| Next changeset 1:8c4e2933a17a (2015-08-26) |
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Commit message:
Imported from capsule None |
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added:
alignment.xml chimera.xml clustering.xml dereplication.xml masking.xml search.xml shuffling.xml sorting.xml test-data/AF091148.fsa.bz2 test-data/AF091148_first_rep.fsa.bz2 test-data/BioMarKs5k.fsa.bz2 test-data/PR2-18S-rRNA-V4.derep.fsa.bz2 test-data/Rfam_11_0.repr.fasta.bz2 test-data/alignment_result1.fasta test-data/chimera_result1.fasta test-data/chimera_uchimeout_result1.tabular test-data/clustering_blast6out_result1.tab test-data/clustering_centroids_result1.fasta test-data/clustering_notmatched_result1.fasta test-data/db.fasta test-data/dereplication_result1.fasta test-data/masking_result1.fasta test-data/masking_result2.fasta test-data/query.fasta test-data/search_blast6out_result1.tabular test-data/search_dbmatched_result1.fasta test-data/search_fastapairs_result2.fasta test-data/search_matched_result2.fasta test-data/search_userfields_result2.tabular test-data/shuffling_result1.fasta test-data/sorting_result1.fasta test-data/sorting_result2.fasta test-data/three_human_mRNA.fasta tool_dependencies.xml vsearch_macros.xml |
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| diff -r 000000000000 -r fae6527990af alignment.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/alignment.xml Thu May 21 03:58:09 2015 -0400 |
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| @@ -0,0 +1,66 @@ +<tool id="vsearch_alignment" name="VSearch alignment" version="@VERSION@.0"> + <description></description> + <macros> + <import>vsearch_macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="stdio" /> + <expand macro="version_command" /> + <command> +<![CDATA[ + vsearch + @GENERAL@ + $acceptall + --id $id + --iddef $iddef + --allpairs_global "$infile" + --alnout $outfile + --query_cov $query_cov + @USERFIELDS@ +]]> + </command> + <inputs> + <param name="infile" type="data" format="fasta" label="Select your FASTA file" help="(--allpairs_global)" /> + <expand macro="id_and_iddef" /> + <param name="acceptall" type="boolean" truevalue="--acceptall" falsevalue="" checked="False" + label="Output all pairwise alignments" help="This option overrides all other accept/reject options including identity. (--acceptall)"/> + <param name="query_cov" type="float" value="" optional="True" label="Reject if fraction of query seq. aligned lower than this value" + help="(--query_cov)"/> + <expand macro="userfields" /> + </inputs> + <outputs> + <data name="outfile" format="fasta" label="${tool.name} on ${on_string}" /> + </outputs> + <tests> + <test> + <param name="infile" value="Rfam_11_0.repr.fasta.bz2" ftype="fasta" /> + <param name="acceptall" value=""/> + <param name="id" value="0.97"/> + <param name="query_cov" value="0.95"/> + <param name="userfields" value="query,target"/> + <output name="outfile" file="alignment_result1.fasta" lines_diff="4" ftype="fasta" /> + </test> + </tests> + <help> +<![CDATA[ +**What it does** + +Pairwise alignments of all sequences. + + +Alignment options (most searching options also apply) + --allpairs_global FILENAME perform global alignment of all sequence pairs + --alnout FILENAME filename for human-readable alignment output + --acceptall output all pairwise alignments + +@EXTERNAL_DOCUMENTATION@ + +------- + +@REFERENCES@ + + +]]> + </help> + <expand macro="citations" /> +</tool> |
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| diff -r 000000000000 -r fae6527990af chimera.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/chimera.xml Thu May 21 03:58:09 2015 -0400 |
