+\n+ - Use bootstopping criteria for number of runs :\n+ If selected, overxwrites the number of runs to use bootstopping criteria.\n+\n+ - Algorithm to execute (-f) : allows to choose what kind of algorithme RAxML shall execute.\n+ Default : Rapid bootsrap and best ML tree search (-f a).\n+\n+ - Multiple model assignement t oalignment partitions (-q) : an optional parameter. Permits to specify the file name which contains the assignment of models to alignment partitions for multiple models of substitution. For the syntax of this file please consult the manual.\n+ This option allows you to specify the regions of your alignment for which an individual model of nucleotide substitution should be estimated. This will typically be useful to infer trees for long multi-gene alignments.\n+\n+ - Rapid bootstrapping random seed (-x) : Specify an integer number (random seed) and turn on rapid bootstrapping.\n+ In addition to the best tree search.\n+ By default, this option is choosen. \n+\n+--------\n+\n+**Inputs**\n+\n+ - Files from Filter Assemblies : a set of fasta files (one file per species), e.g. the outputs of the first tool of the AdaptSearch suite.\n+ Used to retrieve all the species names.\n+\n+ - Alignment files without indels : a set of fasta files with aligned sequences (with the same species than into the previous parameter), e.g the outputs of the CDS_Search tool of the AdaptSearch suite.\n+\n+--------\n+\n+**Outputs**\n+\n+This tool, produces the following files :\n+\n+ - Phylogeny :\n+ the general output. It gives the information about the concatenation (statistics) and the RAxML run.\n+\n+ - Phylogeny_concatenation_fasta_aa :\n+ contains the sequences concatenated in fasta format when you choose the option proteic.\n+\n+ - Phylogeny_concatenation_phylip_aa :\n+ contains the sequences concatenated in phylip format when you choose the option proteic.\n+\n+ - Phylogeny_concatenation_nexus_aa :\n+ contains the sequences concatenated in nexus format when you choose the option proteic.\n+\n+ - Phylogeny_concatenation_fasta_nuc :\n+ contains the sequences concatenated in fasta format when you choose the option nucleic.\n+\n+ - Phylogeny_concatenation_phylip_nuc :\n+ contains the sequences concatenated in phylip format when you choose the option nucleic.\n+ it\'s this output which is used for the RAxML run.\n+\n+ - Phylogeny_concatenation_nexus_nuc :\n+ contains the sequences concatenated in nexus format when you choose the option nucleic.\n+\n+ - Phylogeny_RAxML_BestTree** :\n+ the output of RAxML run which contains the Best Tree found.\n+\n+ - Phylogeny_RAxML_BiPartitionBranchLabel :\n+ the output of RAxML run which contains the Best Tree found with supported values as branch labels.\n+\n+ - Phylogeny_RAxML_BiPartition :\n+ the output of RAxML run which contains the Best Tree found with supported values.\n+\n+ - Phylogeny_RAxML_BootStrap :\n+ the output of RAxML run which contains all the boostrapped trees. The number of boostraped trees depending of the option -N (number of run).\n+\n+---------\n+\n+**The AdaptSearch Pipeline**\n+\n+.. image:: adaptsearch_picture_helps.png\n+\n+---------\n+\n+Changelog\n+---------\n+\n+**Version 2.0 - 06/07/2017**\n+\n+ - NEW: Replace the zip between tools by Dataset Collection\n+\n+**Version 1.0 - 13/04/2017**\n+\n+ - Add funtional test with planemo\n+ - Planemo test with conda dependencies for raxml and python\n+ - Scripts renamed + symlinks to the directory \'scripts\'\n+\n+ ]]>\n+\n+\t</help>\n+\n+ <citations>\n+ <citation type="doi">10.1093/bioinformatics/btu033</citation>\n+ </citations>\n+\n+</tool>\n' |
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| diff -r 000000000000 -r b186cae246bd README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Fri Feb 01 10:27:42 2019 -0500 |
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| @@ -0,0 +1,14 @@ +Changelog + +**Version 2.0 - 06/07/2017** + + - NEW: Replace the zip between tools by Dataset Collection + + +**Version 1.0 - 13/04/2017** + + - Add funtional test with planemo + + - Planemo test with conda dependencies for raxml and python + + - Scripts renamed + symlinks to the directory 'scripts' |
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| diff -r 000000000000 -r b186cae246bd macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri Feb 01 10:27:42 2019 -0500 |
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| @@ -0,0 +1,32 @@ +<macros> + + <xml name="python_required"> + <requirement type="package" version="2.7">python</requirement> + </xml> + + <token name="@HELP_AUTHORS@"> +.. class:: infomark + +**Authors** Eric Fontanillas created the version 1 of this pipeline. Victor Mataigne developped version 2. + +.. class:: infomark + +**Galaxy integration** Julie Baffard and ABiMS TEAM, Roscoff Marine Station + + | Contact support.abims@sb-roscoff.fr for any questions or concerns about the Galaxy implementation of this tool. + | Credits : Gildas le Corguillé, Misharl Monsoor + +--------------------------------------------------- + + </token> + + <xml name="citations"> + <citations> + <citation type="bibtex">Credits : ABIMS team, Roscoff Marine Station</citation> + <citation type="bibtex">Contact support.abims@sb-roscoff.fr for any questions or concerns about the Galaxy implementation of this tool.</citation> + <citation type="bibtex">Version 1 : Scripts by Eric Fontanillas -- Galaxy integration by Julie Baffard</citation> + <citation type="bibtex">Version 2 : improvments by Victor Mataigne, Gildas le Corguillé, Misharl Monsoor</citation> + </citations> + </xml> + +</macros> |
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| diff -r 000000000000 -r b186cae246bd scripts/S01_concatenate.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/S01_concatenate.py Fri Feb 01 10:27:42 2019 -0500 |
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| b'@@ -0,0 +1,361 @@\n+#!/usr/bin/python\n+## Author: Eric Fontanillas\n+## Last modification: 17/06/2011\n+## Subject: find and remove indels\n+\n+###############################\n+##### DEF 0 : Dico fasta #####\n+###############################\n+def dico(F2):\n+ dicoco = {}\n+ with open(F2, "r") as file:\n+ for name, query in itertools.izip_longest(*[file]*2):\n+ if not name:\n+ break\n+ if name[0] == ">":\n+ fasta_name_query = name[:-1]\n+ Sn = string.split(fasta_name_query, "||")\n+ fasta_name_query = Sn[0]\n+ fasta_seq_query = query[:-1]\n+ dicoco[fasta_name_query]=fasta_seq_query\n+ return dicoco\n+###################################################################################\n+\n+\n+####################\n+###### DEF 11 ######\n+####################\n+## Concatenate sequences\n+###########################\n+def concatenate(L_IN, SPECIES_ID_LIST):\n+ ## 4 ## Process files\n+ ## 4.1 ## Create the bash and the fasta names entries (name of the species)\n+ bash_concat = {}\n+\n+ for species_ID in SPECIES_ID_LIST:\n+ bash_concat[species_ID] = \'\'\n+\n+ ln_concat = 0\n+ nb_locus = 0\n+ pos=1\n+ list_genes_position=[]\n+ ## 4.2 ## Concatenate\n+ for file in L_IN:\n+ nb_locus=nb_locus+1\n+\n+ ## a ## Open alignments \n+ dico_seq = dico(file) ### DEF 0 ### \n+ ## b ## Get alignment length + genes positions for RAxML\n+ key0 = dico_seq.keys()[0]\n+ ln = len(dico_seq[key0])\n+ ln_concat = ln_concat + ln\n+\n+ pos_start = pos\n+ pos_end = pos+ln-1\n+ pos=pos_end+1\n+ position="%d-%d" %(pos_start, pos_end)\n+ RAxML_name = file[:-6]\n+ sublist = [RAxML_name, position]\n+ list_genes_position.append(sublist)\n+\n+ ## c ## Generate "empty" sequence with alignment length * "-"\n+ empty_seq = "-" * ln\n+\n+ ## d ## Concatenate\n+ ## d.1 ## Detect missing species in this alignment\n+ list_ID=[]\n+ list_absent_ID=[]\n+ bash_fastaName={}\n+ for fasta_name in dico_seq:\n+ ID = fasta_name[1:3]\n+ list_ID.append(ID)\n+ seq = dico_seq[fasta_name]\n+ bash_fastaName[ID]=fasta_name\n+ for sp_ID in SPECIES_ID_LIST:\n+ if sp_ID not in list_ID:\n+ list_absent_ID.append(sp_ID)\n+\n+ for ID in SPECIES_ID_LIST:\n+ if ID in list_absent_ID:\n+ bash_concat[ID] = bash_concat[ID] + empty_seq\n+ else:\n+ fasta_name = bash_fastaName[ID]\n+ seq = dico_seq[fasta_name]\n+ bash_concat[ID] = bash_concat[ID] + seq\n+\n+ return(bash_concat, ln_concat, nb_locus, list_genes_position)\n+####################################\n+\n+\n+########################################\n+##### DEF 12 : get codon position #####\n+########################################\n+def get_codon_position(seq_inORF):\n+\n+ ln = len(seq_inORF)\n+\n+ i=0\n+ seq_pos1=""\n+ seq_pos2=""\n+ seq_pos12=""\n+ seq_pos3=""\n+ while i<ln:\n+ pos1 = seq_inORF[i]\n+ pos2 = seq_inORF[i+1]\n+ pos3 = seq_inORF[i+2]\n+\n+ seq_pos1 = seq_pos1 + pos1\n+ seq_pos2 = seq_pos2 + pos2\n+ seq_pos12 = seq_pos12 + pos1 + pos2\n+ seq_pos3 = seq_pos3 + pos3\n+\n+ i = i+3\n+\n+ return(seq_pos1, seq_pos2, seq_pos12, seq_pos3)\n+###############################################################################\n+\n+\n+\n+#######################\n+##### RUN RUN RUN #####\n+#######################\n+import string, os, time, re, sys, itertools\n+\n+list_species = []\n+SPECIES_ID_LIST = []\n+fasta = "^.*fasta$"\n+i=3\n+\n+## Arguments\n+infiles_filter_assemblies = sys.argv[1]\n+format_run = sys.argv[2]\n+\n+## add file to list_species\n+list_species = str.split(infiles_filter_assemblies,",")\n+\n+## in SPECIES_ID_LIST, only the 2 first letters of name of species\n+for name in list_species :\n+ name'..b't[0]\n+ positions=sublist[1]\n+ OUT_PARTITION_gene_NUC.write("DNA,%s=%s\\n"%(name,positions))\n+ OUT_PARTITION_gene_NUC.close()\n+\n+ # c # Mixed partition (codon + gene)\n+ for sublist in list_genes_position:\n+ name = sublist[0]\n+ positions = sublist[1]\n+ S1 = string.split(positions, "-")\n+ pos_start1 = string.atoi(S1[0])\n+ pos_end = string.atoi(S1[1])\n+ pos_start2=pos_start1+1\n+ pos_start3=pos_start2+1\n+ partition1 = "DNA, %s_1=%d-%d\\\\3,%d-%d\\\\3\\n" %(name,pos_start1, pos_end, pos_start2, pos_end)\n+ partition2 = "DNA, %s_2=%d-%d\\\\3\\n" %(name,pos_start3, pos_end)\n+ OUT_PARTITION_gene_PLUS_codon_12_3.write(partition1)\n+ OUT_PARTITION_gene_PLUS_codon_12_3.write(partition2)\n+\n+ OUT_PARTITION_gene_PLUS_codon_12_3.close()\n+\n+\n+ ## Get "ntax" for NEXUS HEADER\n+ nb_taxa = len(bash_concatenation.keys())\n+\n+ print "******************** CONCATENATION ********************\\n"\n+ print "Process nucleotides concatenation:"\n+ print "\\tNumber of taxa aligned = %d" %nb_taxa\n+ print "\\tNumber of loci concatenated = %d\\n" %nb_locus\n+ print "\\tTotal length of the concatenated sequences [All codon positions] = %d" %ln\n+ print "\\t\\tTotal length of the concatenated sequences [Codon positions 1 & 2] = %d" %ln_12\n+ print "\\t\\tTotal length of the concatenated sequences [Codon position 3] = %d" %ln_3\n+\n+\n+ ## Print NEXUS HEADER:\n+ OUT3.write("#NEXUS\\n\\n")\n+ OUT3.write("Begin data;\\n")\n+ OUT3.write("\\tDimensions ntax=%d nchar=%d;\\n" %(nb_taxa, ln))\n+ OUT3.write("\\tFormat datatype=dna gap=-;\\n")\n+ OUT3.write("\\tMatrix\\n")\n+\n+ OUT3_pos12.write("#NEXUS\\n\\n")\n+ OUT3_pos12.write("Begin data;\\n")\n+ OUT3_pos12.write("\\tDimensions ntax=%d nchar=%d;\\n" %(nb_taxa, ln_12))\n+ OUT3_pos12.write("\\tFormat datatype=dna gap=-;\\n")\n+ OUT3_pos12.write("\\tMatrix\\n")\n+\n+ OUT3_pos3.write("#NEXUS\\n\\n")\n+ OUT3_pos3.write("Begin data;\\n")\n+ OUT3_pos3.write("\\tDimensions ntax=%d nchar=%d;\\n" %(nb_taxa, ln_3))\n+ OUT3_pos3.write("\\tFormat datatype=dna gap=-;\\n")\n+ OUT3_pos3.write("\\tMatrix\\n")\n+\n+ ## Print PHYLIP HEADER:\n+ OUT2.write(" %d %d\\n" %(nb_taxa, ln))\n+ OUT2_pos12.write(" %d %d\\n" %(nb_taxa, ln_12))\n+ OUT2_pos3.write(" %d %d\\n" %(nb_taxa, ln_3))\n+\n+ ## Print outputs\n+ for seq_name in bash_concatenation.keys():\n+ seq = bash_concatenation[seq_name]\n+\n+ ## Filtering the sequence in case of remaining "?"\n+ seq = string.replace(seq, "?", "-")\n+\n+ ## Get the differentes codons partitions\n+ seq_pos1, seq_pos2, seq_pos12, seq_pos3 = get_codon_position(seq) ### DEF 12 ###\n+\n+ #print seq FASTA FORMAT\n+ OUT1.write(">%s\\n" %seq_name)\n+ OUT1.write("%s\\n" %seq)\n+ OUT1_pos12.write(">%s\\n" %seq_name)\n+ OUT1_pos12.write("%s\\n" %seq_pos12)\n+ OUT1_pos3.write(">%s\\n" %seq_name)\n+ OUT1_pos3.write("%s\\n" %seq_pos3)\n+\n+ #print seq PHYLIP FORMAT\n+ OUT2.write("%s\\n" %seq_name)\n+ OUT2.write("%s\\n" %seq)\n+ OUT2_pos12.write("%s\\n" %seq_name)\n+ OUT2_pos12.write("%s\\n" %seq_pos12)\n+ OUT2_pos3.write("%s\\n" %seq_name)\n+ OUT2_pos3.write("%s\\n" %seq_pos3)\n+\n+ #print seq NEXUS FORMAT\n+ OUT3.write("%s" %seq_name)\n+ OUT3.write(" %s\\n" %seq)\n+ OUT3_pos12.write("%s" %seq_name)\n+ OUT3_pos12.write(" %s\\n" %seq_pos12)\n+ OUT3_pos3.write("%s" %seq_name)\n+ OUT3_pos3.write(" %s\\n" %seq_pos3)\n+\n+\n+ OUT3.write("\\t;\\n")\n+ OUT3.write("End;\\n")\n+ OUT3_pos12.write("\\t;\\n")\n+ OUT3_pos12.write("End;\\n")\n+ OUT3_pos3.write("\\t;\\n")\n+ OUT3_pos3.write("End;\\n")\n+\n+ OUT1.close()\n+ OUT2.close()\n+ OUT3.close()\n+ OUT1_pos12.close()\n+ OUT2_pos12.close()\n+ OUT3_pos12.close()\n+ OUT1_pos3.close()\n+ OUT2_pos3.close()\n+ OUT3_pos3.close()\n+\n+print "\\n\\n\\n******************** RAxML RUN ********************\\n"\n' |
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| diff -r 000000000000 -r b186cae246bd test-data/Phylogeny_RAxML_BootStrap.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Phylogeny_RAxML_BootStrap.txt Fri Feb 01 10:27:42 2019 -0500 |
| b |
| @@ -0,0 +1,100 @@ +(Ap,(((Pf,Ph),Pg),((Pu,Te),(Am,Th))),Ac); +(Ap,(((Pf,Ph),Pg),((Pu,Te),(Am,Th))),Ac); +(Ap,(((Pf,Ph),Pg),((Pu,Te),(Am,Th))),Ac); +(Ap,((Ph,Pg),(Pf,((Pu,Te),(Am,Th)))),Ac); +(Ap,((Ph,Pg),((Am,Th),(Pf,(Pu,Te)))),Ac); +(Ap,(Pg,(Ph,((Pf,(Pu,Te)),(Am,Th)))),Ac); +(Ap,(Ph,((Pf,((Pu,Te),(Am,Th))),Pg)),Ac); +(Ap,(((Ph,Pf),Pg),((Pu,Te),(Am,Th))),Ac); +(Ap,(((Pu,Te),(Ph,Pf)),(Pg,(Am,Th))),Ac); +(Ap,(Pg,((Ph,Pf),((Am,Th),(Pu,Te)))),Ac); +(Ap,((((Te,Pu),(Th,Am)),Pg),(Pf,Ph)),Ac); +(Ap,(Pg,(((Te,Pu),(Pf,Ph)),(Th,Am))),Ac); +(Ap,((Ph,Pg),(Pf,((Th,Am),(Te,Pu)))),Ac); +(Ap,((Pf,Ph),(Pg,((Th,Am),(Te,Pu)))),Ac); +(Ap,((Pf,Ph),(Pg,((Th,Am),(Te,Pu)))),Ac); +(Ap,((Pf,((Te,Pu),(Th,Am))),(Ph,Pg)),Ac); +(Ap,(((Te,Pu),(Th,Am)),((Pf,Ph),Pg)),Ac); +(Ap,(Pg,(((Pf,(Te,Pu)),(Th,Am)),Ph)),Ac); +(Ap,(Pg,((Pf,((Te,Pu),(Th,Am))),Ph)),Ac); +(Ap,((Pf,Ph),(((Te,Pu),(Th,Am)),Pg)),Ac); +(Ap,((((Am,Th),(Ph,Pf)),(Pu,Te)),Pg),Ac); +(Ap,((Ph,(Pf,((Pu,Te),(Am,Th)))),Pg),Ac); +(Ap,((Pg,((Pu,Te),(Am,Th))),(Ph,Pf)),Ac); +(Ap,(((Ph,Pf),Pg),((Pu,Te),(Am,Th))),Ac); +(Ap,(Pg,(((Pu,Te),(Am,Th)),(Ph,Pf))),Ac); +(Ap,(Pg,(((Pf,(Pu,Te)),(Am,Th)),Ph)),Ac); +(Ap,((Pf,Ph),(Pg,((Pu,Te),(Am,Th)))),Ac); +(Ap,(((Pu,Te),(Am,Th)),((Pf,Ph),Pg)),Ac); +(Ap,(((Pu,Te),(Am,Th)),((Pf,Ph),Pg)),Ac); +(Ap,((Pf,((Pu,Te),(Am,Th))),(Ph,Pg)),Ac); +(Ap,(((((Pu,Te),Pf),(Am,Th)),Ph),Pg),Ac); +(Ap,(((Pu,Te),(Am,Th)),((Pf,Ph),Pg)),Ac); +(Ap,(((((Pu,Te),(Am,Th)),Pf),Ph),Pg),Ac); +(Ap,(((((Pu,Te),(Am,Th)),Pf),Ph),Pg),Ac); +(Ap,(((((Pu,Te),(Am,Th)),Pf),Ph),Pg),Ac); +(Ap,((((Pu,Te),(Am,Th)),(Ph,Pg)),Pf),Ac); +(Ap,(((Pu,Te),(Am,Th)),((Pf,Ph),Pg)),Ac); +(Ap,(Ph,(Pg,(Pf,((Pu,Te),(Am,Th))))),Ac); +(Ap,((Pf,Ph),(Pg,((Pu,Te),(Am,Th)))),Ac); +(Ap,(Pg,(((Pf,(Pu,Te)),(Am,Th)),Ph)),Ac); +(Ap,((Ph,Pg),(((Am,Th),(Pu,Te)),Pf)),Ac); +(Ap,(Pg,(((Am,Th),(Pu,Te)),(Pf,Ph))),Ac); +(Ap,((Pg,((Pf,(Pu,Te)),(Am,Th))),Ph),Ac); +(Ap,(((Pf,(Pu,Te)),(Am,Th)),(Ph,Pg)),Ac); +(Ap,(Ph,(Pg,((Pf,(Pu,Te)),(Am,Th)))),Ac); +(Ap,(Pg,(((Pf,Ph),(Pu,Te)),(Am,Th))),Ac); +(Ap,((Pf,Ph),(Pg,((Pu,Te),(Am,Th)))),Ac); +(Ap,((Pf,((Pu,Te),(Am,Th))),(Ph,Pg)),Ac); +(Ap,((((Pu,Te),(Am,Th)),Pg),(Pf,Ph)),Ac); +(Ap,(((Pu,Te),(Am,Th)),(Pg,(Pf,Ph))),Ac); +(Ap,(((Th,Am),(Pu,Te)),((Ph,Pf),Pg)),Ac); +(Ap,((Pf,((Pu,Te),(Th,Am))),(Ph,Pg)),Ac); +(Ap,(Pg,(((Pu,Te),(Th,Am)),(Pf,Ph))),Ac); +(Ap,((Pf,((Pu,Te),(Th,Am))),(Ph,Pg)),Ac); +(Ap,(Pg,((Pf,((Pu,Te),(Th,Am))),Ph)),Ac); +(Ap,(Pg,((Pf,((Pu,Te),(Th,Am))),Ph)),Ac); +(Ap,((Pg,(Pf,Ph)),((Pu,Te),(Th,Am))),Ac); +(Ap,((Pg,Ph),((Pf,(Pu,Te)),(Th,Am))),Ac); +(Ap,(Pg,(Ph,((Pf,(Pu,Te)),(Th,Am)))),Ac); +(Ap,(((Pu,Te),(Th,Am)),(Pg,(Pf,Ph))),Ac); +(Ap,(Pg,((((Pu,Te),Pf),(Am,Th)),Ph)),Ac); +(Ap,((((Pu,Te),Pf),(Am,Th)),(Ph,Pg)),Ac); +(Ap,((((Pu,Te),(Am,Th)),Pg),(Pf,Ph)),Ac); +(Ap,(((Pu,Te),(Am,Th)),(Pg,(Pf,Ph))),Ac); +(Ap,((Pu,Te),(((Am,Th),Pg),(Pf,Ph))),Ac); +(Ap,((((Am,Th),(Pf,(Pu,Te))),Ph),Pg),Ac); +(Ap,((((Am,Th),(Pu,Te)),(Pf,Ph)),Pg),Ac); +(Ap,(((Am,Th),(Pu,Te)),((Pf,Ph),Pg)),Ac); +(Ap,((Pf,((Am,Th),(Pu,Te))),(Ph,Pg)),Ac); +(Ap,(Pg,(((Am,Th),(Pu,Te)),(Pf,Ph))),Ac); +(Ap,((Ph,Pg),(Pf,((Te,Pu),(Am,Th)))),Ac); +(Ap,((Pf,Ph),(Pg,((Te,Pu),(Am,Th)))),Ac); +(Ap,(Pg,(Ph,((Pf,(Te,Pu)),(Am,Th)))),Ac); +(Ap,((Pf,Ph),(((Te,Pu),(Am,Th)),Pg)),Ac); +(Ap,(((Pf,(Te,Pu)),(Am,Th)),(Pg,Ph)),Ac); +(Ap,(((Te,Pu),(Am,Th)),(Pf,(Pg,Ph))),Ac); +(Ap,((Ph,((Pf,(Te,Pu)),(Am,Th))),Pg),Ac); +(Ap,((Ph,((Pf,(Te,Pu)),(Am,Th))),Pg),Ac); +(Ap,((Ph,((Pf,(Te,Pu)),(Am,Th))),Pg),Ac); +(Ap,((Pf,Ph),((Pg,(Te,Pu)),(Am,Th))),Ac); +(Ap,(((Pu,Te),(Am,Th)),((Pf,Ph),Pg)),Ac); +(Ap,((((Pf,(Pu,Te)),(Am,Th)),Ph),Pg),Ac); +(Ap,(((Am,Th),(Pu,Te)),((Pf,Ph),Pg)),Ac); +(Ap,((Pf,Ph),(Pg,((Am,Th),(Pu,Te)))),Ac); +(Ap,((Pf,((Am,Th),(Pu,Te))),(Ph,Pg)),Ac); +(Ap,(Pg,((Pf,((Am,Th),(Pu,Te))),Ph)),Ac); +(Ap,(((Pu,Te),Pf),(Ph,((Am,Th),Pg))),Ac); +(Ap,(((Pu,Te),(Am,Th)),(Pg,(Pf,Ph))),Ac); +(Ap,(((Pu,Te),(Am,Th)),(Pg,(Pf,Ph))),Ac); +(Ap,(Pg,(Ph,(Pf,((Pu,Te),(Am,Th))))),Ac); +(Ap,((Pu,Te),((Pg,(Am,Th)),(Pf,Ph))),Ac); +(Ap,((Pu,Te),((Am,Th),(Pf,(Pg,Ph)))),Ac); +(Ap,(((Ph,Pf),((Pu,Te),(Am,Th))),Pg),Ac); +(Ap,(((Ph,Pf),((Pu,Te),(Am,Th))),Pg),Ac); +(Ap,(((Ph,Pf),((Pu,Te),(Am,Th))),Pg),Ac); +(Ap,(((Ph,Pf),((Pu,Te),(Am,Th))),Pg),Ac); +(Ap,(((Pu,Te),(Am,Th)),((Pf,Ph),Pg)),Ac); +(Ap,(((Pu,Te),(Am,Th)),((Pf,Ph),Pg)),Ac); +(Ap,(((Pu,Te),(Am,Th)),((Ph,Pg),Pf)),Ac); +(Ap,(((Ph,Pf),((Pu,Te),(Am,Th))),Pg),Ac); |
| b |
| diff -r 000000000000 -r b186cae246bd test-data/Phylogeny_concatenation_fasta_nuc.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Phylogeny_concatenation_fasta_nuc.fasta Fri Feb 01 10:27:42 2019 -0500 |
| b |
| b'@@ -0,0 +1,18 @@\n+>Ac\n+gtacatgggcaagtttttcttcgaatgataaggtgcatatggatcattggcataatacttgggtatcttaaagtatctgttgaccattctgtccagcatccagcactggcgctgtgtgcagaagacatggtgctgcaggtgtgccactctggcacccttcttcttccacagcttctcgtgtcggccgtgcatttcagagcttcctcagcgtactccagaagagtaacaaagctctctttggagccctcgggcagaattccattggggatctccacaatgagcttccgaccaagaagcagcgtttcccagctgacctccaagcaatctgtcagagtgatacggaagcacaaactcgaggcagtctgtgccttcgccaatgtgtttacattttccggcaggccattggcgctgacagggggctcttttaacacccccacaccgttgccctctgtcttttcagacacgttgacggcgtggggctcatcaggagcaccaccgaggcccaggacccaatcgtatacaataccgcgagggcaaaccaaagccataaccgtgcattgttcctgctgctcggttttcaatgacaactccaaacaaaccacgattcacacgcgagtcttccttttctttgccacttgttgtgaacccatattcaaatacttggtttatttgattatgaggaatgccaccaccacggtcagatattcttataatgaaatcaattttgttgttggcaatagtaacagacacaggtggcatattctccagggaattcagatgattttctactgtagctctcattgcattcttcagcatctcatgtataatgtactcaagtggtggtgcaatgtatggaaaggttgcatttacatgaccattgatacgaacatctggccagatcttgttgtatacatgtccttgtcttcaggatttgacatgccatggtcttctttgggtttcactgtctctgtgcttcctggtttgtctacaagtttgactacatccttatcagatgatggagctttgttctctgactgctttgaagaacttggatcagtcttggaaatattttcacctggaagtcttgctggtctccagaactccttggcttgttccttcgtcagaatccaggcttgtttagatatatccagagcctggtctgggatgggtgacgataataagaacaatgaacatattaacctcaaggttacaggacaggatggcagtgttgtacactttaaaatcaagaagaacactcccctgaggaagctgatgaatgcatactgtgacagaacaggtgtcaagagtggagcaatgcgattccgatttgatgggcaaccaatcaatgaaacagacactccaacacagctggacatggaagatggtgatgtgattgatgtattccaacagcagactggaggcgtcgagttgacccacgtaatgcttcacgtctggacacaagggatcccagacaggctgaaccacgacgtgctgcatcgcaaccagcagcacctaccccagcacaaagattacaggctccaccatcatctggaggaagcaatgggccaatttcatctcaggatcaggaaaagactgctctcatcatgcaggtgttacaacgtgctggtgctggtgccgaactatcaggtgatgaatgtggtgatcacgtcgttcgtgttcgtctgcgccgcccacgagatccactcgctgaccgtcaagctgacggactacgccgtgccaaacgactggagaatactgctgaggaacatggtctgctttactgccgttctgatacctgtggccataacacacggtgcatttggcgtatgtctgggaattgagtattctgtggcaatgacctacagaatggtgtcatgtcaaaagcatccacttctgcatcctttaaatgaggatctttatttattgcaggatttggtggataagggtgtgagatgccacttggtaccgaggtgtccttgctcgtggcaccaactgctgtatatgaaggtggtacagtcaaaagaaatgcaacgaataaaccggagctaccagaaaaaccaaaagtttcaagaatggagcaagtttatgaaaacataccgatgtccgaacaaaaacaaggtctgcagagagacgaaagtaatggaaaacgtcaccttccattccagcttcgtggagttgatggcacaacttacgctgacctcgagatcattctggtggcttgggctggcactgatagcagatggtgctcttggtggcggtgctatgcgtgtgcctcctgggggaggtggcagtattcccgtgccatgtccacggctacgctgcttgctggcattgcttgggctaccatgctccctgtttttctttgtagctatatttatcctaatggtttggccctctttgaagccaagatccagcttaggtccagagctaagtaggtctttgttgtccttctgttcttcaagtcttcagtacaacctggtgatcatgttatcccattgtacatccctcagtgtggtgaatgcaaattctgcaaaagtccgaagaccaacctctgctcgaaaatcagagctactcaaggtgcaggtaagatgcctgatggcacaagcaggttctcttgtaatggcaaggagctgtatcacttcatgggctgcagcacattcagtgaatataccgtggttgctgaaatatctgtgtgtaaggttaatccagaagctccactgggcaaggtttgcttacttggctgtggaatatcaactggttatggagctgccttccggaactgtagctgttttcggcttcctgtcgtcgtctggtgcggaagaacgcgcgcctgtccacctggctgtgtgtgcatgttgctgtttatgcatgttcatgtcagtgcttgtgatcggtgagttagaacgagcgagtgagcgggtgcgtgagacatccgacaacatcctgtctggtcgttcactgtgtactgcttttgaatcatttcctaaaggtgaaggtcgtctcgtggctgcttgccctcgttgtgtggagtgcgtgattgaccctgtaatgttgggagccaaacataatgtactgtggcgccacctggtggagaagaatgttgagcgccaagatgatgtacatgaggtgaaaggaagccatcagcaaggcttgaggcctcatcttatgtggccggatcttgaacaactgaatccaaagaaaccgaatgccaattgcttccattccaccaatggcacagctgagcaggaacaagattccactgtgatgtgtaccttctgtccctgtatgtcaatggattttaccaggtcgccatctgtcagtgtctgtttacgttctctggaatatttgggcatgagagtatctttgagagttctatgttcagttccttgttgtctgtcatcaatggcagcaattgtccatggcaatcctaagccaaggaagacattgacagagttggacccagttacatttccaattgagttgtcagcatatttctcctgtgtggcagcctgcttgctggcaaacagatctggcaaacttgttcccagagctacaaatgtgatggcagtgacgctgtccttcaggccaaccaaacaaccgaagatagatgccaagtccccaacaacggcagtaagtagaccaatcatgataagggcaatgaagaaggctaaccagccaccccagatggaaggaggaggcacaagtgcaaaaatgatcttccagccaaaggttaagaagtgcatgatgtctgtcttcactcgactgagatccgtccccaacgctgacgtcacaaatgtccggcccccgcgctgcgggaagaccttcaccattcacttcatgcgaatcctcgaccgccgctcgttcccctccataggcctccactgcctgctgaatgaccgactggacgaaatctctgacctgcacgtggaagcccatttccaactcagacgacatatacatggacagatatctcgct'..b'--------ggcttgtttgcatgcttttcctcaaatttgccattcagaggatttttatgtcggaatatgaagtgtagcttgttgtcattgccacatttgtctggcccgaacataatcgtg------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tattttaacgtgcaccgcctcaatcctgaacctatgtgccattgctatagaccgctactatgctattcacgacccaatacgctatgctcagaagcgaacgctcaagcgcgtgctgatcagtattttgttggtttggctggtcagtatcctgatctcagtgccgcctctgattggttggaacaacagcggcggcagttccctgtacaacgtcatctacagctcttctggatccttcttcatccctctcttcatcatgacctttgtgtacttcaacattttccgtgcaaccagaaaacggctccgagcacgcgccaaagcagcggc------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------cacggagaagccgtgtggattgggtcgatagtcacagtggaagatctcgatgatctccccgcgtcgcttgccgccctcccacacattgccgaggctctgcatgtagtcccgggaaatgtccgggtagttatccaacagcaccaggttgttggcccgcaccatccgcctcagatggaagtagtcagacagactctcacggaaggtgtgtccaccgtcaatgaccacaatgtcacaacggaactccttgttggcctcacggacgcgggg\n' |
| b |
| diff -r 000000000000 -r b186cae246bd test-data/RAxML_bestTree.nwk --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/RAxML_bestTree.nwk Fri Feb 01 10:27:42 2019 -0500 |
| b |
| @@ -0,0 +1,1 @@ +((Th:0.14924410568595378179,(Pg:0.09556296125671981390,Am:0.18536781449475758787):0.03651339268974715391):0.09478352424348672478,(Ap:0.01138298824199455994,Ph:0.14438335285430420329):0.01626011361346790460,Ac:0.01818704284736943205):0.0; |
| b |
| diff -r 000000000000 -r b186cae246bd test-data/RAxML_bestTree_test3.nwk --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/RAxML_bestTree_test3.nwk Fri Feb 01 10:27:42 2019 -0500 |
| b |
| @@ -0,0 +1,1 @@ +((Th:0.14927144427385935499,(Am:0.18539294342267700899,Pg:0.09554925527172976329):0.03654579746795907913):0.09478496426471696990,(Ap:0.01138646621287440173,Ph:0.14439022038764615097):0.01625809813917244995,Ac:0.01818713970915995445):0.0; |
| b |
| diff -r 000000000000 -r b186cae246bd test-data/RAxML_bipartitions.nwk --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/RAxML_bipartitions.nwk Fri Feb 01 10:27:42 2019 -0500 |
| b |
| @@ -0,0 +1,1 @@ +(Ph:0.14438335285430420329,(Ac:0.01818704284736943205,(Th:0.14924410568595378179,(Pg:0.09556296125671981390,Am:0.18536781449475758787)75:0.03651339268974715391)98:0.09478352424348672478)86:0.01626011361346790460,Ap:0.01138298824199455994); |
| b |
| diff -r 000000000000 -r b186cae246bd test-data/RAxML_bipartitions_test3.nwk --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/RAxML_bipartitions_test3.nwk Fri Feb 01 10:27:42 2019 -0500 |
| b |
| @@ -0,0 +1,1 @@ +(Ph:0.14439022038764615097,(Ac:0.01818713970915995445,(Th:0.14927144427385935499,(Am:0.18539294342267700899,Pg:0.09554925527172976329)78:0.03654579746795907913)99:0.09478496426471696990)86:0.01625809813917244995,Ap:0.01138646621287440173); |
| b |
| diff -r 000000000000 -r b186cae246bd test-data/RAxML_bootstrap --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/RAxML_bootstrap Fri Feb 01 10:27:42 2019 -0500 |
| b |
| @@ -0,0 +1,100 @@ +(((Pg,Am),Th),(Ph,Ap),Ac); +(((Pg,Am),Th),(Ph,Ap),Ac); +((Am,(Th,Pg)),(Ph,Ap),Ac); +((Th,(Pg,Am)),(Ph,Ap),Ac); +((Th,(Pg,Am)),(Ph,Ap),Ac); +(Ph,(Ap,(Am,(Th,Pg))),Ac); +((Th,(Pg,Am)),(Ph,Ap),Ac); +((Th,(Pg,Am)),(Ph,Ap),Ac); +((Th,(Pg,Am)),(Ph,Ap),Ac); +(Ph,(Ap,(Th,(Pg,Am))),Ac); +((Ap,Ph),(Am,(Pg,Th)),Ac); +((Ap,Ph),(Th,(Am,Pg)),Ac); +((Ap,Ph),(Th,(Am,Pg)),Ac); +((Ap,Ph),(Th,(Am,Pg)),Ac); +((Ap,Ph),(Th,(Am,Pg)),Ac); +((Ap,Ph),(Am,(Pg,Th)),Ac); +((Ap,Ph),(Th,(Am,Pg)),Ac); +((Ap,Ph),(Th,(Am,Pg)),Ac); +(((Th,Ap),Ph),(Am,Pg),Ac); +(Ap,(((Am,Pg),Th),Ph),Ac); +((Ap,Ph),(Th,(Am,Pg)),Ac); +((Ap,Ph),(Th,(Am,Pg)),Ac); +((Ap,Ph),(Th,(Am,Pg)),Ac); +((Ap,Ph),(Th,(Am,Pg)),Ac); +((Ap,Ph),(Th,(Am,Pg)),Ac); +((Ap,Ph),(Th,(Am,Pg)),Ac); +((Ap,Ph),(Th,(Am,Pg)),Ac); +((Ap,Ph),(Th,(Am,Pg)),Ac); +(Ph,((Th,(Am,Pg)),Ap),Ac); +((Th,(Am,Pg)),(Ap,Ph),Ac); +((Th,(Am,Pg)),(Ph,Ap),Ac); +(Ph,(Ap,(Th,(Am,Pg))),Ac); +(Ph,(Ap,(Th,(Am,Pg))),Ac); +((Th,(Am,Pg)),(Ph,Ap),Ac); +((Am,(Pg,Th)),(Ph,Ap),Ac); +((Th,(Am,Pg)),(Ph,Ap),Ac); +((Th,(Am,Pg)),(Ph,Ap),Ac); +((Th,(Am,Pg)),(Ph,Ap),Ac); +((Am,(Pg,Th)),(Ph,Ap),Ac); +((Am,(Pg,Th)),(Ph,Ap),Ac); +((Am,(Th,Pg)),(Ap,Ph),Ac); +((Am,(Th,Pg)),(Ap,Ph),Ac); +((Th,(Pg,Am)),(Ap,Ph),Ac); +((Th,(Pg,Am)),(Ap,Ph),Ac); +((Th,(Pg,Am)),(Ap,Ph),Ac); +(Ph,((Th,(Pg,Am)),Ap),Ac); +((Am,(Th,Pg)),(Ap,Ph),Ac); +((Th,(Pg,Am)),(Ap,Ph),Ac); +((Th,(Pg,Am)),(Ap,Ph),Ac); +(Ph,((Am,(Th,Pg)),Ap),Ac); +((Ap,Ph),((Am,Pg),Th),Ac); +((Ap,Ph),((Am,Pg),Th),Ac); +((Ap,Ph),((Am,Pg),Th),Ac); +((Ap,Ph),(Am,(Pg,Th)),Ac); +((Ap,Ph),((Am,Pg),Th),Ac); +((Ap,Ph),((Am,Pg),Th),Ac); +((Ap,Ph),((Am,Pg),Th),Ac); +((Ap,Ph),((Am,Pg),Th),Ac); +((Ap,Ph),((Am,Pg),Th),Ac); +((Ap,Ph),((Am,Pg),Th),Ac); +((Ph,Ap),((Am,Pg),Th),Ac); +((Ph,Ap),((Am,Pg),Th),Ac); +((Ph,Ap),((Am,Pg),Th),Ac); +((Ph,Ap),((Am,Pg),Th),Ac); +((Ph,Ap),((Am,Pg),Th),Ac); +((Ph,Ap),((Am,Pg),Th),Ac); +((Ph,Ap),(Am,(Pg,Th)),Ac); +((Ph,Ap),(Am,(Pg,Th)),Ac); +((Ph,Ap),(Am,(Pg,Th)),Ac); +((Ph,Ap),(Th,(Am,Pg)),Ac); +((Ap,(Th,(Pg,Am))),Ph,Ac); +((Th,(Pg,Am)),(Ph,Ap),Ac); +((Pg,Am),(Th,(Ap,Ph)),Ac); +(Ap,(Ph,(Th,(Pg,Am))),Ac); +((Ap,((Th,Pg),Am)),Ph,Ac); +(((Th,Pg),Am),(Ph,Ap),Ac); +(((Th,Pg),Am),(Ph,Ap),Ac); +(((Th,Pg),Am),(Ph,Ap),Ac); +(((Th,Pg),Am),(Ph,Ap),Ac); +((Th,(Pg,Am)),(Ph,Ap),Ac); +(((Pg,Am),Th),(Ap,Ph),Ac); +(((Pg,Am),Th),(Ap,Ph),Ac); +((Am,(Th,Pg)),(Ap,Ph),Ac); +(Ph,((Th,(Pg,Am)),Ap),Ac); +(Ph,((Th,(Pg,Am)),Ap),Ac); +((Th,(Pg,Am)),(Ap,Ph),Ac); +((Am,(Th,Pg)),(Ap,Ph),Ac); +((Am,(Th,Pg)),(Ap,Ph),Ac); +((Am,(Th,Pg)),(Ap,Ph),Ac); +((Th,(Pg,Am)),(Ap,Ph),Ac); +((Ph,Ap),((Am,Pg),Th),Ac); +((Ph,Ap),((Am,Pg),Th),Ac); +((Ph,Ap),((Am,Pg),Th),Ac); +((Ph,Ap),((Am,Pg),Th),Ac); +((Ph,Ap),((Am,Pg),Th),Ac); +((Ph,Ap),((Am,Pg),Th),Ac); +((Ph,Ap),((Am,Pg),Th),Ac); +((Ph,Ap),((Am,Pg),Th),Ac); +((Ph,Ap),(Am,(Pg,Th)),Ac); +((Ph,Ap),(Th,(Am,Pg)),Ac); |
| b |
| diff -r 000000000000 -r b186cae246bd test-data/input_filter_assemblies/AcAcaud_trinity.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input_filter_assemblies/AcAcaud_trinity.fasta Fri Feb 01 10:27:42 2019 -0500 |
| b |
| b'@@ -0,0 +1,15294 @@\n+>Ac1_1/1_1.000_629\n+CCACCACTGGCACAAAGGATTATCAAGGCTCATGACAAAGGTATAAATAAGACATTTTATGGCCAGCTGGTCGGTCGATGTGCTAAGGAGTTGTCTCTGGTGCAGATTAAACTGCTGCCAGAAAAGGTCAGAGAACCAGTCTTAAAGAGATACAAGATCTATGAGGAGAGAAAAAAGCTGGAAAAAATGACACCAGAAGAAAAAGAAGAATACATGAGAAAGAAGAAGGAGGAATACAGAAAGAAGTTAAATGAGATGCTGAAGAACCGAAGACTTGAAAAACACAAACGTTTTGAAGACACCGATTTGGAACTGAAGCCCATTCCAACTCCACGCCTTGTGGAAACTCCTGATGGTCTGGCAAATGAATTGTTTGGTTATGTTGCTATGGTGACTGAATTCATTAGCTGCTACAAAGACCTCTTCACGCCAAAGGATGACAGCACTGTAATCAATGTGACCACAGATGCCCTGATGACCAGCTTAGTGTCTGATGGTAGGCAGTCTGGACCAGTAGCTAACATCCTGACAACATTGCTGCAGACTTTGTTACAGGATGGCATCACAGAGGATTACACAGAGCTCGGTTTGAAGATGTCTGAAATCCCAGTCAACCAGTACACAGCCAG\n+>Ac2_1/1_1.000_896\n+ATGTTAGTAAAAGAGATTAAAGAGTACCGAGAGATAAAAGAGAAGGCTAGAACCTATCTATGTTATATTATAAGTAGTAACCTATCTTATGGTTCAAGCATAAATGAGGAGACTCTTCAAGAGAGTATGGAGATGTTAAAGAGGGCAATCCCAAAGAGTGAGGTCATCTATGTTTTAGATAGCGAAGGGATGCAGATAACAGATAACATATCACAATTCTCTAATCTACATGGTATAAATAAGGGTAAAGATAGGAGTAATCGTTCTTACTACTATAATACAAAAGCACAACATCGTTGTGAAATATCCGACCCTTATCCATCAATAGCGAGTAAACATCTGATTGTTACATCTAGTTTTCCTATTTATGATGAGTTTGATAATCTTCTATACATTATATGTGTAGAGCTTAGTTTGCAAAATATCCTAAGAGTGGTACACCCAAGCTCTGTGGACTCTATGTTTGGAAATGGTAGTAAGGTTGTTTATACAATATTCTCTTTAGCTCTATTTTTTGTGGCTATGCTTCTTTTTGTAAAGGGAATTACAAGTTTTGTGGGGTATGGAATAGATTTCCATAAAGTAGAGATAAATGATATGTTTAAATCGACAATTCTACTTACTCTATCTTTGGCTATTGTTGATTTGGTAAAAGCGATATTTGAAGAGGAGGTTTTAGGAAAAGAGAAGAAGCATGGAGACGGGGATACCCATCAAACTATGGTTAGATTTTTGGGTTCGATTATTATTGCCCTATCTATTGAGGCTTTGATGTTGGTATTTAAATTTGCACTAAATGACCCAAGTCAACTACTCTATGCTGTATATATTATGTTTGGTGTAACAGCTCTGCTTCTTGGTTTATCATACTATCTAAAAGTGAGCCATGATAGTTG\n+>Ac3_1/1_1.000_252\n+ATCTGTAATGTCGTTTACCACACACTGGACACTGATATTTCCGCTCGCCAGTGTGTGGTAAACGATATTACAGATCAGATGTGCTGGCAATCCATATCAGTACACACAGCAGTGAAAAAAATCATAAATGTGACATCTGTGGCAAGGCTTTCTCAAATGCTAGTTATGTCCACGTGCACAAGAAGATGCACAGCAGTGAAAAAGCACACTTGTGTGTTCAGTGTGGGGAGAGGTTTACAAGAGCACAATCAC\n+>Ac4_1/1_1.000_165\n+AAACAATGCAATCCTCTACCATTGCCAAGATATGAAGAACAAGTAAATGGCACATCAACAACAATGATAATAATAAGTGCTAATAACAATAAGAGTAATACAATTACCACAATATCTGAGAACAAGGGGCTTAAGCATAGCTATCATTATTTGGGAGGGGAGGAT\n+>Ac5_1/1_1.000_447\n+GCACCGGGATGCGGATTTGCTGACGATATGGCAAAAGCATTGTCAGCGTGCGGAACCTGTTTATGTCACACCACTGGCATCTTCCTGGCCGTCGCAGCCTTCGTTCTGACGGCACTCGGTATTGTCTGCGTCACGCGATCAGCTGACCCGAGCCTTTGGTACAAACTCGGTCTGGGAGCCTTCGCAGTGGCCGGCCTGTTCGCGCTACTTCTCACATGTTACGCCTGCTTCACGATTCACCGAGGTTGGAAGCTGTTCGGGTGCTGTGGCGACTGGACACAAGGGAAGCTTACCGAAAGACAGGCCCCCGTCAACTTGTATGCCACTCGTATCAACCCCAGAACAGATCCAAGGTTAGCTTCTAGACAGACTTCAAAGACCGACTCAGTGCCGGATCGAGGGACGGAAACGAGCGCCAGTCTACCTTCTAATGTTATTGGAATGGTG\n+>Ac6_1/1_1.000_393\n+CAGCCTACCACTGAGAAGAGATACTTCAACATGTCTTACTGGGGTAGAAGTGGTGGTCGTACAGCGGGTGGTAATGCAGGACGTGGTCGTGGCGGCGGCAGCGGCAGTGGCAGTAGTCAAAGTGGTGGTGGCAGCTTTCTACAGGAACGTATCAAAGAGATGAGTGCCCAAGAAAAACTCATTGAGCAGAAGAAAAAGGAAATAGAAGCTAAGCTCCTTGAACAAAAACAGAAGGAACAAGAAAAGGTTCTCTCAAAACTTCAGTCAAAAGCAACTGCTAAGACATCACTTACAAAGATTGGAAAAAGACCTGGTTATGGACGAGGTGGCATATTTAGTACCAAACGTGTGAAGCAAGAGGAGCCAGATGCTGAAACTGACACAACTCCACAG\n+>Ac7_1/1_1.000_614\n+GCACCTAGAATTACCCGAAGTTGCTTGGCAATAGCGACACCTAACGGTCGCCATGATATTTGCAGGAAGAAGGCATGTGGTACCATTGGGAACCGTCAAGCGTTTCCTCAGCCCTGTGGCAGCTGCCCGTCTGCGCCCGTGTTTGACCTTGAGCACCAAGTCACGACCTCTGTGTCCGTGTGGGTGTGCGCCCGCGCGCGCGCTGCCAGGCTCGGTTCAGACACGTTAAGGCACCTTCGTTCCGGTGGCGTTGGAATGGACGCGTTGGTGAGGCACTGGGACACGACCGTGAATCAAACTGGACGGAACCCGGTCTGGCACGCGCCGACACACGCACACACACCGATAGCAGCCGACACGCCGTGGTCCTTGGCTCCGGATTACAACACCCGGCACGGCATCCTCGGAACGGCGTCTCGGCGAAATGGAGAAACGATCCAAGTCAAGTCTTCGTCTACTGATTTGTCTACGGCGACAATGTACAACGGATGGCTGGGATATGTGTACCGCTGTCAAACCGGTCGCAGACGCAGGGGCCGTGCCCAGGACACGAACAGAGACACATTACAGTCACACCTGTCTGGGCCGACCACCCAAACAGTCCCATCGTCCAC\n+>Ac8_1/1_1.000_332\n+ATCAAAGAAGAGCAACATCGAGCTACTGGCACTGGCAATGGAATCCTAATTATAGCAGAAACAAGCACTGGTTGCCTGTTGTCTGGGTCAGCAATTGGTAGTAGAGGTGTTCCTGCTGAAGAAGTTGGGGTCAAAGCAGGACAGATGCTTTTGGATAACTTAGGTCATGGTGGCTGTGTTGATGACTATTTACAAGACCAGCTTATTGTACTGATGGCCTTAGCTAAGGGCACATCACGAGTCAGATGTGGGCCAGTCACATTACACACACAAACGGCCATCGAAGTTGTCAAGATGTTAGCAGAGGTGAATTTCACCATAACACAAGTATC\n+>Ac9_1/1_1.000_303\n+GCCATTCGTCTTAGGAGAAGTTTGTCGTCAGGAAAGATACATGAGGCCTGGATT'..b'CTCTGAAGTGTCTGAAACAAAAGAGCCTCCTGTTACTAAGGCTCCTCCCCCACCATACACCATCATACAAGAACCACCTGAAGGACATCCAGACTACTTAGTGGCTGAGATGCATTTGCCCAAAGTGAAGTCAGTGGATTCTGT\n+>Ac7635_1/1_1.000_231\n+AATAAAGTTGATCAGTTGATGCCAATACATGACCCTGACCCCCTTATATCCTGTGATCTCATGGATGGTCGTGATGCTTTCTTGACCATGGCTCGTGAGAAGCACTACGAGTTTTCATCATTGAGGAGAGCCAAATTCTCATCAATGGCTCTGCTGTATGAACTGCATAACCAGGGCAAAGATGCATTTGTTTATACATGTAATAGTTGCAAAGCACATGTTGAAACCAGA\n+>Ac7636_1/1_1.000_213\n+GCAATGGAGGGAAAGGACAAACTCTTGCGAACAGTAAGTGGTGTAGAAATTGAAGAACCCCATGCCAAGTTAACCATTGTAGGTGTGGGACAGGTGGGAATGGCTGCAGCTTTTTCAGTTGTCACCCAAGGCCTGGCAGCAGAGTTGGCTCTAGTTGATGTCATGGCGGACAAGTTGAAAGGGGAGATGATGGATCTTCAGCATGGCATAGCC\n+>Ac7637_1/1_1.000_113\n+ACTAGAAGCGACATTAATGAATGCTCCCTTCAGTGTTTACATTTCCTTACTCTAACTAATAAAGATGATAGCAAAGTTCTAAAAAGACAACGAACGAACATGGCATTATGTAA\n+>Ac7638_1/1_1.000_221\n+ACGTACGAATATGTATGCGTGCGTGTGTTAACCACGCTTCGCTGTACACCTTACTGTACACCTTACTGTACACCTCACAGGTCGGATTTATCCGGTAACGCGTACAGAGAAACAAAAGCCGACGTACGTCACGCTGAGCTAACCAGATGTAAAATTATACATTTGGCAATATTCTTTGCCTGTCATCAGTCACGATACATCGCCTTTAATCACGTCAACGA\n+>Ac7639_1/1_1.000_168\n+ACACGCATGAGAATACATTTTAAAAACTTCTACAGACGTCAAAGTAACTGTCAGACGTCAAACTTCTCCAAGCACAAATTAAAGCCATGCTCCTCGTACTCTGTCTTGGTGATAACCTGTTTGTCGAAGTCTTCGCTCTCTGCAAACATCACTCCTCCTTGCCAGGGG\n+>Ac7640_1/1_1.000_174\n+AATGAAAGTGAACACATTTGCAAAGAACATGATTCAAACATTAAAAACTATCTCATATCCTTAGAAGTCAACAAGCATCAATCACGTTACATGAACACTTTTATGGTGTGTGAGGGAGGCACTAAGTGCTCATTGAACAAGTTCATGCAATTTTATATTGAACAGTTACACTGC\n+>Ac7641_1/1_1.000_294\n+GTTGAGGGTGAGAATGAAGCCTGGTACTACAGCACAAAGGTACAAATTGATGAGCTGCTGGAGTGTCTGGATCAGAGCAAGTGGGAAAGTGAGCTGGTTAGAACAATCAGGGAAATGAGAAGTGAGATTGAGAAACACATGGACATTACAGAAAAACTAACCAATGAACAGAAAGGAAACAAGAAATCAGCACTTGAACTAGAAGTTGCTGAAATCAAGAAACGTCAAGTGGAGAGAACTGAGAGAAAGAAGAGGGAGGAGGAAGAGAGAAAACAGAGGGAGATTGAGATGAAA\n+>Ac7642_1/1_1.000_201\n+ACTGCAACTGGTAAATACACGTTCTGCCTGCAAATTCATATTAGATTTTACTCGCTAGCAATTGCTAAACGCTGGCATGACGTTTTCATTCGCATGTTTTACATAATAAAACCGTACACAAGCGGAGACCTACAATATAAAATTACTGTACTCGGCGCAGGTAATTTCCGAGAGAAATTCACTTCTGAAATCCAATTGATG\n+>Ac7643_1/1_1.000_382\n+TTTTCACCATCACTGTCTTGGTGGCTAGCTCACTGGTGGCCAGACTATGTCCCTGACTCTCTTCTGGAGAGCTGTCTGTCTTTCCTGGTTGCCAACCCCTCAATATTCCTTGACTTTGATGCAGACTCTGAGGTGTACACACTGAAGCCTGAAGTGACCCTGCCTTCGGACATCTGGGAGAAATTGCTAACAAAATGGGGGGAGTGCAGCATTGTGGACAAGAAGTTCCTGCACATATTCAAGGACACGCAGCGGACCAAGCTGAAACGGCTCAACCTGGCAGAGACAGATGTCAGCGATGATGCCCTTGAGTGTCTGATGGCTCATAAACCAAGGGAAGTCAACCTGTATCAGTGTGAGGAGTTGACAGGTGAGGCACTTG\n+>Ac7644_1/1_1.000_253\n+AAAGATTTGCCTGTTTCGCCCGATGCAAGCCATGTGTCATCACAGCAGACGTCTGATGAAATGGATCTTATTATGATACAAAAACAATTTAAAGAAGGAAAACTGACTATGGATGAGGTTGAAGCAGAGTTCCAGAAATGGAAGAAGAAACATTTCAGTCATGAAGAAAAGTCATTTAAATCTAAACAGGTCGTTCTTAAAACAATTAACCAGAAGCTCAGTGAGCTAAGAAGCAAAACAAAGAAGCAAAAGA\n+>Ac7645_1/1_1.000_327\n+GATACAATGTCGGAAAGCGACCTGCCAGTCGAGTCGTGGAATGAGACTAAAGATGGGCCGTTATCTGTTGAAAACATGAAGAAGAAACTGAGACTACAAGGCTATGACTTCACTCAATATGAATTTGCACCTGGCACGGTTTTCCCAGATCACAGCCATGGGATAACGAAAAAGGACGCCATCGCTTCAGGACATTTTCGTTTTTCTATGTTGAACAAAGAGGTTATTATGAAGCCCGGTGACATGCTTGAGGTGCCCAAAGGAGTTGTACACAACGCTGCTGTAGTCGGCAATGAGCCTGTGATCTTTTTTGACAGTACTAAACAT\n+>Ac7646_1/1_1.000_313\n+AGCCCGGCCACCGGCCAGTTCGCGGCCAGGTGGATGCGGAACTCGGATGGCCGAGTCGTCCCGCGCCTTGAACTGCTGAAGACTCTCGATCGCGAGGAGGTCACGACTTTTGACTTGACCGTCACGGCCACCGACGGCGGATCACCACCCAAATCGGCCATCTTGTTGGTTCACGTTGACGTCCTGGATGCGAACGACAACATACCAGTGTTCAAGGAACCGACGTACGAGGTGCGGATCCAGGAGGATCACGGCACTGGGTCGAGGCTTATTACTCTCAAAGCCGAGGACCAGGACTCGGGCAGCAACGGAC\n+>Ac7647_1/1_1.000_639\n+AAACTAGCTCAAGACCTTGGAAGCAATGCTGCTTTCAGTCCAATGGATGTGACATCTGAAGAAGATGTAATGAAAGCTATGGAGCTTGCTAAGAAGCAGTTTGGTGGTTTACATGTTGCTGTCAATTGTGCTGGTGTTGGTGTTGCTGTTGTTACGTATAATGCAGGAAAGAACAGAGTACACAAATTGGAAGAATTCCAGAGAGTTATAAATGTGAACCTGGTTGGAACATTTAATGTGATCCGTCTGGCAGCTCAGCTCATGAATGAGAATGAGCCAAATGCTGATGGTCAGAGGGGTGTCATAGTCAACACAGCAAGTGTGGCAGCCTTTGATGGTCAACGTGGCCAGGCTGCTTACTCAGCAAGTAAAGGTGGAATTGTTGGCATGACACTACCAGTAGCAAGAGACCTGGCTCACATTGGCATCAGAGTTAATACCATAGCTCCAGGTCTTTTTGATACGCCATTGCTTGGAGAGCTACCAGAGAAAGTACGCAAATTCCTTGCCACCAGTGTGCCATTTCCACAAAAGCTAGGTGTTCCTGATGAGTTTGCTCATCTTGTACAGTTCATTGTTGAGAATCCAATGATGAATGGTGAGGTGGTCAGATTGGATGGTGGCATCAGGATGCAGCCA\n' |
| b |
| diff -r 000000000000 -r b186cae246bd test-data/input_filter_assemblies/AmAmphi_trinity.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input_filter_assemblies/AmAmphi_trinity.fasta Fri Feb 01 10:27:42 2019 -0500 |
| b |
| b'@@ -0,0 +1,16208 @@\n+>Am1_1/1_1.000_262\n+GAAGAAGTATTAGATAGACTTTCTGCAGAGGAAATTAAACACATCTTACTGAACCAACTGAGAAACCAGGATTCAAAACCAGTTGTTGCACTTGGTATCCTGTTCCCCCGCGTGTCATATCCATATCTAGGTGAACAGCATTGCGTCAGATGTCACATGACATTCAATTCGAGATCTCAGACGCCATGTTTATTACGTCATCCAACCAAAGCAGTGTCAAAGTTTAAACAAAGTCCCACAGGAGCACATTTTCACTGTCGTG\n+>Am2_1/1_1.000_279\n+CTGAAATGGAAGAAGGAAGTAAAGCAGGCAGTGCAAAAGTATTGGTTACAGGAACTGAAAAATGAGGCCAGATATAAAACGACATTGGCATACCTAGATGTAAGCGATTGCCAACCAGGCCTGATGCATAATGTCTGGAGGAGAACACCACTCAACAAGGCAGCTGTACTGCAGGCTAACATCAGAGCACAATTACTTGTAGGTCGATATCCACTGCAGGACCAAGCAAATAAGTTTAATAAAACCAACCATAAGTGCCCAATATGCAAGGTAAATGAC\n+>Am3_1/1_1.000_150\n+TTATCATATATTCTGATCAATACAATTCATTTATTGTCAAGTAGAAAGTTCAACAAGCCTCAAGATGTTGACTCTTTTATGACTATTTTATCTTATTTGTTTTATCTCAGGATAATGAACATGTGTGCTTTCAAAGAATCACCTTTCATT\n+>Am4_1/1_1.000_144\n+ACAGTTCTAAATAGCATTCGCCAAATGATATTGAAAGCATATTTTATGAATAGTGGTTCACAGATGAAAGATCATTATTGGGAACCCGTTCCAGCTTTTGTAGATCATTTTGTTCTTGCTATAGATCATCGACCCAGAATACAA\n+>Am5_1/1_1.000_224\n+TACTGCTGTCGAAGTGATGGCGCTTGGAACAGTGTGATAACCTTGCCTACAAATAGGCCATTCTATTTGCTCAGATACACAAGTCAATGTCAGCTGGTGAAAGGAATGAAAGTCAGAAGGGAAGTATTCTACTGGGATAATGAAGATATTAACAATATTGATTACACTACAGGATATCACCCGTATGAAGATGGAGGCAGATACAACCATAAACTACATTATTG\n+>Am6_1/1_1.000_361\n+ACCACACAATCATCTAGTGAAACATTTACCAAAACACCCTCTGAAACTGTTCGGTCAGAAGAAGACAGTGCTAAAAAGCAGAAAACTTTCATCAAAAGCCCACAGGCAGTTGCTGTATCTGAAGAATCTACAAAAACAAATTTAACTTTTGTTGCTAAATCATCCGACGTTAACAGCAACTCTCCATTATCTACAGTACACCAGGCATCAGGATCAGGAGAAACATTTACCAAAACACCTGTAGAAACTGACCATACGGAACAACCTTCTGGTCAACCAGAACATAAACAGGCCTCCACTGACCTTGTTCCTCCAGAAAGCACCAAAGAACCGCTGATCCATTCTGGTAATGTGCTGGGTT\n+>Am7_1/1_1.000_325\n+GGGGCCCGGGATGTCGAGGATGTTGTACTCGTAGTTGCTGTGGTTGACGTGGTATTGTTGTTCCTGGCTGTGGCTCCGTTACCACTTGACGTGGCTGTTGTGGTGCTGGTGGAAAAACGACTAGTGGTTGTGTCTGCAACTAATTCCTCGCCTCTAATCAGAATTAATGGACTGTCTGCAATACGAATTCCACGCAGGCTTTTGTCCAATTTGGCAGATTTTTCCTTGCTGGTTATTTTAGGTTCAGTTTTGGTCAAATCCAGTCTGTCACTGATCACACCATACGCCAATCTGCATACTCTCCCATCCTCCAGATCGGAAGAGC\n+>Am8_1/1_1.000_144\n+GTATTAATAAAAGGACAAGACTATTATTTAATACCAAGAAATCTGGCCTTAATAAGCATGGTTGCTTATATCATAAGCATGGTAAATCACATTGTGTTTTCCATGTGTTTACCCATCAGATGTAAAAATATTCTGCATGAAATA\n+>Am9_1/1_1.000_242\n+AGCCATCAAAGGTTGCTAATCATGTTGAGTTGTATTGTCAAGCATTTCTACTCGAGGCAACCATTAATAATTGAAGTTATCAGTTATATTGTCAACTCAATGGAAAATCAAATGGATTTAATTAAGGAAGGAAGATTTTGTACTTGTAAATCTGCATTTTATTACAAAATGTGTAATAAAATTACAATTCTCAAATGGATTCATATATATGCAAATAAAGGATTTATGGTTGGTTTGAAGAG\n+>Am10_1/1_1.000_318\n+AGCAACTTTGCCACCACCACCACCACCAACAATAACAACAACAGCTGCAACACCGCGACCAATAACAACAACAACACTGGTAACACTAACCACGTCACCACCAGAAATAACATCTTCACAACCATCACCAACACTACCATTAACTCAACTTATAACAATAACAACACCTCAAGTGTTGCTACCTACATCACTCAAAACAATTACAACAACATCAGAATCGCCTTCGACACATACACAAGCAACAATTTCAACAACTTTTGTGCCACAAATATCTGCCACAACAGTCCATTCAGCTCCCCCTACCTCACCACTCACTAC\n+>Am11_1/1_1.000_207\n+ATTTTTTGTAGATATTTTTATCTATTTACATTTCTATCTTTATTTCTCCCTACGACCGAAGGCCTCAAAGAGCATATGATTTATTTCTGTCCATTTATCGACCGTGCGTCTGTCTGTCCATCCGCCTCCCTTCCACAAACAGCTGCCGCTACTGTTATATTTAAAGTTTTCTGGTATCGCTTAGTCCGTTTTCTGGTATCGCTTGGT\n+>Am12_1/1_1.000_120\n+ATAAAGTGGGCCATACAAAGTGAGACCTTACACATATATGAATGTCTAAATTGTCCTATGTTGTCCCATTTAACATGTTTAGTTTGTGGTATTTTTCAAACAAATATAACATGGGGTTTG\n+>Am13_1/1_1.000_264\n+ACAACTCCTCCAATAGTACTACCAGCTTGTCAGGGTGAACCAGATGGTAATGCACCTGATCCTGACTCGTGCTCACGATATGTAGTATGTCTCAATCAGGAACCGGTTAATGACTATCCATGTGATCCAAGTACCTTCTTCAACGACCTACCCGAGTACAGGGAATGTACAGACCCAGACCTACTGAGCAATGAGCGATATTTTGAGTGTTTTGGAATCACAAAGCGACCTACTGCAGCCATTGAATCTACTTCAGTAGCCCAA\n+>Am14_1/1_1.000_153\n+TACTTTCCTGAAATTAGTTCTAATGGTTTCATTGTGATGACAAAGTTTAATATGTCAAGCATAATAAACTTGATTGTGTTTTTCCACCTCAGCAGTCATTTATACATTTTATTGAATGTAGAGGGTGTTGAGACATTCAGTGTTGTTATACTT\n+>Am15_1/1_1.000_241\n+AAAACTACCATTTTGTATTCCACCACTGACATGGATAGCCCCAAGCCACCCACCCATACCATATCAAGGTTTGTGGGTAGAGGAATGGACAACAGTGTATATCTAATTCTAGGAGTTGTATTTCTGGTGGTGATTGTTGTGGTTGTTACAGTTATTCTGTTTATCAGTTTTAACAGAAGGAAAAAGAACAGCGAGTCTTCATCATCAAATCTTATATGCACCAGTAAAAATTATCCCCAAG\n+>Am16_1/1_1.000_298\n+CATTTTTTTTATTTTTCAACTGGTACTCATTATCCAGGAACAGTACTACTCAAGTACCAAAATATCAAAGAAACACAATGTCCACGTTTGTGTCGACAGTACTTTGAGTGCCATGGTTTTCTCATGAAACTTAATGGAGGAATAATTCCAACTGATCTTGGCACTTGTTATTTGCTTTCAAGTAAAT'..b'CCGAAGAGCTTCTACAACACACATCAGTGCTTGCGGGTTACAAATTTTTACCGAGGAAACCGTATAAACAATACAACCATACATTGAAGATAATGTTTCAGGTTTCTTGTTTACATAAGTTGACATGGAGATGCAGAACTATATACCGC\n+>Am8091_1/1_1.000_236\n+CATGTTAGAGAAGCCACCATGTTGTTGTATATAGTAACTTGTGTGGACATCACAATTACTAGAAGAATGCTGGATTTCTCAATTGATACATGTTCAGGAACTTATTACTGGAAAATATCACCAGACTACTATTTTACTTACAAGTCGAAAATACAAAATCATGTGATTTATGTGAACCTTGTCGATTTGGGATCCTGTGCATGCATTTGTTCACATTCAATTGATCATAAATGTAT\n+>Am8092_1/1_1.000_225\n+AACAATGTTGCTTTGATAATCTATGCAACTTTGGTCTTCGAACTGGACCGGGATTCGCAACTGCAGTTGTTGGTCTCATGGTCACCTGGATTTCACTTCAAGCATTCGCATAAATCGAAATCGATAGAAAAGAATGTGTATCTTACACTTACCCGTATCATAAATGTTTCTCAATGTGTTTATGACTTTATAATTTCACGTGTTCAATTTTCTGTTGTGTTTGTT\n+>Am8093_1/1_1.000_138\n+TGTCTCACAGTGACTCACATGATTCTGACTGGTAAAATGGTATTTAAGCTGGATAAATCAAGTACCCACTGTGGATTAAGTGTTGATTATCTCAGCGTAGGTTGGTCAATTTGCCAATACCCATTTGCAATGCCCTGT\n+>Am8094_1/1_1.000_402\n+GAGGGGTCCTCTTCTCTCAATGCTACTGCTGATGCTGCTGATTCTACAACAGCAACCGGTGCTCCATCACGTTTACCATCCACAATGGAAATTAGCACAGAAGCACTTTCATCTTCATCATCTACAACCAGGATTAATGCAGATATGAACCACTTTCAAAATGAAATATCTCCTCCTCCAGCTTATACCGAACAGCATGTACACATTACATCCCCAGTGAGAGCAGCTCAATTTGACTGGGATGGTCAACCCTTCTACAGCCCCATGGCAGTCCAGCAGTCAAGTCATCCTAACTCCAGACATACAACCCCTGAGAGTATACAGAGTATTCAGGAGTTTGGACCACATCTACATCTGTTATACACGGCTCAGCCAGTCTTAGGGGATGCCCAGTATTGGGTT\n+>Am8095_1/1_1.000_201\n+GAACTGAGTGTGGCCCTAATACGCTTTCGTGCTTTGTTTACCTTTCACAATGCTGTATATATATATTTATTTACCCACATAATATATGTATTTCATTCAGCTTACATGTCTTGTAGCAAACACTGGCAAATCTCCAAATTAAATATCTATGTAAAAATTCACCATGATAAATATATTTATAATGTACTGTATGTTTACCAA\n+>Am8096_1/1_1.000_170\n+AATGTATTACGAAAGCATTGTTTATTCACCCCTATTGTATACAGCTTCATATTGTGTAACTGTTGTGTTGAATATTTTAAACACGTAGGGTTCTTTAAAAATTCTGTGTTCTGTGGAATTCGAAATTTTGATGTTGACAGTCTGAATGGCGAGATCAGTTTTTCTCATTG\n+>Am8097_1/1_1.000_735\n+TTAAATAAAAAAGGTGTATTTTGGTTGCTTGCCAATAATATATATTTATATTTTGAACAGTCAATATTATTAAGGAATAGCTCAAATAATAAATTACATGTATATATAAGAGTGCATATCAAGATACTACAGGATAATATAGTGAAGATGGAATACCATAATAACTACACACTGGATGATATCAGGAATGTTACTGATCTAATAAATGTTGTAACAATACAATGTACATCCCCAATTAACACATCAACAGGGAACGATACGTGCATAAAACCAGATTCAACAGTGCATTTCATCTTGAACACAGTTATAATTGGAATAATATGTATCTTTGGGTTGGTTGGTAATACACTCTCCCTGTTGGTGCTAAGAATCGATACGACAAGTAAAGTGGCTCTTTATTTTCTTAAAGTGCTAGCTGTTGCAGACAACTGTTTGTTGTTGTATTCCTTCTGTTTTCTGTCTTTATGGCATGGATTATTGCCCTTCCTGAGGGACACTTTGAATATTGGAGGTGAAATATATGCCAAAAGTTGGCCTTTTATTTATATTGGAATAAATCAGACTGGACAATTGTTTCAGTTATTGGTCATCTGGATAACAGTATTATTGGCAATCAACAGGTACATTGCTGTGTGTTACCCTCTACAAGCTGCTAAATGGTGTACATTGTCAAAGGCCAAATTACAAATGTCCTTGATTTTTATGTTTGTCATAATTTTCTATTTGCCAACATAT\n+>Am8098_1/1_1.000_178\n+TTCTCCATTGAAAGTGTTTCTGGATTCAGTGAATGTCGAAGAAACCTTCTAAGATTCGTCAATGTACACTTGTATCTTGTATTTCAGGCTACACACATAAAAGATCATGATATTGAACGTATCAACACAACTTATCTACTAAATATGATAATTCAGATGTGCATGGTGTCTAATTTTG\n+>Am8099_1/1_1.000_168\n+TATGTCAGCAAAAAACCCATGTCTTTATGCTGCCTCCACTACAGCATGGCTTCAAGAGGTCTCCTAACAGTAAGACTAGATCTAAGTAGGCCTACATCAGTCTGTACATGTACTGATTCTAGAGTCCAGGCCCAGTCCTCTTTAAAAAAGCCATATTCAGTCAATCTA\n+>Am8100_1/1_1.000_239\n+AAGTTCCAGGTTAAATTAATATTATTTCTCCATGTTTGTTTGGTACCCGTTTACTGTGCACCTTACCCCCAGAGCTATCCCCAACACAAGGAACTACGAACTACTACTAGTAGGGCCAATCTTGACCGACTAGCTTGTTACTTTCCAAACTGGAAAACAAGTTTTGGAATCAGTGACATTAATGCCAACCTCTGTACCCACCTTCTCTTTGCCTTTGCCAAAATTATAGGAAACAATCT\n+>Am8101_1/1_1.000_171\n+GGATTTGTAGGCAGTTTTCACCATGAAAACTATGTAAGAGATCTATCCGTTCTTTCCGGGTCTAATCTAAAACTCATCATGATCAACAGGACTTTTTTCTGCGTGGATGCATTCGCATGTCATTTTAGATGTAAAAAGTCCTTGCCTATGTGCAGACGACGACCAGGCCTG\n+>Am8102_1/1_1.000_198\n+AAGTCAGATATATATATGTTAAATGTACTTGGACACAGGCTGTCATACTATATATGTACAAAGACATGGAAAATATTTTATTTCTCTATGCTAGATTTATGGATCTTTATGTACTCAGTGTTTTGTTTTCAGATATATTTTTGTAATTATTTGTTGTATATATTGTTAGGTACTGTATGTATTATGTATTATTTGTTG\n+>Am8103_1/1_1.000_192\n+TTTATGTTCTGCCCTGCTAAATTTAATGTGAATCCTTGTCAAACAAAGCCCTACTTGAAAATTGCAAGAGGGACCTCATATGCAACATGTCAAAATTCCCTCAAATATAAAAGGAAATGGAAAAATATATTTCACATTGTTTTGAAGTTGAATTTCCCAAAAAATAATGTTCTACTATATGACCTCAGGTAT\n+>Am8104_1/1_1.000_246\n+GCGGCTGTTGCATCGTGTCTGGATAACAGGGCCAGTGATGATAATCCTACAGATGAGTCAGGCAGTGATAGTGATGGAGCAGAGAGTACCAGTTCTTCATACTCCTCGCTGTCTGACTTTGTTATTGACATACAGAACAGTGAGATCAATGGAGAGACCCCTGAAGTCTATGCAGAAGATCAAGTATTGACAGTAGATGAGTCACGTGTGTTCTCACCCCCGAGTAAGCTCCAGGTTCCAGATACA\n' |
| b |
| diff -r 000000000000 -r b186cae246bd test-data/input_filter_assemblies/ApApomp_trinity.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input_filter_assemblies/ApApomp_trinity.fasta Fri Feb 01 10:27:42 2019 -0500 |
| b |
| b'@@ -0,0 +1,13338 @@\n+>Ap1_1/1_1.000_168\n+GGTCGCCTTATAAAAACCAATCCGAAACAGTTTTCCTTTGAAACGTGCCAAAAACCAAAAACATACTTCAAATCTTCCAGTGTCTGTTATAAAGGGGTGAGCGTAGAGAGGGCACTTGTGAGATTGGTGTCTGGGTTAAAGATTTTGCCAAAAAGCGATTGCTTGGTT\n+>Ap2_1/1_1.000_174\n+ATACTCAGGCACACAGCATTTGTCGTACTAGGCGAGAGAGAGAGAGGAACGACTAATTGCAACCACGATTACGTTACATTTGTTTACAAACCAAACGTACTGGCGTCGAAGATAATTAAGAGGAAGCTGACTGAATGCGATTGGCGTTGGTCTACGGGTTTGAGTTCTATTATA\n+>Ap3_1/1_1.000_546\n+GCCATGCAGTACACTGGACTTCTGTTATTCTGTTTGTTTGCCTTGACGGCAGCCAAACCCGCGGAAGACCTTCAAATGCTCATCCGAGCCCTGCTCCATGAAATAGAAGAGGAAGGTGAACTCCAAGAGCGAGGCATTGGCGCCGTGAAGTATGGTGGAACGAACGTTGGAGAAGACTACGTCGAGGTGAAGGTGATCAGGAACATGGAGGAAGTGAAGGCCGACCAGAAGAGCCACAAGCCACTCTACTCTCTTATATACGGCAAAGGAACCCACGATCCGAATTCCTCTCAACATTCGCTTACTTCCTGGACCTGGAGCCAACTGGATAAGTGTCAGAACGGTGCAGAGGGATGTTTCATGATCAGAAATCTGAAGCCAAACACCGAATACTGGTTCCAATTAGAAGTTCAGATGTGGATCAATGGAGCATATGAATACATCGAGAGCAGGAAGGATGTTGAACAGATCAGGACGAAGGGAAGACAGGAGAACGCACCATGGATGTCTTCAAAAAGTTACAAACCTGACGCAGACATTCGTACC\n+>Ap4_1/1_1.000_225\n+CGGCCGCGGCGCGTCGTTCTCAGCCAAGCTGACTTCGACTTGAGCCGTCCATTCGCTTATTTACACGACGACTGCTCGACCCTTTACGACTTAGTCACACTTCCGTTTAACCAGGCCCTGCTACCCTCCAATCTCGTCCAATCGGTCTCTACGCATCCGATCGATACAAGTTTGTTGACAAGGTCAAACATCAGCACCAATGAAGGTCAAGACCGTCTCATTGTG\n+>Ap5_1/1_1.000_271\n+AATCTACTGACAGATACCTGGAACGAGATGCAGGTCAAGTGGTCGTGTTGTGGTGTGGATGGCTACTCCGACTGGACGCAAGCTGAAGGTCTGGCCACGGGTCACTACGTGCCGCAGTCCTGCTGTCAGAACACGATGAGTACAAGCTGCACGTCACAGAACAACCCGACACTGTGGTGGCAAAAGGGCTGTCTCGGAGAGCTGAAGTACCGCCTGAAGGAGAACCTGTACATCATCGGAGTGATTGGCATCTCCGTCGGCGTGGTGCAGG\n+>Ap6_1/1_1.000_141\n+TGGCGAAATGTAGTGGTCATTGATGGATTTTATTGCAATCAGTGTTACATATTACAAGCATTTCTTAATAAACAAAAAGTTGCACGAGATATTTTTTACTTAAAGGTTTTATGGGATGAACACAGTCAATTATATTCATGT\n+>Ap7_1/1_1.000_421\n+TTCGTAATGAATCTTTTTGACTGGTATTCCGCAGGATACTCAATAATTATTGTCGCATTCTTCGAAGTTATCGCCATTTCTTGGATATACGGTCTCCAACGGTTCAAGAAGGACATTCAGATGATGGTTGGCAAGGGGCGATGGATCAATGCTAGTTTCTATTACTACTGGTATCCTACTTGGTTTATCATCAGTCCAGCTTTGATGCTGTACATCCTGGTTACCATGAGCATGCAGTTCGCACCAATAACGTACGGGGGTAGCATCAGCTACCCAAGCTACGCTGACGGCATTGGCTTTCTGATGGTTGGCCTCGCCTTGATCTACCTCCCAGTTCTCGCCATGATTGAATATTGCAAAGCTCATGGTTTTTTCAGCACGATGCAAAAGATCCTGCGACCGAAGCCTGATTGGGGTCCGG\n+>Ap8_1/1_1.000_417\n+GCGAAAACTGGTTTTAACACAAATAATTGTTACAGTACCAGGTTTCGGAACACGTTTGCATATAACCAGCGAGAGTGGTGCTCAGTTCTGTTATGTATGACAGTCCTTCTCCTCAACATGCAACGGAAGCGAGCACTTCCATCATCACATTTGTCAATAAATACTGCATGGTACTCCGGCCAGGGTGAACAGGAAGAAAGACTGATTGTCAGCACTCGTGCATGCTCACCAACACACACACACACATCCTCACATGTATGCACACGCACACGCAGGCCAAAACACACTAACACGCACACAGGCTCAAGAATGTTTATTAGACATAGTAGTAGTAGTAGTTGTCATTCAACTCGAACAACGAGTCGCCTATCACTAGGCATCATCTTTCTGTGGGCAAACCGTGGACCGATCAGACAG\n+>Ap9_1/1_1.000_470\n+TTGGAAGAAGAAATAGAAGAATTAATGCATGAGAATGATGATGAAGATGGAGTTGAAGTTGAAAAATCAAAAGATAAACATGAAAGTGTGGAAAGGGCTGAGAAGAGAGGCAGCAATAAAAATGATGTAAAACATGATGAGAAGGATAGAAGTAAAGACAACAAAGAAAATGAGTTAGGTCAGATTAAGGAAGTAGAAGATATGGGTCCTAGTGTTGATAGGAGTGAGAATGAACGTGAAGCAGTTGGGAAGGGAATCAAATCAGAACAGGAAGGGTCTGGTTCTAAAGCCAACAAACACCAGGTATCACCAACAAATCAGGGTTGTTCTCACACAACCAATGAGAGTGAGAAGAAAGAACCCTCACACCCTAGGAGTCAGTCTCAACAGGACAGTGATGATGATGATGGGGAGGGTGAGACATTGCATGAGAAGAGTTCATCTGAAGGGGATGATGAAGGGAATCAAAT\n+>Ap10_1/1_1.000_338\n+CCATACTCAGCCGCCAAGACCACGGCCCAGGCTGCCACAGATGACCTGAAGAGACGTCAGGAAGAACTGGAGAGGAAGGCTGAGGAACTACAGAGAAAGGAACAGGAATTACAGAGAAACATGGGACACCAAGCCAGGGTGAACAACTTCCCACCACTGCCTGAGAAATGCTGTGTCCAGCCTTGCTTCTATCAAGATTTTGAGCTTGACATCCCATTGGAATTCCAAAGAATTGTAAAAACAGTGTATTATGTGTGGATAGCCTACATATGTCTGTTGATTCTGAATGTACTGGGAACACTGGCCTACTTCATAGCTGCGTCCAAGGCAGGTCATGG\n+>Ap11_1/1_1.000_303\n+ACGACAGAGGTCCTCTGCTTGATGAATATGGTTACACCAGAGGATTTGGAAGATGAAGAGGAATATGAAGAAATTTTGGAGGATGTCAAAGAAGAGTGCAGCAAATATGGTTATGTGAAGAGTATAGAGATCCCACGGCCCATTAAGGGTGTGGAAGTGCCTGGAGTTGGCAAGATCTTTGTTGAGTTTAATTCAGTGATAGACTGTCAGAAAGCACAACAGGCACTGACAGGAAGAAAATTCTCCAATCGCGTGGTTGTCACATCTTACTTTGACCCAGACAGATATCACCGACGAGAGTTC\n+>Ap12_1/1_1.000_582\n+GATGGTGTTGCGCTGTTCTGCTTTCTGCACGCATTTTATCTCGTCAAAACGCAGCCGTTGCTTCTCAGTTTGTTTATGTTTGTTGTTGTTTTGTTTTGTTATTTCCTTTCAAGTCGCCCTGATACAATGCTGTCACATAAACACGAGGTCATCGGACGTTTTCCGTCGATGTCGACATATATATATTTTTCCCCGCTACTTGTCCATCCATCCATCCATTCGTCTACCTGTCTGTCTTC'..b'TTTCAGTCATGGCAACTGACGCCGAGACAATTGCAATCGCTGTCGGGGTGACGGCCTTACTCCTCATCGTCATCGCCATCATCGTCTTCGTCGTCATATGGCAGAAGGGCAAGAAGCTGAAGGCCGAGGGCAAATTACCGACATCCAGCAAGCCGACCACCCAGTACCAGCGCCAGCCACCGGCAGTACGCTACCAGCCAAGTCCGATGCCGCAGTATGTGTCTGGAATGCCGCGTGCTTATGCCCCGTTCAACAGCTACAACAGCTGGCCCAGGGCTTCCAGCACCGAGGCTTCGCCGTGGCCGCAGAATGCCATCCAGTACGGCATGTCATCGTACGCAGCTGCCGGAGCCAGCGAGAACGCGTCGTCGGCTACGACGGACACCGTGCCACTGTACGTGGTCAACCGAACGAACAGCGTCCAGGATCTTTTCGCGGCATCGAAGGCCGATCCGGAGGCCTTCATTCTGCCGAAGCTGCCGAAGCTCTCCGAGCCCGAGCCGTTCATCTTGCCGACGACGAAGCTGAAGGTTGAGAAGACGGACGAGACGCTCCAGAACTTCATCCTGCCGACGACGACGACGACGAAGTCGACCACCCTGACCGAACTCCAGTCGGACAACTTCATCCTGCCAACGACGAAGTCGACCACCCTGACTGACCTCCAGTCGGAAAACTTCATCCTGCCGAAGACCGAAAACAATGAGCTGGTGCAGACAGCCGGACAGCTGACGATACCCGGGATACAGCAGCCGGGGCCCAACGAGCCCATCCTGATGACGACGAACGTCATCCCGGGCACGTCGACGGTCACGTCGATCCTGTACAACCCGTACGCCCCGCCCGAGCTCGAGAACCGCTACCAGCAGCCGGAAGGGCCCAGCGACAACTACGACCCGTTCAAGCCTTACGACCTGAAAGGCTATTTGTCGATGAAGCCGACGACGACAAAGAAGAAGAAGAAGAAGTCGACGACGACGACGACGACGACGAAGAAAAAGACGGCCACGAAGTCAACCAAGAAGTCGGCTGCTCCCAAAGAAGAGAAGCAGCAGTCGGTCCAGAACATGAATCCGGAACAGATCTACTACTACCTGACGAAAAAGGCGAATAAGAAGTCGAAGACGTCAAAGCCAGCTAAAAAGGAGCCGGAGAAATCGAAACCGAAGCAAAAGAAGAAAGAGGAAGTGAAAGAGGAACAAGAAGAGGAAGAAGAGGAAGAGGAAGAAGAGGAAGAAGAGGAGGGAGAGGAGGGAGAGGAGGAAGAGGAGGAAGAAGAGGAGGATGAGGAGGAAGACGACACGACGACGACCGCTGCCCCGACTGGAGCCTACTCGCCGTATTACATCCCGGCACCGCCTCCACCGAAAAGCAAATCGAGTCAGCCCAAGGCCGTCCTCAACCAGGTCCAGCCCGGCTCGATGGCCGTGGCGCTGCCGGCCAGCCAGCCGCTGAATCAGCGACTGAAACAGCCGCTGAACCAGCCGCTGAACCAGCCACTGAACCAGCCACTGAACCAGCCACTGAACCAGCCGGCGACCAGCCAGCTCTCCGGACCGTACTTCTTGTCCATCAGCAATCCACCTGTCTCTGGCAGTTCCGACATCCACCTCGCCGGTTACGCCATCAGCCGTCAAACCAACTGCGTGCTGAATGTCAAAAAGCCTGACGAGATGAGCTGCACGTCGAAGCAGACCGTATACCGGCTCCAATCCGTACCAGACCAGCCACAGCAACCAGCATCTAATCAACAACAACAACAACAGACACAGCAACCAACCACGTATATCGTCACGGCTTCACAG\n+>Ap6666_1/1_1.000_1596\n+AAAGATATAGGCAAGATGGCGACGAATGGGAGAGGTTTTATGAGACCGAGCAGTGGTGGCAGAACGCCTCCCTTCCTAATAGTAGGCCTTCTGGTCGTGATTGGCATATTGGCCTTCAACTACTGGAATCTCTCGTCCAAAAACAGTATGCTGACTGTGACTGTCAGTCAGCTAGAGGCGAAATATCGCTCGATTCAGGCCAACAAGCTGGACGTCGAGAAACGCAACGTCGAACTGAATTCCCAACTGGAGGAGGCCAAAAGATATAGGCAGGAGGCACAGGACAAGGATATGAAACTCAGGGAGGCCGAACAGAAGGCAGCAGAACTGACCGACAAGATTGATAACTTGGCAAGCGACCTGGAAGTGGCACGGAATGACTTTAATACGTGTGATGAATCTTTGGGTTTCTGCCATCAGAATATCACAAAGATGACCATTGACCATAAAAGGGAATTGGAAGAAGCTCATATGCAGTGCAACAGGAAAGTGGATGAAGCAAAGTCTGCTGCAGAACAAAGAGCAGCTTCACTAGAAAGTTCATGTCAGCAAGCTGTAAATGAGATGCGTTTGACAGTTCTTCACAAGGTCCAGCAAGTGTTTGGCACTAAGGCAGTACTTCTTCTTCAGCAACAAGCTCATTTAGATGTCTCTGGCATTGACCTTAGTATAATGACTGGAGCTGACCTTGAACAGTCTCAGCAGGTGGCACAGCAGAATGCACAAACACAACAGTATGTCACAGCAGTGCAACAGCAACAAGCACCACAGCAGCAATACCACCAACTGGGACAACAGGAAAGAGAACAAGAGAAACTACCAGGAGAAAACCAAATTGAACAACAACAACCAGGACAAAATGAGCCAGAACAGCCTCAGCTGCAAAATAACCTACCAGAATACCACCATCAGCAGCAGTACCCTAATCTGCAGCATGTATCAAAAGAACAACAGCCTCATCTACAACCTGCTTTACCAGCAGAGCGAGTCCAAGTAATGACACAGCAACAAAAGCAAGTTGAACCACATGACAATGCAGCAGCCCAGGAACAACAACATGCTGAGCCCACTGCACAGCATGTACCTCATGAAAGTCTACAAAATGTCAACCAACAGCATGAGAAACCAGATGTTACTTTGATGGATGACAAGAATAAAGAAGTTGCAGTTAATCCTGGATTATCTCAATCTGATGACCTCATCAAAGCTGCTCAGCATGGCTACTCGGAAGCTAAACAGAATGCAGTAGAACAGCAGCAGGATCAGGCTTCTGAACTCCAGAAACCAGAAAACCAGCTGTCAGTCATCAATCAGGCACCAGTTGCACAACAGGGCATTGATGAAACTGTTAGATCAAGTGAAATTAGGCCGAAAATTGATGACACACAGAAACAAGATGCAGAAGATGCCCAAATAGTATCACAGAGAGGAGAAGCTGCTTCAGCACCTGCTGGTGAACTGGTTATCAACAGACAAGTTGAAGATGCAGATAAACAGGAGGAACTCCCTGTCTCGGACCAAAAGCGTGATCAGCAAGAATATGTAGCAAGAGGACTGGATGATGCAGCTCCCCTTGGTCAGGCGATTCCACCTAAA\n+>Ap6667_1/1_1.000_150\n+TGGAAAACCAAGTACTTGTTGTTCAACACTTGTCTTGCAACCATGCTTCTGTGTTTATTTGTAAAAGAAGAACCCAACTACCATACTTCTGTTGTAAACATTAAAAATCATATCATCCTAGGAGATTTGACAGGTTATTATAAAACTGTT\n+>Ap6668_1/1_1.000_205\n+TTCTGCCCCACTTCAGCGCAGACTTCTGCCTCTCTTGACAGCGTCACCGTACTAGCCAGCTTCTGTTCTTCATCTTTAGCTTCCGATTTCCGCGATGTTTTAGGCACACCAGCCTTCAGCGTGGGTGGTGGTGACTCTGCCTTGGCAAAGGCATATGGCTCCACTTCAGAAATGACTGCCTTTTGTTTGAGAACAGAAGTCTTAG\n+>Ap6669_1/1_1.000_141\n+CTACATCTGGTTCAGACTGGTTTTACTTTGCTTATTTATTGTGTGTATCCAGCTCACCAGAAAAATAGATATTTCCAGGTAAATTACTGTTGTGTTTTGTGTGTAAAAGTCCAGCTACTTAACAGTGCAATGTCTACATGT\n' |