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| @@ -0,0 +1,135 @@ +<tool id="vsearch_chimera_detection" name="VSearch chimera detection" version="@VERSION@.0"> + <description></description> + <macros> + <import>vsearch_macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="stdio" /> + <expand macro="version_command" /> + <command> +<![CDATA[ + vsearch + @GENERAL@ + --abskew $abskew + --chimeras $outfile + --dn $dn + --mindiffs $mindiffs + --mindiv $mindiv + --minh $minh + --xn $xn + $self_param + $selfid_param + #if $detection_mode.detection_mode_select == 'denovo': + --uchime_denovo $detection_mode.infile_denovo + #else: + --uchime_ref $detection_mode.infile_reference + --db $detection_mode.db + #end if + + #if 'nonchimeras' in str($outputs): + --nonchimeras $nonchimeras + #end if + #if 'uchimealns' in str($outputs): + --uchimealns $uchimealns + #end if + #if 'uchimeout' in str($outputs): + --uchimeout $uchimeout + #end if + +]]> + </command> + <inputs> + <conditional name="detection_mode"> + <param name="detection_mode_select" type="select" label="Detect chimeras" help=""> + <option value="denovo">de novo</option> + <option value="reference">using a reference database</option> + </param> + <when value="denovo"> + <param name="infile_denovo" type="data" format="fasta" label="Select your FASTA file" help="(--uchime_denovo)" /> + </when> + <when value="reference"> + <param name="infile_reference" type="data" format="fasta" label="Select your FASTA file" help="(--uchime_ref)" /> + <param name="db" type="data" format="fasta" label="Select your reference database" help="(--db)" /> + </when> + </conditional> + + <param name="abskew" type="float" value="2.0" label="Minimal abundance ratio of parent vs chimera" + help="(--abskew)"/> + <param name="dn" type="float" value="1.4" label="'no' vote pseudo count" + help="(--dn)"/> + <param name="xn" type="float" value="8.0" label="'no' vote weight" + help="(--xn)"/> + <param name="mindiffs" type="integer" value="3" label="Minimum number of differences in segment" + help="(--mindiffs)"/> + <param name="mindiv" type="float" value="0.8" label="Minimum divergence from closest parent" + help="(--mindiv)"/> + <param name="minh" type="float" value="0.28" label="Minimum score" + help="(--minh)"/> + + <expand macro="self_and_selfid" /> + + <param name="outputs" type="select" multiple="True" optional="True" + label="Select output formats" help="(--qmask)"> + <option value="nonchimeras">Non-chimeric sequences (--nonchimeras)</option> + <option value="uchimealns">Chimera alignments (--uchimealns)</option> + <option value="uchimeout">Chimera info to tab-separated (--uchimeout)</option> + </param> + + </inputs> + <outputs> + <data name="outfile" format="fasta" label="${tool.name} on ${on_string}" /> + <data name="nonchimeras" format="fasta" label="${tool.name} on ${on_string}: Non Chimera"> + <filter>'nonchimeras' in outputs</filter> + </data> + <data name="uchimealns" format="fasta" label="${tool.name} on ${on_string}: Chimera Alignments"> + <filter>'uchimealns' in outputs</filter> + </data> + <data name="uchimeout" format="tabular" label="${tool.name} on ${on_string}: Chimera Information"> + <filter>'uchimeout' in outputs</filter> + </data> + </outputs> + <tests> + <test> + <param name="detection_mode_select" value="denovo"/> + <param name="infile_denovo" value="PR2-18S-rRNA-V4.derep.fsa.bz2" ftype="fasta" /> + <param name="outputs" value="uchimeout"/> + <output name="outfile" file="chimera_result1.fasta" ftype="fasta" /> + <output name="uchimeout" file="chimera_uchimeout_result1.tabular" ftype="tabular" /> + </test> + </tests> + <help> +<![CDATA[ +**What it does** + +Sequence chimera detection based on a different scoring functions. + +Chimera detection options + --abskew REAL min abundance ratio of parent vs chimera (2.0) + --alignwidth INT width of alignment in uchimealn output (80) + --chimeras FILENAME output chimeric sequences to file + --db FILENAME reference database for --uchime_ref + --dn REAL 'no' vote pseudo-count (1.4) + --mindiffs INT minimum number of differences in segment (3) + --mindiv REAL minimum divergence from closest parent (0.8) + --minh REAL minimum score (0.28) + --nonchimeras FILENAME output non-chimeric sequences to file + --self exclude identical labels for --uchime_ref + --selfid exclude identical sequences for --uchime_ref + --uchime_denovo FILENAME detect chimeras de novo + --uchime_ref FILENAME detect chimeras using a reference database + --uchimealns FILENAME output chimera alignments to file + --uchimeout FILENAME output to chimera info to tab-separated file + --uchimeout5 make output compatible with uchime version 5 + --xn REAL 'no' vote weight (8.0) + +@EXTERNAL_DOCUMENTATION@ + +------- + +@REFERENCES@ + + +]]> + </help> + <expand macro="citations" /> +</tool> |
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| diff -r 000000000000 -r fae6527990af clustering.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/clustering.xml Thu May 21 03:58:09 2015 -0400 |
| [ |
| @@ -0,0 +1,167 @@ +<tool id="vsearch_clustering" name="VSearch clustering" version="@VERSION@.0"> + <description></description> + <macros> + <import>vsearch_macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="stdio" /> + <expand macro="version_command" /> + <command> +<![CDATA[ + vsearch + @GENERAL@ + --cluster_fast "$infile" + ##--cluster_smallmem FILENAME cluster sequences using a small amount of memory + ##--clusters STRING output each cluster to a separate FASTA file + + #if $maxrejects: + --maxrejects $maxrejects + #end if + #if $maxaccepts: + --maxaccepts $maxaccepts + #end if + + $cons_truncate + --id $id + ##--iddef $iddef + + #if '--msaout' in str($outputs): + --msaout $msaout + #end if + #if '--consout' in str($outputs): + --consout $consout + #end if + #if '--centroids' in str($outputs): + --centroids $centroids + #end if + #if '--alnout' in str($outputs): + --alnout $alnout + #end if + #if '--blast6out' in str($outputs): + --blast6out $blast6out + #end if + #if '--notmatched' in str($outputs): + --notmatched $notmatched + #end if + #if '--fastapairs' in str($outputs): + --fastapairs $fastapairs + #end if + #if '--matched' in str($outputs): + --matched $matched + #end if + #if $qmask != 'no': + --qmask $qmask + #end if + #if $sizein: + --sizein $sizein + #end if + #if $sizeout: + --sizeout $sizeout + #end if + --strand $strand + --usersort $usersort + +]]> + </command> + <inputs> + <param name="infile" type="data" format="fasta" label="Select your FASTA file" help="(--cluster_fast)" /> + <expand macro="id_and_iddef" /> + <param name="cons_truncate" type="boolean" truevalue="--cons_truncate" falsevalue="" checked="False" + label="Do not ignore terminal gaps in MSA for consensus" help="(--cons_truncate)"/> + <param name="usersort" type="boolean" truevalue="--usersort" falsevalue="" checked="False" + label="Indicate that input sequences are presorted" help="(--usersort)"/> + <expand macro="qmask" /> + <expand macro="sizein" /> + <expand macro="sizeout" /> + <expand macro="strand" /> + <expand macro="maxrejects" /> + <expand macro="maxaccepts" /> + <expand macro="general_output"> + <option value="--msaout">Multiple sequence alignments</option> + <option value="--consout">Cluster consensus sequences</option> + <option value="--centroids">Centroid sequences</option> + <option value="--notmatched">Write non-matching query sequences to separate file</option> + <option value="--matched">Write matching query sequences to separate file</option> + </expand> + + </inputs> + <outputs> + <data name="msaout" format="fasta" label="${tool.name} on ${on_string}: Multiple Sequence Alignments"> + <filter>'--msaout' in outputs</filter> + </data> + <data name="consout" format="fasta" label="${tool.name} on ${on_string}: Consensus Sequences"> + <filter>'--consout' in outputs</filter> + </data> + <data name="centroids" format="fasta" label="${tool.name} on ${on_string}: Cluster centroids"> + <filter>'--centroids' in outputs</filter> + </data> + <data name="alnout" format="fasta" label="${tool.name} on ${on_string}: Alignment"> + <filter>'--alnout' in outputs</filter> + </data> + <data name="notmatched" format="fasta" label="${tool.name} on ${on_string}: Non-matched queries"> + <filter>'--notmatched' in outputs</filter> + </data> + <data name="matched" format="fasta" label="${tool.name} on ${on_string}: Matching query sequences"> + <filter>'--matched' in outputs</filter> + </data> + <data name="blast6out" format="tabular" label="${tool.name} on ${on_string}: BLAST like tabular"> + <filter>'--blast6out' in outputs</filter> + </data> + <data name="fastapairs" format="fasta" label="${tool.name} on ${on_string}: Query/Target sequences"> + <filter>'--fastapairs' in outputs</filter> + </data> + </outputs> + <tests> + <test> + <param name="infile" value="BioMarKs5k.fsa.bz2" ftype="fasta" /> + <param name="id" value="0.99"/> + <param name="maxaccepts" value="1"/> + <param name="maxrejects" value="2"/> + <param name="sizeout" value="--sizeout"/> + <param name="outputs" value="--centroids,--alnout,--blast6out,--notmatched" /> + <output name="centroids" file="clustering_centroids_result1.fasta" ftype="fasta" /> + <output name="blast6out" file="clustering_blast6out_result1.tab" ftype="tabular" /> + <output name="notmatched" file="clustering_notmatched_result1.fasta" ftype="fasta" /> + <!-- The result following result files would be too big --> + <!--output name="matched" file="clustering_matched_result1.fasta" ftype="fasta" /--> + <!--output name="alnout" file="clustering_alnout_result1.fasta" lines_diff="2" ftype="fasta" /--> + <!--output name="fastapairs" file="clustering_fastapairs_result1.fasta" ftype="fasta" /--> + <!--output name="msaout" file="clustering_msaout_result1.fasta" ftype="fasta" /--> + </test> + </tests> + <help> +<![CDATA[ +**What it does** + +vsearch implements a single-pass, greedy star-clustering algorithm, similar to the algorithms +implemented in usearch, DNAclust and sumaclust for example. + + +Clustering options (most searching options also apply) + --centroids FILENAME output centroid sequences to FASTA file + --cluster_fast FILENAME cluster sequences fast + --cluster_smallmem FILENAME cluster sequences using a small amount of memory + --clusters STRING output each cluster to a separate FASTA file + --consout FILENAME output cluster consensus sequences to FASTA file + --cons_truncate do not ignore terminal gaps in MSA for consensus + --id REAL reject if identity lower + --iddef INT id definition, 0-4=CD-HIT,all,int,MBL,BLAST (2) + --msaout FILENAME output multiple seq. alignments to FASTA file + --qmask mask seqs with dust, soft or no method (dust) + --sizein read abundance annotation from input + --sizeout write cluster abundances to centroid file + --strand cluster using "plus" or "both" strands (plus) + --usersort indicate that input sequences are presorted + + +@EXTERNAL_DOCUMENTATION@ + +------- + +@REFERENCES@ + + +]]> + </help> + <expand macro="citations" /> +</tool> |
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| diff -r 000000000000 -r fae6527990af dereplication.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dereplication.xml Thu May 21 03:58:09 2015 -0400 |
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| @@ -0,0 +1,93 @@ +<tool id="vsearch_dereplication" name="VSearch dereplication" version="@VERSION@.0"> + <description></description> + <macros> + <import>vsearch_macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="stdio" /> + <expand macro="version_command" /> + <command> +<![CDATA[ + vsearch + @GENERAL@ + --derep_fulllength $infile + #if $maxuniquesize: + --maxuniquesize $maxuniquesize + #end if + #if $minuniquesize: + --minuniquesize $minuniquesize + #end if + --output $outfile + #if $sizein: + --sizein $sizein + #end if + #if $sizeout: + --sizeout $sizeout + #end if + --strand $strand + --topn $topn + #if $uc: + --uc $uc + #end if +]]> + </command> + <inputs> + <param name="infile" type="data" format="fasta" label="Select your FASTA file" help="(--derep_fulllength)" /> + <expand macro="topn" /> + <expand macro="sizein" /> + <expand macro="sizeout" /> + <expand macro="strand" /> + <expand macro="uclust_like_output" /> + <param name="minuniquesize" type="integer" value="" optional="True" label="Minimum abundance" + help="(--minuniquesize)"/> + <param name="maxuniquesize" type="integer" value="" optional="True" label="Maximum abundance" + help="(--maxuniquesize)"/> + </inputs> + <outputs> + <data name="outfile" format="fasta" label="${tool.name} on ${on_string}" /> + <data name="uc" format="fasta" label="${tool.name} on ${on_string}: UCLUST like output"> + <filter>uc is True</filter> + </data> + </outputs> + <tests> + <test> + <param name="infile" value="AF091148_first_rep.fsa.bz2" ftype="fasta" /> + <param name="strand" value="both" /> + <param name="minuniquesize" value="1" /> + <param name="maxuniquesize" value="100000" /> + <param name="sizeout" value="--sizeout"/> + <param name="topn" value="10000" /> + <output name="outfile" file="dereplication_result1.fasta" ftype="fasta" /> + </test> + </tests> + <help> +<![CDATA[ +**What it does** + +Merge strictly identical sequences contained in filename. Identical sequences are +defined as having the same length and the same string of nucleotides (case insensitive, +T and U are considered the same). + +Dereplication options + --derep_fulllength FILENAME dereplicate sequences in the given FASTA file + --maxuniquesize INT maximum abundance for output from dereplication + --minuniquesize INT minimum abundance for output from dereplication + --output FILENAME output FASTA file + --sizein read abundance annotation from input + --sizeout write abundance annotation to output + --strand dereplicate "plus" or "both" strands (plus) + --topn INT output just the n most abundant sequences + --uc FILENAME filename for UCLUST-like output + + +@EXTERNAL_DOCUMENTATION@ + +------- + +@REFERENCES@ + + +]]> + </help> + <expand macro="citations" /> +</tool> |
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| diff -r 000000000000 -r fae6527990af masking.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/masking.xml Thu May 21 03:58:09 2015 -0400 |