| b |
| diff -r 000000000000 -r b186cae246bd test-data/input_filter_assemblies/PgPgras_trinity.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input_filter_assemblies/PgPgras_trinity.fasta Fri Feb 01 10:27:42 2019 -0500 |
| b |
| b'@@ -0,0 +1,16594 @@\n+>Pg1_1/1_1.000_200\n+AATATAATATGTAAGATTTGCAAGAAAACAATGAATCCAATGAATGGATTTTTTAATATTTTTGCACTTACACAATGCAAAATTATGCATGAAGAATGGACATATTTGCTGTTAATTGATAGCAATAATGAGCGACCACATAGCTCTATCTTGTTTATATATCATGACACCTTAGTCTTAAATACTGATTTGCTCCAAAT\n+>Pg2_1/1_1.000_207\n+GAACACCGACTGGCCCATCTCAGAATGGATGTTTCATCTTTCGCTTCGAAGCGAACCGTGCGCACAAATGTGGTCGAAAAACGACAAAATTTACAGTTTACATTTCGGACGCTTGAACACCAAATACAGACATCACCAAACAATTACCAACAGACAGACCATTACGTCACAACAGACAGTAAACAAACCAAATCTCAGACGATGTTA\n+>Pg3_1/1_1.000_218\n+GAGACAGCTACAGATCGACAGATATCTAAATTTGACCAAGCCGTTGGTGGCACGGAGCAGGTGATTACAAAAAAGTCAAAGAAATCCAAGCGAAAGAAGAAGGGGAAAAAGAAGGCAACGGAAGCAGTAACCATGGAAACAGATTCTGAGCAGACAGGACAACAGGCTACACAGGAAATTATTCCCGAATCCTCCCATCAGGAGTCGGCAGAAGTGCA\n+>Pg4_1/1_1.000_258\n+CATCTGACTAGGACCTATGCCACCCTGGAAAACGACCAGAAAGCCTATTATAGACCCGTAAACTTTGATCTCACACAGCCGGAAATGAACGTTGACTTCTCCGCTCTGGACACCCTCGAAAAGAACCAACCACCGTGCTTTGATACGTCATGTGACCGAAACGCGGCTCGTATTGATCAGAGCACATGTGCAACATTGCCAACGCGCGCTTGCGCCTGCGATGAACGACAAAGTATATATAACTCAATAAAATCAACG\n+>Pg5_1/1_1.000_123\n+TTAATGCTGTCAATTTATTTCAGTCTTTGGTTACCTTTAATAATGACATACGCAGAAGAAAATAAATCACACTCACTATCATTGTATTATCCTTATAGCTTGGTAATTATCAGTCAGCACAAC\n+>Pg6_1/1_1.000_174\n+CATATAAAAATACGCTGTGTAATAATTAATCTTGACAGATTCAGCGGAGATGGAAATTCACTTTCCCTATATTCAACAAATGACATGTACATAGAGGTGGTTAAATTTCCACACATATACACACAAACAATAATTACCAAACAATTAAAACAAATCTTAGGCATTCATTGGGTT\n+>Pg7_1/1_1.000_270\n+AAAGGAATCCACTGCATGGACAAGTCCTACATAGGACAACCAGGCTGGGTATTTCAATTTAACCGGATCACATTCTTCGTTACAACATTTGCTCCATTCTATCCCGAGACGCATTCCAGACACAGCTTTGGAACGGAGAATGGATACATCCTTTTCCAGCCCGAAATATCATTTGCCCAACACGATATCCCCGATGATACACCACACACAAACTGGGCTGAGCCTAAAACAATCAGAGATCAAATCAGAGTAGCATTTAATAAAGCAGGC\n+>Pg8_1/1_1.000_422\n+CTCAACTTCACTGTGACGAGTCTACGACCTAACATACGCTATTGGCATAGAGTGGATGCTGAGACTGTAGCAGGAAGTACAAAGGGGCCCGTGTCATCCTTTGATGTGCCTCAAGTGACACCTGAAGGCATACATGCCCCAACGAATGTCACAGTACTTGGACCAGAGTCCATATTTGTGACCTGGCAGGAGCCCGAGATTATGAATGGCATCATTGACCAGTACCGTGTGTTATTAAATGGTGGCACTGATAGACAAATCACACAAGGCTTTGGACTTAGTCTTAGTGGAGAAATAAATGGTTTGAAGCCATACACCTCGTATGACGTCCGCATACAAGCGTGTCTACGTGGTGTCTCTAATGGTTGTAGTACTGGACCGGGGATAGTTGTTTGGACTTTTGAGGCAGGACCACAAGGGCA\n+>Pg9_1/1_1.000_147\n+ACAGATGTGTTTACAGATACGTTTACAGATGTGTTTATAAATACGTTTACAGATGTGTTTACAGATGTGTTTACAAATACGTTTACAGATGAGTTTTATAGTAAACATCGAAAATCTATTCTCACGAAGAAGCAACGGTTACTCACC\n+>Pg10_1/1_1.000_324\n+GGCAGTGAGTCCGATGTCTTGGCGCTGGCTTCTAACGTCCTACTTAAGGATAGAAGTATTTTGATAGGCTCAGTTCTGTTGATAGTTGATGGACATGTGTTAGATAAGGTGGCTGTGAAATTCAACTGGAAAAGAGCACCTTCCATAGAAGATGTTCTGAAACATTTCTGGACTATAATCAAGATAATGGAACCAAGAAATAAGGCGAAGTACTTAGCAGCGATTCTAGAAATATATCGGTTTCTTCAGAAACAACCACCGGATTGTGTGAAGAAAGCTTTAGATAAACGAAATATAAATCAATGGATATGGAACGGATATGGC\n+>Pg11_1/1_1.000_150\n+CGAATGGGCCCTGGAGATCAGCCATTTAATGCTACAAAATCACCGATTATAAGGATATTGTTGGGTCACGGTTGGACACTGGCACCATTCGGTGTTACGCTGTATTTTGACCCATTTCGGCCAAAGATGAGAATCACCATGCATTATGTA\n+>Pg12_1/1_1.000_583\n+AAAAATCTCATGCCAGTTCCACTGCAGAGTCTGATGCTGTCTGAGAATTCACCAGTCAAAGATTACTACCCCGTGGATTTCAAGACGGATCTCAATGGCAAACAACAACAATGGGAAGCTGTTGTGTTGATCCCATTCATTAATGAGAATCGTCTCATCAGTGCCATGACTCCTCTTGAGGAGAAGATGACGGATGAAGAGAAGAGCCGTAATAAGCATGGACCTCACGTAATGTTCGAGTACACGCCAGAAAGTTATGGAACCTACACCTCGACCATGTTTCCAGACATCTACAATCATCAGACCAAAATCACAAATCTGCCTCTGGATCAGTTCTGGATGAGGGATAAATCAAAACTGCGACAGGGACTATGTCCAGGTGTCAGAGTGGATGTGTATTTTCCTGGATTTCCGACAATGAAGCACATTCCTCACAAGGCTGAGCTACAGAGATGTGGTGTGAAGGTTTTCCAACATGTCAGTAAGGGAGAGAATATGATGCTCACTATTTTGAAGGAGAACAAACAGACCTTAGATGAGCTGGCCCATGATATGATCGGACAAAGTGTTTATGTTAGCTGGC\n+>Pg13_1/1_1.000_309\n+CAAACATCCAACAACAACAGGACTACAGGTGGTGCTAAAAATGATTCAAACATTAAACAAACAACCAAAGTTGATAACATACAGGAGAATCATTATGTAGATGCAGTCTCATCTGTAACAGACACACCATCACAACCGAAATGGGATAGTCAAACTTCGGATGATCTGGTAAGCCAGGATGAGGCACAATCAGCTACAGCAAACAGAGCTCAAATAGTGCAGATCACTAATCCTGTATTTAGGTCAGAGAGTGTAAACAAACTACCAGATTTACCATATCATTTACCATATGCTTCATTATATCATGAC\n+>Pg14_1/1_1.000_465\n+ATAAATGTAGCCAAAATATGTGAAAACAGAAAAGAGATAAAACCTGTGCTTCATATATCAGTAAACCATAGTGCTGAAATACAGGAGCAGAGGTTGAAGTTACCAATACTGGGAGAAGAGCAAATAATTATGGAAACAATCAATGATAATCCTGTTACTATTTTATGTGGGGAGACAGGCTCTGGAAAGACAACTCAAGTACCCCAGTTCTTGTATGAAGCAGGCTATGCCCTTGATGGTTCTATAATTGGTGTGACAGAACCTCGTCGTGTGGCTGCAATT'..b'CACAGCTGCATCTGCAGCTTCCCAGCCTACAGGGTTTTCATTTGGCCAGACACCCCAGCAGACTGCAGGTGCATCTATGGCTGGACAACCTGCTGGCTTTTCATTTGGCCAAACACCCCAGCAAACCACAACTGCATTAACAGCTGGTCAGCCTACAGGCTTAATACTTGGCCAAACACACCAGCAGACAACAGCTGCATCTACAGTTGGTCAGCCTGCAGGCTTTTCACTTGGCCAAACACCCCAGCAGACAACAGCTGCGATGACAGCTGGTCAGCCTGCAGGTTTCTCACTTGGCCAAACTCCCCAGCAGACAACAGCTGCACCCACAGCTGTACCCACGGCGGGTCAGCAGACAGGATTTTCATTTGGCCAGGCATCCCAGCAGATGTCAGCTGGATCTACAGCTGGTCAGCCTGCAGGATTCTCTTTTGGTCAGACTCCACAACAAAGTACAGTAACATCTACAGCATCTCAGCCTGCAGGCATCTCATTGGGTCAATCAGTACAGACACAGCAACAAGGCACAGCTGCACCAGCAGCTGGCTTTTCTCTTGGTCAGACCACACAACAACAAAATAGTTTCCTGTCTGGATCAACACTTGGCACATCGAACGTAGGTGGATTGTCATTTAACAAGCTTGGCCAGCAGACAAAGGCTTCTACAACCACCACATCACAACTAGCAGGACTCCTGTCTGGCAACTTACAATCAGCTCAACAGAAGCTTTCTGGCACAGCTACTTCTACAACACCTAGCCTTCTGACAGGTGCTTCTAAACCACCAGGTGCTGCCCCCACCTCAGCACCAAATATGTCAGCTCCTAGTTCACAGGGCCTAACTTTAGGTGGTACAGCACCAACATTCCCACTAGGTGGAGCCACATCAACTCCAGGCCTGACACCTGGAGTGTCAAAGACAACAAGCGCGACCACGACAGTTACTACATCGAGCAGCATTCCTGGTTCCGGTTTCTCCTTCGGTGCCCTTGGTGCGGCGAAAACGACAGCCGACTCGACACTGGCGACATCCACTCAGTCTGGCGCCACAACAGTGACCACTATTGCTACAACTCAGCCAGCGGCTACCCTCAGTACTGCCACTTCTATCTCTGCTTCAACAGCCACATCGAGTACCATTAATTACCGTCAGCTCGAAGAATCGATCAACAAGTGGACTTTGGAGCTCGAGGAACAGGAGAAGATTTTTCTAGAACAGGCAACACAAGTGAATGCCAGAGATAGACTACTGATAGATAATGAAGATAAGATTACCGACTTGAACATGAATATGGAGCGAGTGAAGTTAGACCAACAGAGACTTGACCAGGAGCTAGACTTTATAGTATCACAACAGAAGGAACTGGC\n+>Pg8290_1/1_1.000_519\n+CTCTTCCTGGGAGCAGCTTTCGGCAAAGGCGGTGTCTTCGTCCACCTGGCTGAGACGTGTCAGTTCCTGAGAGCTATTGGCCGTGCTCTGGATCTCAGTGTCCTGGGGGCGATGTTCGGGATCCTGGTCGGCTTTCCTTGGTTGAGATACGTCGGTGGTGCCGCGGCCGTGTTCTACATTATGAGTGGCCTCAACGAGTACGTCTCTACCATACATGGTACTCTGGTGTACAAGGATGACGATGGTGACGTGGCCAGGTACACCATCGACAGAGAGGCCAAGCAAAGACAGGTGGAGCCACCATCACTTCCTCTGCCAGCCTACGTCATCGTTTCCGCCTCACTGCTGGTGGCCCTTGTCGCCATGATAACGACTGGTGACGTCATACCCTTCCTCTTGCAAGTAGTTACCATCACTGGTCACATGATGATGACGTCATCCAATAAGAGCCAACACATCTACAGTAATCTGTTCCGGATGTTGAGGGTTGCCAGTCTGTTGCGTGTAGAACGATATGTT\n+>Pg8291_1/1_1.000_232\n+AAGGAACACGTGAAGTTGTGTGATTCAAAAGTGGAAGTGTTAAAAGATGGGGACAGTGTAGACACTGATGAATGCCGTGAAAGCTCAGTGGATACGCTAAGTGAAAATTGTAATGATGAGAACACAGCTGGCTCTCGCAAGTCCAGTGTACTACCTTCTGGTACGCATTTCATGGAACAACACAATCTGAGCTGCCTTCAGTATGTCTTTGTGTTAGCTCTGACAGCCTGGG\n+>Pg8292_1/1_1.000_255\n+GTCGACGTGAACGATGTTGATCCGGATCATGCTGTAGATCCAGATCAGGAAGGGAATTCAGATGCTACCGAACCCATGAAAGTGATGCAGGGATCGATGATGACTGATGATGATTATACAAACATTGAGATAGGAGACCTGTCGGATGATAGAGCTATCTCACAGAGCAGCAGCATGGATACACTCTCAGAGGCCCACAGCAGTCCAAAACTTGCCAGAATGTGCAAACGTGCCAGCATTGATTGCACATCTATG\n+>Pg8293_1/1_1.000_138\n+AAAGGCTACTTCGACATGTTTAAGGCTGTACGAGTACTAGGCCTGTGGTTACGTATTAAGGCTGTCTACACTGTTCACGATCCGTCTTTCTGTGTTCTGACAGCGCCAGTACAAAATCTCGGATTAGGTGTACTTAAG\n+>Pg8294_1/1_1.000_198\n+GTCGTCGTTGCCGCCGCTGCTGTTGTTGCTGCTGTTATTGTCCTGGATCCATATATACTAGCCATATTAAAGGACGCTGTCGTTGGTTATGGCATACCACTCGACGTATCCGGAATAACGTTAAGTCAGTTGGTAGTCGACAGCAGCGCCACCAAACATAACCGTCTGGATACAGGAAGTTCGCAAAACATCGGGCTG\n+>Pg8295_1/1_1.000_360\n+TGTCTGTTAGCTAGATGTCTTCATAATTGCTGTTTCGTAGATGGTTCGAAATTAATACTGGCTGTGGGCCGTGTACAGTTCGGATGTTTCCACGTAAACAGTCATAATCTGATAGTACTGTGTCATGTGGTGTTGTCGGTGTCGTTGAGTGGTCTGTTTGTGATTTGTAATATGTTTCCTGTCCCTTCGTGCCCACATCTTGTATCCAATTCGGCGTCATTGTTCTTGCCACAGACGCCACCGCCGTTATCAGTGGACCGGTGTCAGGTGTCTTGTCTCATCACCTACCATATCGGGTGTTCATCAGGTTTGGGACATGTATATGTAGTGTTGTTACGGACGACGGCGCCCTCCTCCTCC\n+>Pg8296_1/1_1.000_446\n+GAACCTTCTCGTGCGGAAGATGAGGGAGCAGGAGAACCAATGGGAAGAGCCGACGACGTCGCTGGCCGACAACAAGAAGCTGTTCAAGCCCGTCGCCACCTTCCCCACCGAAGTCAAGAAGCCGAATGCGGCTCGGAAATACATCGGCGGCGGTTTGCCGACGATGCCGAACCAGTTCTTGCCCTTTCCCTTCCAGAACGCCATGATCTCGCCGTTCGGACACCACGACGTCCTGGAGCCGGGCGAGCGGCTCCGAGGCGGTCACGTGAAGATGTCGCCGGGAGGTCATCTCCATCACATGCCGATACTGTTGCCGAACGGCGGCATGCCTCCGCTCTACGCCCTGAACAATATCTTCCCGGTCGGTCCCTATCCAGGCCTGGCCCCGTGGAACATGTACCCGCCGACCTTCCCCGGAGCGATGCAGGGCCCGAGCCCACTGGCCG\n+>Pg8297_1/1_1.000_282\n+GTTGGCGCATTAAATGCATGTTTCTTCGCTAAAAGAGGATATCATGTCCAGATGTATGAAATGAGAAAAGATATTCGTAGAGAACCTTGGGCTAAAGAGAGAAACATCCACATGACTTTATCAAGTAGAGGACGAGATGCGTTAAAGGCTGTTGGTTTAGAAGACTGCGTCGTAACTAATGGTACACCAATGTATGGCAGGATGATACACGATCTTTATGGTAACAAGAAGACAATTTATTATGGACGTAATGATCAGTACATCATGTCCATAGACCGTCGG\n' |
| b |
| diff -r 000000000000 -r b186cae246bd test-data/input_filter_assemblies/PhPhess_trinity.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input_filter_assemblies/PhPhess_trinity.fasta Fri Feb 01 10:27:42 2019 -0500 |
| b |
| b'@@ -0,0 +1,16274 @@\n+>Ph1_1/1_1.000_126\n+CAGTCACAATATTACCTGTCTGTAGATATATTCGTACTAAGTAACCTCGCTATCAGCAGATCTGTAGTCAATACCTCGTGTATTATACATATACTGTGTATATTTGTATGTGTGTGTGTGTGCGCG\n+>Ph2_1/1_1.000_225\n+ACAATGGCCAAATTGGAATATGTCTGTGAGATTCTTGATCAGAGCCGGCAGAATATGAGACATGTTGGATTAGATATCACTAAACTAGAGGCTGTGGCTGGTATAAGATTCAGTTTAGTTGAAGTAGCCAAGATGATGCATGCTTTGTATGTGGAGAAGAGAGATCTTAGAAAAGAAAGAAGAGTTCTTGAAAGACTCTTTGAACATGCCCAGCAGGTCTGTGTA\n+>Ph3_1/1_1.000_150\n+CATCTTTATAAAGTATATCCGGCTTTTGCAGACGCCTCCTCCACAAAATGGTCTTACAAGATGGGTGGTCGTACATTACAGGTTTGTTTCATAACCTGGGGAACATTTCTCCAGTTGCAAAGGTGGTCTTATGTGTTAGATGCCCTTATA\n+>Ph4_1/1_1.000_156\n+TTAGAAGCAGATGTTTGGTCAGCAAATGTAAAATACACATTGGAAAAGTGTTGGTCATTTAGTCCAGGATTCATTGAGATTGATGATCATAGAGGATTCTACCATATCATCCTGTGTTATCATTTGTTGATGGAGAGTAATTACTCTGGATTGATA\n+>Ph5_1/1_1.000_147\n+TTATGCAAAACAATGCTAAATTTCTTCTTCACCTTGCTTTTATTTCATTCTTTTTTTGTATTTTCAAATGGAATCAAAGAGAAATTTAAGACTTTTGGCAACCTTCTCAAAGAGCATTTGATAATATTCAATAAATTTCTCCAACTC\n+>Ph6_1/1_1.000_120\n+GACCATGTTATTTATTACTCAGTGCTACAGATACAACTAGTGATCTGTGTTGTTTTTAATATTTTTATTTCAGTTAGAAATCAAGTTGATATGTCAAATCTCAGATATAATGCATGCATT\n+>Ph7_1/1_1.000_105\n+AATCAAGACGTACACTCTGTTCATGTGCCATTTCATTTACATGAACAGTTCACAGTTATTTCTCCGGGGAGTGAACTTTGGATAATTCAAAGGCCACCGGACTTA\n+>Ph8_1/1_1.000_159\n+TTAAATGTCATTGTTTCTTCAGTGATTGATAGACTGTTGAATAATTCATTATTATATAACTTTTCCTACCTAAGTACATTAGAAATATATTTATTTCTTACTGAAATAGTGCATTCAGGCGATGACAACTTTGTTTGGCAAAAGGGAAAGAGTATTAGA\n+>Ph9_1/1_1.000_138\n+GATAATTTAAGTAGCAGTAATCAACATTTATATTTCTTTTTGTTTAAAATGAATCAGAATGTAACAATTTTGTGGGTGAAAGTACATAGCGGTTGCATTTATATTAATGTCAGCCCTTTAAACAAATTTGAAGGAAAA\n+>Ph10_1/1_1.000_405\n+GTGGAGGCACCAGAGGAAGAAATCATCGAGAAGCTGTCCAAGAACATATCATCATTACCTGACGCTGAGGATGTTGCCACCGAGCAGACTGCAGCCCAGGCCATGATGGCTAGTGGACTCCAGCTGCTGACCAATCAGGGACAGTCTCTAATGTCACATGGGCAGGCTTTGGTTTCCGCACTAGGCAGTACAGATATCTCTGGTCTCATGGCGAGTACCATGGCTGGCCTGAGCACCATTCGGGATACGGTTTCGACGGTGGTCCAACAGTCAGCAGCGGGTGATGACAAAGACAGCGCCCAAGACAGACAGGGCAAACCACTTGAAGCAGAATTTGAATTTCTCAGTGAGGCAGACTTGAACCAAGCAGTACTAGAAAACCTGGGCAGCATTGATGAAAGCAAC\n+>Ph11_1/1_1.000_180\n+TTAGTTATGCAGGCTTATAATATTTATCGTAGGGTTATGAAACGTGGCTTAATTGCAGACATCAGAGCATGCAGCAGAAGCTGGTTTGCGATATTGTACACACTAATTGTTATCATTATTTCAAATTATTTTATAATAATAAATATTAAATGGATACAGTCAATTTTTTTGTATAATGTA\n+>Ph12_1/1_1.000_148\n+AATACAAACTGCCCCATTTCTAGATTTACTCAATATATTTTCTTTCTACCACCAAAATCGGTCACGCTACCCACACACTGTATAACACACGCACGCACACACATACGCCTATACACACGCAGAGAGGGCACAATCATGACGCAGAAAC\n+>Ph13_1/1_1.000_234\n+TTGGGAATATACATCACACATTATAGAAGCTTCTATGTCGCTGTTAAATGGACACCATTACGGATGGGACCATCCCTCTGTTTTGGTTTTAATTTGATTTTCAGGCTCTGGGCTACGGGTCAGTTTATTCACGATACTCGCCACAAGCACACCAGCTATCACACATACGTTTCAATAAACTATTTCTCGCCAAATACTGCACGCCACGGAAACACTACGGTGACATACACAATC\n+>Ph14_1/1_1.000_189\n+CAACTGTGGTTTCTACAACCCTATATCAACATGTATATAGATGATGATATACATATATTGATTTTATATGGGGCTCTACACAGTATGTATATTATTACTATTATTAGCATGAACCAGCAAACAGTTTATCGGTCCAGGCAGAGCACTTCTAACTCATTAGCGAATCACACTTATTTTACTGAGTCAACG\n+>Ph15_1/1_1.000_147\n+CGTTGTTACTACCTCATTCAGTGTAAACTTACAGAAAATCCAGCTGTATTTCTGTCACTTTATCACAGAATGATACTTGTCATTTTATTAACTAGCAGGCATATTTTTATAATAACAGGAGCCTGTTTACCAGAAACTTCTGTCGAA\n+>Ph16_1/1_1.000_123\n+TTAATTGTAACAACTAGCGTGCGTGTGTGTGTATGTGTACACAGATACATATGTACATACACACGTACACAAACACGTAATCCGATATCTAATCAGCACTATATCAGTATGTTTTTAAGTCTC\n+>Ph17_1/1_1.000_277\n+GGCATTGCTAGAGAGTTATCTGATCTGAGTATCTACTGTAGACCTGTACCTTTTGATAAATCCGATCCGAAGAACATCTATGAGATGTGCTCATTCCCGGAAACTAAGGTGGACACGTTTGTCAAGAAGCGACAGTGCTCCGTGCTGATTGACTTCAACCGCAAGAAACTGAGCCGCGTCTATCCAAAAGGACAACGAGTTGAATCGTCCAACTACGATCCAATGCAGATGTGGAACTGCAACATTCACATGGCTGCACTGAATTATCAAACACCAG\n+>Ph18_1/1_1.000_453\n+TGTGGGAAACTGACTGAAATATTATTACACGAAGGTGCTGATATTGAGAAGCGAGATCGTCGCTGTTTTACACCGATACATTGCGCAGCACAAAGTGGCAACGTAGATGTTGTTGTCGCCCTACTGAGTGGTGGATCTGAGGCCAACTCACGAGGCTTTGCTGGCACCACACCTCTTCACATATCAGCCATCAATGGCAATGCTCAGGTTATCGCAAAGCTGTTGAGTTATGGTGCCGATGTTCGTCTGGTTGATGATGGTGGCCTCACGTGTGTTGATGTTGCCAAAACTAAACGAGTGAAGGCTGCTTTGAAGGAAGCATGGTCTGAAGTGACGCAGGCAAAGTCGTCCGATCTGAGCCCGGTGAAGTCGCCCAGTGCTGAAGGCCTGCAGCGAAGCAGTCAATCAAACAGCATCAAGGCGATGACACAGAATCACACGAAGAAAACAGGC\n+>Ph19_1/1_1.000_187\n+CTTCCTTTGATCAATTTAAAAGTATCACCAACATTTAACATTAAACAGCAATCAAACACTTTCGTGTTCA'..b'ATATTTGTCACGTGTGATGAAGCAGTTGTCTTTTTATCA\n+>Ph8122_1/1_1.000_258\n+CATATCGTGTCAATGGTTGTTTACAGCGCAGGTGTTGGCCGTACAGGTACGTTCATCACCTTAGACAGGTTGTTTCAGACGGTGGAAGAGCATGATATTGTCGATATATACGGCATCGTGCACGAGATGCGACTAAATAGACCGTTTATGGTACAAAGTGAGCGACAGTACATCTTCATCCACGCTTGTCTCAAGTACGAACTGGAAGCGAGGGGACTCTGTAACGAAGCTTACGATGATGCTGACGAGGACGGTAAC\n+>Ph8123_1/1_1.000_335\n+AATTCAGTGGCTGATGCCTGTATCCAGATCCAGGCAAGCAGAATTCTCATCAAAGAAAGCATTAATTGTCTTTGTGGAACCATCGTTTGTCATCATGTACAAGTTCTACACATCTGGAAGAATGCTTCTAGCACAGATTTCCACAGTTCACAATGGAGTGTTTTCATTAGAATGGAGTTGCTAATGATAGTATGCTGTATGTTGGATTGGTCAAGTGATATGGAACATCCACTCCATTTTGTTTATTCTTTATTTAAATTATTTATCATAATTTGTAACTGGTTATTTTATCAGTGTATTTACTGGACTTGCCATGTGTTTGTGTGTGTGTGTGT\n+>Ph8124_1/1_1.000_171\n+GTCAATTCCATGTTTACGATGTCACTGGTAAGCAATTACCTTATTAAAGAAAGCTTTCTATGGATACAGTTTCATTGGCACTACACCTGGTTTCTTGGATCAAATCATTTTCGAAATGCATACCCCTTAATCACAGACCAAACTACTGTGCGCAATCTAATGATTTGTCAG\n+>Ph8125_1/1_1.000_135\n+ATACCTGCTTGTAGACTTGAGAATATTACCTATCTGTATGTTCCTGCCATGTTCCAATTATTAAATGCTCTTAGAGATTTACTGATGTGGCATATACCCCCTTGTAATGAGCAGAACCTTTGTCTTAAAAGTTTA\n+>Ph8126_1/1_1.000_282\n+TTAGGCGTTGGCATATTTACTGTCGATGGCTGGCGTATTTACTTTACTCTGTTGCTGACTCACGTGTACTGGTCGGACGAACAGTTCCACACAAACACCACCTTGCAATTACCTGTCACGACTGCTGTGTTCCAAAATGTGTCGCTAAACAAAACAAGTATTTACTTTTCTCGCAACTACGTACAAGATCAAATAACAGACATATGGCGACAACATCCGTTCCAAGTTATTCGCCCATATGTTTATATTAATTCATCGGCTACCTCAGGATTTCTGTATTTC\n+>Ph8127_1/1_1.000_336\n+ACAGACATCCTTCTACCCAGTGATTTCTTGTTCTGCCTGGTTATGTATAAATGCTGTTCTTTGCTTCAACCAGATGCAAGGAAAGGGAATAATATCATTAGCCTAGGCAGAAGTCAAACCCCATTTGTGAAATGTCACCGTCAATCTACAGAACACCCTGGATGCCTGAACTGTCACTGCTATGGTCTACACCATATTCAAAAAATATGGCTAAAATCCACTAAACACTTTACTGCTGCCAAACAGAAAATATTAAACACATGCTTAACAAATATGCAAATAACTTCTTATTGTTTCACAATTAAAAACAAAACATTTATAAATTTAATAAATAAA\n+>Ph8128_1/1_1.000_129\n+GCTGAAGCTAAGATGAATGGGCACCTAAGTATCAGGCAATTACAGATGCTTCATTGTATAACAGTTATTTGGCTAACAGACAAATTCCATTACCCATGCATAGCCAAGAAGTTAATAAATGGACCCAGT\n+>Ph8129_1/1_1.000_171\n+CAAGTGTGTAATCAGTACGGCCACATAACACTGTTGACAAAACCCTTTGAATATTGGCTGTTACTGTCATTATCCTGTATTTATTCAATTCCGAATCATTTTCAGACATTACCGAAACATGTTTGTATGGAATTTCTAAAGAAAGCAAACTTGACTTTTAAGGCAAGAAAA\n+>Ph8130_1/1_1.000_183\n+GTGAAATGTCCACATTTGTATTCATATTATGTTGAATTTATGTGCAAGAATATACTTTTATATGTCTGTGATGCATTTTTTGGGTTATTTATCAAGGGATTTGAAAAAGAGCTGCACATATCCCAGAATTTTTTTGTCATACACTCACTGTGCTTAAAAATGTACCTCTTTTACTCATTCTCT\n+>Ph8131_1/1_1.000_279\n+GAAGATAAGCTGCAGTTGTGTCGGAAGTATTATTTAGGAGGTTTTGCCCTGCTTCCATTCCTGTGGTGTGTAAACAGTGTGTGGTTCTTCAGAGAAGCATTCATTAGGGACCAGTTCCAGCAACAAAAACAAATCAAAACCTATGTGACACGGTCGATGATAGGAACGCTCATCTGGATTGCGATCATCACGACGTGGGTGGTGATATTCCAGAAGTACAGAGCTCAGTGGGGCAAAATAGCCGATGACATGTCATTTATCATACCGAGAGGAGAGCTA\n+>Ph8132_1/1_1.000_126\n+ACTACGACTAAAAGCTACATTAAGAACAGCAACAGCGGAGCAATATTACACAGTGTGTCTGTGATGCTTTCTCGTAATAACTGGAATACAACCTCGTTAAGGCATTACTGTGACAAGAAGAACAGG\n+>Ph8133_1/1_1.000_269\n+ACCGGATATGCCTGCTTGCCGCCGAAATACGAAATCACCTATCAGTCGTTTATCAAATATTCTTTCGTTAACCGAATTGGACCACAATTCTTGCAGCCTAAACTATTATCTACAGTCTTCCGGTGTCAATATTTAGTGACATGCGTAGGAGTGTACTCGATAAGTACTACTTGTTCGTGTGTGTATACGGCCCAGTGTAAGGACATGGCTATCTTAACCTTTGCCTTATCTTTATTGCACGCCTGTCATAATAAATTAATTGTCAGGTC\n+>Ph8134_1/1_1.000_302\n+ACATCTTTGGGCAGAAGTGTATCGGACAAGGATCAAAGTGAAACCGAAGTATTTGTTGGCAGAAAGAACGGTACGATGAACGGATACGAACGCCTGAGAACATTACGTCTCTCGTATCGCAATGCTAACTACATTACTCGCGTGTTTAAACAACCAACACACCAAGCAAAGGCACGCTTAAAAAGGCAGCCTGATGTTTTATTATCGCAGCCTGATGCTGAAGCGGGTACATCAGTCGGCAGTAAGGACAGAGCACAATGTAAGGTCGACGATTCTTTGATTTGTTCAGGTTTCAGAGACTG\n+>Ph8135_1/1_1.000_225\n+ACCATCCGGACATTCCATGTGGTCCGAGATGGCTTTGTTGATAAGCGTGAAGTCAGACAGTTCCAGTTTACAGCTTGGCCTGACCATGGTGTACCTGACCACCCTACACCATTACTGTTGTTTATGCGTCGTGTTAGAGCAATGACTCCTCCTGAGTGTGGTCCTCTTGTAGTCCACTGTAGGTTAGTAAGAACACTGAAACAAACCATAGAGGACGTGCTGGGT\n+>Ph8136_1/1_1.000_157\n+CCGAAATCGAGTTTGCATTATTTATTTACCAAGCCATCAGTGCACGGTTTGTGGAAATATGCAAATTGTCTTGTAATTAATAATAATTCACTGGAGAATACACGTTATCTTATAGAAATTGCTGATTACGCACATCTGCTGAATCGGAGAACGTCAG\n+>Ph8137_1/1_1.000_201\n+ATGTGCTTATGTATAATCTGGAAACTATCTGCAGATAACGAGAGATATCTACCACTCATTGAAATATGGCATCAGAAAATATGCAGCCAAGTCTCTTATAATGACACTTCACTCCTACTAATATGCAATAAAATATGGCTGCTACAGCTAAATCAAATAGGAACAAAGCTAAACCATAACTTGACTAAGATAACTACTCAA\n' |
| b |
| diff -r 000000000000 -r b186cae246bd test-data/input_filter_assemblies/ThThelep_trinity.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input_filter_assemblies/ThThelep_trinity.fasta Fri Feb 01 10:27:42 2019 -0500 |
| b |
| b'@@ -0,0 +1,15700 @@\n+>Th1_1/1_1.000_222\n+CATGCATTGGTTCCTGGAGATGTCTTCAGCCAGTTAAAAAGCTTCCCTGCTAATTTCTCTCTGTGCCTGGGACCGAGACCGAGCAGACTCCCACTTCACAGAGGCAGTCAACCAAACACAACCTTCTCCTCGCCCGGCCACAAAAACTTCCCTGCAGCCCGCAGCCCGGTCTGCCACACAACGTTCGTTCACAGACTCACAGGCCACGCCGATTACATACTC\n+>Th2_1/1_1.000_250\n+CGTAACAACAATTCTGGTAAAACGACGAATATATCGAATGATAACAACAATTGTAATACTATTCGCAGTACTAGCAATTGTAGTAGCATTAGGAATTTTAATAGTAATCCTAAGAACTCTAACATTGAAGGTACTAGCGCTAGTAGTTGTACTACCAGTACTAGTAGCGATGGTAGTTCTACAGAGACTAAATCAAGGTCTGAAGATGGAGTTTTAAAGAGAAGGGGCGCGGTAGAGGAGATGTCGTATG\n+>Th3_1/1_1.000_211\n+TTCCATCGAAATTGGGCCGCCCACGTTTGTAGCTCCTCCATCCTTATATTTTCACATGGAATGGGGAGAGTTTTGGTATTTAGGAGTGAAAAGTTTGTGACTAATCTTAAGCTGAAGTCCTTTTTCGGAACAGAGAAAGATGGTGATATAAACTTAGCGTGGTTCCGTGCTATAGCAACAAGGATACCTCTATCTATTAGAGGTTTAGCCG\n+>Th4_1/1_1.000_126\n+TCAAATTGGGACATTGTTACATCCTTAGCCGTGTATTTGCCCTTTGAGGAGGACGCTTGGCTCTTTCTCTCAAGTAACGCTTTGCGGTCTTTATCCAATTTTGGTTTCGTAATCACGACCTTACTT\n+>Th5_1/1_1.000_168\n+TTTCTTATTCCGAAAACTTTTTTTGTTTCCAATGAATACGACCATCGAAATTTAAACTCCATAAAAACTTATCTGTCCGTATTCTTTCCAAACAAAGCATTTAATTTGGTCTTTATTTTCGTTCGATGGAGTGACGTAAAAGAATTTTTATTCAAGGGTGTAGTGGAA\n+>Th6_1/1_1.000_249\n+AGGCTGCAAAGTCTATCCCCAGATTGCTTCCGGGTAGAATACATTGTGTATATCATACATGTATATATATATAGACGGTTGCCTGTCAGATATAGTCATGTGGTCATCAGTGTAACTATGGGATTAAAATATAATTATGTACATGTATTTAATCACATACCTGTGTACAATAAACGATGGAATACACCTACACGTACATCAACCATGTGTACTGTATTGTGCTTTACATCAATGATTCTATGTTCCTTT\n+>Th7_1/1_1.000_150\n+ATAAGTATAATTACACGCCACATGAAAATCATTCACTTATTCCTCACAAAAATAATAATGTGCCTAGCTCACATTTTCATTCCGGTGGGGTCATGTTTCTGTTCATTTCATGATCATCATGAAATAAACAGAAATGTGATTTTGCTGGAA\n+>Th8_1/1_1.000_216\n+GATAATCTCCATATGCTTAATATGCTGGTGATGTTGGAATTCCATACTGTCAAAATGAAACCATATTTGGGAAGGAAGGATGTCTTTATGATGACCAAAGCAACCCTTACATGCCTGATGATCAAAAAATCAGTTTATAGATGGGATTTAATGAATTCTAAAGAAAAGTTATTGACCATATTCATGAACAAAATAAGAAAATCCCTCTCATTACAG\n+>Th9_1/1_1.000_250\n+AAATTAATAAAGGAATTTAAGTACAGTGTCTCCCAAGCTGCAGCTACTGGAATGGTTAATAGAGAAGTCAATGTAGAAAAGGAACATCAATGGTGGAATGGCGGAAAGCAACAACTCGTGGAGGAGAAGGGTAAAGTTAGAGAGAAAGCTATTGAGAGAGGATCAGACAGACGGAAGCAATTCTCTACAGCTGCTTCACTCACTTGGAAACCTATTATCGATTACAACGAAGAAGAGGAAGAAGAGGAAG\n+>Th10_1/1_1.000_272\n+CTACTACATGTACACATTTCTACTCGATTGAATCACTGGGGGGTCATGTTTCTCTCCGCATCCGTATTCAAATGGTTCATTATCATGATTATCGTATTCCGATATTCCACATTGAGGGCAAGTACAAGTGAAGCGCTGGATGTTTCTTCTCCCAGTGCAACCCGTAGAATGTTAACGCCGAGATATTCCCGCCAGTCACACACAGCTCGTGGCCACCTCTGTGCACATGTCAGCGTCAAGTGCTGCAGCAACACATCTGTGGTCGCACTGAA\n+>Th11_1/1_1.000_177\n+TTCACAATTGTGCCCTTTCCAACACCCCAAAGATGGACAACTGTGTCATATTCAGACACCACATGTGCTGCCAGACATTGGGGCACAATTTGTGCATGCTTCTGTGTTGTCGCTTTGATGTCAACTGACGATCTGCCTCGACTTATACCAGCCATCACAATTCACAATATAACAGGT\n+>Th12_1/1_1.000_202\n+TGGGTGGCACTTGTGAATAAACACTATGGAAAAGTGACGCAGCGTGCAATCACCCGATGTCCCTACGTCAAATCTCTTTGGTTACACAGGTTGATTGCATTGGCATCGAGGTATGGTATTGACACTACAGAAAAAATAACTAAAGATAGCGGAGACAAAAAATATAGTTGTCAAAGCAGTCAAGTTGACGATTTAGTATTGG\n+>Th13_1/1_1.000_153\n+TTGGATGAACTACAGATAAATCCAAGTCTTACAGAAGACAACATTTTTCTCCTTTCGAAGGTTGTACTCCGAAGTACAGCTAAAGTCAAAAGTACAGCTAAGGTCAAGCCACTGCTTTTCGACATTCAATACAGTTGGACCCTAAGAATATTC\n+>Th14_1/1_1.000_252\n+GGAAGGGAAAATTCGAACATTCAGCACATCATTTCAGAGACAAGAGGGACGGTTGATATTCATATAAAAGGAAAGCCAGTAAATCATTTGCCGCCTGTTGAACGTCTCCACCTCGTTTTGGTCGGAGCGGATCCAAAATGTTTCACAGCGGCCGTTTCACTTTGCCAAGATTTGATAAATTCTGTCGTTGATGAATTTCAAAACCATTTCAGAAGCGAGAATCGGCCGCCACCGGTCGAGTACGGATTTCAA\n+>Th15_1/1_1.000_487\n+AAACTAAGGGGAAGGATGGAGGGAGACGGGAGTGCGTTTTCTGTTGGTATAATGGAAGGACGTTCTCCCATGTCATTGTCATTATATGAAGAAACGGGAAAAGACAGACGAATGCCAAGTGGTGATGAGGTTGGCATGCTGGGCAGCATGCAGAGCTCTACTTATAGCAATTCTACTGGGAGTAACAGCAGTACCAGCAGTAGTACGACTACTAGTTCTAGCAGTAGTAGCAGTTCAAACAGTAGTCACTTGGTGAGCAAAAGTATGAGAGAGGAGGAGGACGATAAGCTGTACTTCTCCGACGCCGGCGAGGACGAGGGAAAACGTGCAGCAGTGGGAGTGAACTCTGAAAATATTACTTATGGAACCAGTACCAACGACGGCACTAGTGATGGTGTAAACGGCAATAATTTGCAACCTGATACGACGACATGCGAGGAGGCTCTTAGCTGCTGCGGTTTTGCTAGTGAAGCTCCTTCTGCTTCAG\n+>Th16_1/1_1.000_180\n+TGTGATGACCCATTGATGGCACGAACCCCCGCGGTGTCGGTTATCTATGCTGTTATCTGGTATTCAGACGTGTCGTCGGTATTTAGCGCTTGTGTGTATCGCAGGCGTTGGCTGTTCCATTTTCTCCGCGGCGAGTGCGAGCACAAGAAGCATATTTCTGTGGGCCGATTGTCAACATGG\n+>Th17_1/1_1.000_222\n+ACTGAAACAAAAAAGTCGCGTATTATAAATGAT'..b'GAACCAAAGAGGAATATTCTGTGACAGTTGCAGTTTGTGGGCGCACACCAACTGCTTGGGAATGGACGTGGACACCTACAACCGGCTCGCTGAAACTCCCGACGCTTGGAGCTGTCCTGCCTGCTCCACAACGAATGTGAGTGTTGATCCTGCCAACATAAGCCAGACGTCAACCCCACCGATAAGCCCTGATGACCATGACAGTTCCATCACAACGTCTGACCCA\n+>Th7846_1/1_1.000_198\n+ATAGGAGAACGATATCATACAAATCTTGTTAAGCAATTACATGTTCCTGACAACATGCATTCATACGCGTCATCAGTAGGGTGGAGTAAAAGTCATCCATCTGCCGTTATTGTTTTGTTTTCATGTCCAGAATACTCGCCAGGAATTTCCAATCTCCTCCACAATTTTAAATGTTGTAACGAATTCTGCAGTCAGCTT\n+>Th7847_1/1_1.000_207\n+TGCTACAATGTCATCAACACATTCTACTTGTCAACATATTCAGTTACATCAGTTGTTCAATTATACAACTTACTTCAAACTTGCATAGCGTGCAATGAGAGTTCATCCAGGAGTATAATCGGTCAACAGCAGTTCCCACCCGAAATAGACAACGTCACATTCGAAGTGTGTTACATCACCATATCTGATCACAGAGCAATCGAATTT\n+>Th7848_1/1_1.000_1839\n+TATGGACAACACCGCTTACTCCCAAGTAAGGAAGTAACGAATGGAGAAGGCTGTGTTAAAAGTCTTATGATGATGATTTGGTATCTCGTTGTGTTGGCTTTATGTGGCGGAGGAGGACTTAAGTGGGGGGAGGGGAATGTGTTGTTAGTTGGTGGAGATGGTTTAAGGTATAATGATAGCAAAGAAACAGATAGTATGTCCAATAAGTATTCTACTAAAGTAGTTAATCGTAGCTCTAGCCCTACCTACAGTAGCAGTACTCCTACCAATAGGAACCATAATGATAGTAACAGTTACAGTGCTTCTCTCGCTGCTGCACCCTCTTCTCTATCTTCTTCACAGTCCACATCCTGCTCCCCCTTTCTTCAGTCAAAACTATACCTTAGTATTATGATATTTTTCTTTGCAGTGATAGGTGGCTGTATTCCTTTATTACTTAACAAACCGAATAATCTCCATAAACCTGTTGACCCCGATCTTGTGTCAACTACAACATTGTCCACTGCTCTCCTTCCACCCTGTCCTTCCACCTCTAGTCCATCTCTCCTTACCGATCACCTCCTACACGACAATTCTCCACCACCTCTAGCAATTGCCTCTCCCCCCCCAAACACCACGTCCACCTCTTCTACTTCTTTAACTTCTCGCGAAAACTGCATGCGCTTAGCACTCGGCTTCACTGGAGGAGTTATGATGAGTGCAGGCCTACTGCACTTACTGACGGATTCTCAGAGACAATTGACTGTGTACAGTCAGGCCTTAGGAGGTGTTCCTCTGGCTGAGTTTTCTCTGATCGTCGGCTTGTTGCTAGTAATCTGTCTGGAAACCATTTCGGAAACTTTTGATGCGAGTCACCATCACGTCCATCACTCGATAACTCATGTGCATGTACATCATCAAGCAGTAGATTGTTGGGGAGAAGGTGGAAGAGGAATAGATAGAAGGGAAGATAATTTAGTAGAAGGATATGTTGGGACTACTTGTAAAGGGAAAAATGCGTTGACAGGTAATCTGACTGATGATGGCACTTTGTTGTTTCAGGGAAGTAATGTATCATCAAATGATGGAATCACTCCAGAAGAGACTTCCTCAGGAGGTACTTTAAGTCTAGAGCCGCTCGTACCTCCTCCTTCACTAACCTCCTCCTCCTTCACTAAGCTCATTTGTCCTCTTCCACCTGTTCCTCTTCCTTCTTCTAATTCTAATGTGACTTCGTATCCTTCAACGACTTATCATCCGGCTAAATATAATTACCACGCTCTGAACGGCAGTGCTCCCTCGTCTGTTTCTTGCCCTGTACGTCACCTTCCGTCAATTCCTCCACCTTCACCTCGAGGCGTTGTCGGTTTTCTCCTCCTCCTCGCTCTCTCATTTCATTCACTGATGGAGGGCCTCTCTCTGGGCACAGTCCTCTCGACGGATGCAAGGTTGGTAGGCATAGCGATTTTGAGTCATAAATGTATAACAGCATTTAGCCTTGGAACAAGCTTGGTGAAAGAGTCAACCCCAGTCCGAAAATATTTGCTGGAAATGCTTGTGTTTGCTATTATGACTCCACTAGGGGTTTTAATAGGTGCAGCGGTATCTGCAGCAGTTGGAGGAGATGTGGGAAAAGAAAGAGGCGATTCTAGCAGCAGTATTAACATGTGGGGGATGGTTCCAGGCATTTGTACTGGAATGGGTGCAGGTACTTTTCTAGAAGTCGCCTTGGTGGAAGTAATAGCACCTGAGGTATATAGATGTCGAATAGATTCGTCTTGCAACGTTAGCGATAGATGGTGTATGTTGTTTATGTGGGCGTTGGGCTGCACTGTCATGGGAGGATTAGCAGTGATTCAC\n+>Th7849_1/1_1.000_222\n+CCATATACCTTAATCAACATCCAACTGAGTAGGCTCATGTACTTATATAATATACAGGATTGCCTTCACCTTTACTTGACATATTCACAACAAATACTAAGTATCATTCACATCACACCAGAGCCAGTAATGATTCCCATTTTCAAATTCGTAACTACCAAAATTCAAAAACTTTTCTACATCAATCCCCCAATATATGGTCAGTCCTGCCTAGTGAAATCA\n+>Th7850_1/1_1.000_1179\n+ATAGAAGAGTCCCGGGAGGAGATGAGGCAGATCACTGCTGACTTCAGTAATAAGAAGCTAAGCCTTTCAACTGACAAATCCGAGCTTGAGCGAGCTGCAAAAGATTGTCAAACGTTAGGCGACAGAATCCGCACTGCCGAGCTGTCAAGGAAAACAGCTGGAGAAACCAAGAGACGAATGGATGAGCTACATGCTGAGAGGCAGCAACTGTCTGACAAAATCAGTTCTAAGAGAGAAGCTATTACATCCAAGCGCTCTGATCTAGAAAACAAGAGAAGCGTTCTACTGACACTTCAACACAACATAGATCTCAAAAAGAAAGAAAAGTTGTTAACAGAAACGGAAGCGGATATCGAAAACACTAAACAACAATTGGGAGGCAAAGATCCTACTTTTCTAAAGCAGCGAATGCAAGTAAAACAGAGTGCCCTCAGTGAAGTAGCAAATGACATCGCTCATCTGAATGGACTGATAGAGTCAAATACTGAGTTGACTCAGCAGCACATTATTGAGTTACGTAATCCGATGTATCGAGACATCGATAGTAAACATAGAGATGCCGTTATTCAATTTACTACTCATGAAATGGCAGCGAAGGATCTAACCAGATACCATTCCGCATTAGATAAAGCGATAATGAAGTTCCACTCTGTGAAGATGGAAGAAATCAATCGATGCATAAAGGAATTATGGAACGAGATTTACACAAACAAAGATATCGACAGCATAGCAGTTCGATCAGATACCGATGAACAAAGTGGTACGGACAATTTGGCAGGAACGGTTGCTGGATCGAGATCATACAACTACAGACTGGTCATGACCGCCCGTGGCGTGGATCTAGAAATGCGCGGTCGGTGTTCAGCTGGCCAAAAGGTGTTGGCTTCGTTGATTGTGCGGCTTGCACTGGCGGAATCTTTTTGTGTGAACTGCGGAATTCTAGCGCTCGATGAACCTACTACGAACCTCGATAGATCGAATATTGAGAATTTGGCGAAAGCTCTAGCCAGTCTCATTCAAACGCGCAGGCACAATAAAAACTTTCAGCTAATCCTAATCACGCACGACGAAGAGTTCGTTCGAAGTCTCGCGCGTCACGGTTTATCTGATCATTACATTCAAGTTTCTAAAAACGAGAGCGGCTACTCTACGATGATAAAAACGAACATAAGTGGATTC\n' |
| b |
| diff -r 000000000000 -r b186cae246bd test-data/input_from_CDS_Search/orthogroup_147_sp3_sp3.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input_from_CDS_Search/orthogroup_147_sp3_sp3.fasta Fri Feb 01 10:27:42 2019 -0500 |
| b |
| @@ -0,0 +1,6 @@ +>Ph48961/110 +------------------------------------------------------------ttagttacctcggcttttactgtctgtggcgtcgattctacaaacttctttgcctgtacaagattcatgccagccataacattctttatctgtttaataagagctactttcttggcttcatcaaaaccagcaagtttaacggtaaatgccaccttttctggcttcttctctgatggcgtttcctcgtcttcctttggagcaatagccggcatggctcccatggccatcataggagtgtctgtaatgttcagtgttttttttaataac------------------------------------------------------------------------ +>Ap66541/110 +tccacttctatctttcctcctactgcctctaaagctttcttcaaagcctctgcttcctctttagttacctcggcttttactgtctgtggacttgattctacaaatttctttgcctgtacaagattcattccaggcatcacattctttatctcctttataagtgctactttctttgcttcatcaaaaccagtaagttttacagtaaatgccactttttctggtttcttctctgctggttcttcttcctctgccttggcagcaacagcaggcatggctcccatggccatcattggagtgtctgtgattttcagtgttttctttaataactcgtttaaatctgctacttctattagggtcagtttactaatctcatcaacaaggttctgtattttttcaggg +>Ac62411/110 +tccacttctatctttcctccgactgcctctaaagctttcttcaaagcctctgcttcttctttagttacctcggcttttactgtctgtggacttgactctacaaatttctttgcttgtacaagattcattccaggcatcacgttctttatctcctttatgagtgctactttcttggcttcatcaaaaccagtaagttttacagtaaatgccactttttctggtttcttctctgctggttcttcatcctctgccttggcagcaacagcaggcatggctcccatggccatcattggagtgtctgtgatgttgagtgttttctttaataactcgtttaaatctgctacttctattagtgtcagtttactaatctcatcaacaaggttctgtattttttcaggg |
| b |
| diff -r 000000000000 -r b186cae246bd test-data/input_from_CDS_Search/orthogroup_17_sp3_sp3.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input_from_CDS_Search/orthogroup_17_sp3_sp3.fasta Fri Feb 01 10:27:42 2019 -0500 |
| b |
| @@ -0,0 +1,6 @@ +>Ac28231/110 +atggatcaggtaatgcagttcattgagccagccaggcagtttgccaaggattccatccgactggtgaaaaggtgtacgaagccagatagaagagagttccagaagatagccatggccactgctattggttttgccatcatgggatttattggcttctttgtaaagctcatccacataccaatcaataatatcattgtgggttc? +>Am49621/110 +atggatcaggttgtgcagtttgtcgagccggcaaagcagtttgcgaaggactccatccgattggtgaaaagatgcaccaagccagatcgcaaagaatttcagaagattgccatggcgactgcgataggatttgctatcatgggtttcatcggattctttgtcaaattaatccacattcccatcaacaacatcatcgtaggttca +>Pg54991/110 +------------------------gagccagcaaagcagtttgcaaaagattctatacgactggttaaaagatgcaccaaaccagatagaagagaattccagaagatagccatggcaactgctattggttttgctattatggggtttatcggatttttcgttaagctgatccatataccaatcaacaacatcattgtgggttcc |
| b |
| diff -r 000000000000 -r b186cae246bd test-data/input_from_CDS_Search/orthogroup_183_sp3_sp3.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input_from_CDS_Search/orthogroup_183_sp3_sp3.fasta Fri Feb 01 10:27:42 2019 -0500 |
| b |
| @@ -0,0 +1,6 @@ +>Th20211/110 +------------------------------gcccgtaagatgaaggaccatcgtcgagaccagaaatggcacgacaaagattacaagaaaagccacttgggtactcgctggaaggccaacgccttcggaggtgcatcccatgccaagggaatcgtgctcgagaaagtaggtgttgaggccaagcagcccaactctgccatccgcaagtgtgtgcgagttcagctgatcaagaacggcaaaaagatcacggccttcgtaccgcgggacggttgtctcaactacattgaggagaacgatgaggtgctgatcgctggattcggacgaaagggccacgctgtcggagatattcccggcgttcgcttcaag------------------------------------------------------------------ +>Ap32511/110 +aagatgggcaagcctcatggacttaggacagcccgtaagatgcgggaccaccgccgtgaccagaggtggcatgataaagactacaaaaagagtcatttgggtactcgctggaaggccaatccatttggtggcgcatcccatgctaagggaatcgtcctcgagaaagtaggtgttgaagccaaacagcccaactctgccattcgtaaatgtgtcagagtgcagttgataaaaaatggcaagaaaattactgcttttgtaccaagggacggttgtctgaactacatcgaggagaatgatgaagttctcattgctggatttggtcgtaaaggtcatgctgtaggagatattcctggtgtacgcttcaaggttgttaaagtggcaaatgtgtccctgttggccttgtacaaggagaagaaggaaagaccaaggtct +>Ac8151/1100 +aagatgggcaagcctcacggactcagaacagcccgtaagatgcgggaccaccgccgtgaccagaggtggcatgataaggactacaaaaagagtcacttgggtactcgctggaaggccaatccctttggtggtgcttcccacgccaagggaatcgtcctcgagaaagtaggtgttgaagccaaacagcccaactctgccattcggaaatgtgtcagagtgcagcttataaaaaacggcaagaaaattactgcctttgtaccaagggatggctgtctgaactacattgaggagaatgacgaagttctcattgctggatttggccgtaaaggtcatgctgtaggagatattcctggtgtacgcttcaaggttgttaaagtggcaaacgtatccctgttggctttgtacaaggagaagaaagaaagaccaaggtct |
| b |
| diff -r 000000000000 -r b186cae246bd test-data/input_from_CDS_Search/orthogroup_334_sp3_sp3.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input_from_CDS_Search/orthogroup_334_sp3_sp3.fasta Fri Feb 01 10:27:42 2019 -0500 |
| b |
| @@ -0,0 +1,6 @@ +>Ap2871/1100 +gaggacttcaccttccttttgctttctagagtctcaatcacattctggtacttccaaccaacctcatgggaaaggcgtccaagaacacagtacttgcgtctagccttcagtctaaggactctcagagctgagggcactaccatgcgtttcttcttgtcatatggaggtggaattccctcaaacaccttcaggtgggacaaagccacctttccacgagtaagcttgtgtggcaacatgccacgcacagttctccagaatatcttgcttggagctcggaagtggaaaggaccacggctcggattagtgttcattcgcttccgcaagaaagccaagtattttaacttgttcctg +>Th30731/110 +------------------------------------------------------------------------------------------------------------------------------------------accatacgcttctgcttgtcatatggaggggggatgccttcaaacactttcattctctccaaagctgccttgccacggggtaacttatgtggcaacattcctctgactgttctccagaaaatcttgctgggagcacggaagtggaatggaccacggcttggtttggtgttcatacgctttctaaggaaatccaagtacttgagt--------- +>Pg43701/110 +gtggacttgagctttcttttgttttctaatgtagtgatgacattctggtacttccagcccacttcatgtgacaggcggccaagaacacatgacttgcgtctagctttaagtcgaaggaccttcaaagccgagggaaccaccatacgtttctgcttgtcaaatggtggagggatgccctcaaagaccttgagacggtccagagcttgcttaccacgtgtcagcttatgtggcaacataccacgcacagttctccaaaatattttacttggggcacggaagtggtatgggccacggcttggattggtgttcattcgtttccttaggaaagcaaggtacttcagtttgttcctg |