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| @@ -0,0 +1,79 @@ +<tool id="vsearch_masking" name="VSearch masking" version="@VERSION@.0"> + <description></description> + <macros> + <import>vsearch_macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="stdio" /> + <expand macro="version_command" /> + <command> +<![CDATA[ + vsearch + @GENERAL@ + #if $qmask != 'no': + --qmask $qmask + #end if + $hardmask + --maskfasta "$infile" + --output $outfile + +]]> + </command> + <inputs> + <param name="infile" type="data" format="fasta" label="Select your FASTA file" help="(--maskfasta)" /> + <expand macro="qmask" /> + <expand macro="hardmask" /> + </inputs> + <outputs> + <data name="outfile" format="fasta" label="${tool.name} on ${on_string}" /> + </outputs> + <tests> + <test> + <param name="infile" value="db.fasta" ftype="fasta" /> + <param name="qmask" value="dust"/> + <param name="hardmask" value="True"/> + <output name="outfile" file="masking_result1.fasta" ftype="fasta" /> + </test> + <test> + <param name="infile" value="db.fasta" ftype="fasta" /> + <param name="qmask" value="soft"/> + <param name="hardmask" value="True"/> + <output name="outfile" file="masking_result2.fasta" ftype="fasta" /> + </test> + </tests> + <help> +<![CDATA[ +**What it does** + +An input sequence can be composed of lower- or uppercase nucleotides. Lowercase nucleotides +are silently set to uppercase before masking, unless the −−qmask soft option is used. +Here are the results of combined masking options −−qmask (or −−dbmask for database sequences) and −−hardmask, assuming each input sequences contains both lower and uppercase nucleotides: + +===== ======== ================================================ +qmask hardmask action +===== ======== ================================================ +none off no masking, all symbols uppercased +none on no masking, all symbols uppercased +dust off masked symbols lowercased, others uppercased +dust on masked symbols changed to Ns, others uppercased +soft off lowercase symbols masked, no case changes +soft on lowercase symbols masked and changed to Ns +===== ======== ================================================ + +Masking options + --hardmask mask by replacing with N instead of lower case + --maskfasta FILENAME mask sequences in the given FASTA file + --output FILENAME output to specified FASTA file + --qmask mask seqs with "dust", "soft" or "none" method (dust) + +@EXTERNAL_DOCUMENTATION@ + +------- + +@REFERENCES@ + + +]]> + </help> + <expand macro="citations" /> +</tool> |
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| diff -r 000000000000 -r fae6527990af search.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/search.xml Thu May 21 03:58:09 2015 -0400 |
| [ |
| b'@@ -0,0 +1,391 @@\n+<tool id="vsearch_search" name="VSearch search" version="@VERSION@.0">\n+ <description></description>\n+ <macros>\n+ <import>vsearch_macros.xml</import>\n+ </macros>\n+ <expand macro="requirements" />\n+ <expand macro="stdio" />\n+ <expand macro="version_command" />\n+ <command>\n+<![CDATA[\n+ vsearch\n+\n+ @GENERAL@\n+ --db $dbfile\n+ --dbmask $dbmask\n+\n+ ##--fulldp full dynamic programming alignment (always on)\n+ ##--gapext STRING penalties for gap extension (2I/1E)\n+ ##--gapopen STRING penalties for gap opening (20I/2E)\n+ $hardmask\n+ --id $id\n+ --iddef $iddef\n+\n+ #if $qmask != \'no\':\n+ --qmask $qmask\n+ #end if\n+\n+ ## --rowlen INT width of alignment lines in alnout output (64)\n+\n+ $self_param\n+ $selfid_param\n+ #if $sizeout:\n+ --sizeout $sizeout\n+ #end if\n+ --strand $strand\n+ --usearch_global $queryfile\n+\n+ #if \'--alnout\' in str($outputs):\n+ --alnout $alnout\n+ #end if\n+ #if \'--blast6out\' in str($outputs):\n+ --blast6out $blast6out\n+ #end if\n+ #if \'--dbmatched\' in str($outputs):\n+ --dbmatched $dbmatched\n+ #end if\n+ #if \'--dbnotmatched\' in str($outputs):\n+ --dbnotmatched $dbnotmatched\n+ #end if\n+ #if \'--fastapairs\' in str($outputs):\n+ --fastapairs $fastapairs\n+ #end if\n+ #if \'--notmatched\' in str($outputs):\n+ --notmatched $notmatched\n+ #end if\n+ #if \'--matched\' in str($outputs):\n+ --matched $matched\n+ #end if\n+\n+ #if $adv_opts.adv_opts_selector == "advanced":\n+ $adv_opts.top_hits_only\n+ $adv_opts.rightjust\n+ $adv_opts.leftjust\n+ --target_cov $adv_opts.target_cov\n+ --query_cov $adv_opts.query_cov\n+\n+\n+ #if $adv_opts.maxid:\n+ --maxid $adv_opts.maxid\n+ #end if\n+ #if $adv_opts.maxqt:\n+ --maxqt $adv_opts.maxqsize\n+ #end if\n+ #if $adv_opts.maxsizeratio:\n+ --maxsizeratio $adv_opts.maxsizeratio\n+ #end if\n+ #if $adv_opts.maxsl:\n+ --maxsl $adv_opts.maxsl\n+ #end if\n+ #if $adv_opts.mid:\n+ --mid $adv_opts.mid\n+ #end if\n+ #if $adv_opts.minqt:\n+ --minqt $adv_opts.minqt\n+ #end if\n+ #if $adv_opts.minsizeratio:\n+ --minsizeratio $adv_opts.minseqlength\n+ #end if\n+ #if $adv_opts.minsl:\n+ --minsl $adv_opts.minsl\n+ #end if\n+\n+ #if $adv_opts.mintsize:\n+ --mintsize $adv_opts.mintsize\n+ #end if\n+ #if $adv_opts.mismatch:\n+ --mismatch $adv_opts.mismatch\n+ #end if\n+ #if $adv_opts.maxqsize:\n+ --maxqsize $adv_opts.maxqsize\n+ #end if\n+ #if $adv_opts.mincols:\n+ --mincols $adv_opts.mincols\n+ #end if\n+ #if $adv_opts.maxsubs:\n+ --maxsubs $adv_opts.maxsubs\n+ #end if\n+ #if $adv_opts.maxrejects:\n+ --maxrejects $adv_opts.maxrejects\n+ #end if\n+ #if $adv_opts.maxaccepts:\n+ --maxaccepts $adv_opts.maxaccepts\n+ #end if\n+ #if $adv_opts.maxdiffs:\n+ --maxdiffs $adv_opts.maxdiffs\n+ #end if\n+ #if $adv_opts.maxgaps:\n+ --maxgaps $adv_opts.maxgaps\n+ #end if\n+ #if $adv_opts.maxhits:\n+ --maxhits $adv_opts.maxhits\n+ #end if\n+ #if $adv_opts.match:\n+ --match $adv_opts.match\n+ #end if\n+ #if $adv_opts.idprefix:\n+ '..b' --blast6out FILENAME filename for blast-like tab-separated output\n+ --db FILENAME filename for FASTA formatted database for search\n+ --dbmask mask db with "dust", "soft" or "none" method (dust)\n+ --dbmatched FILENAME FASTA file for matching database sequences\n+ --dbnotmatched FILENAME FASTA file for non-matching database sequences\n+ --fastapairs FILENAME FASTA file with pairs of query and target\n+ --fulldp full dynamic programming alignment (always on)\n+ --gapext STRING penalties for gap extension (2I/1E)\n+ --gapopen STRING penalties for gap opening (20I/2E)\n+ --hardmask mask by replacing with N instead of lower case\n+ --id REAL reject if identity lower\n+ --iddef INT id definition, 0-4=CD-HIT,all,int,MBL,BLAST (2)\n+ --idprefix INT reject if first n nucleotides do not match\n+ --idsuffix INT reject if last n nucleotides do not match\n+ --leftjust reject if terminal gaps at alignment left end\n+ --match INT score for match (2)\n+ --matched FILENAME FASTA file for matching query sequences\n+ --maxaccepts INT number of hits to accept and show per strand (1)\n+ --maxdiffs INT reject if more substitutions or indels\n+ --maxgaps INT reject if more indels\n+ --maxhits INT maximum number of hits to show (unlimited)\n+ --maxid REAL reject if identity higher\n+ --maxqsize INT reject if query abundance larger\n+ --maxqt REAL reject if query/target length ratio higher\n+ --maxrejects INT number of non-matching hits to consider (32)\n+ --maxsizeratio REAL reject if query/target abundance ratio higher\n+ --maxsl REAL reject if shorter/longer length ratio higher\n+ --maxsubs INT reject if more substitutions\n+ --mid REAL reject if percent identity lower, ignoring gaps\n+ --mincols INT reject if alignment length shorter\n+ --minqt REAL reject if query/target length ratio lower\n+ --minsizeratio REAL reject if query/target abundance ratio lower\n+ --minsl REAL reject if shorter/longer length ratio lower\n+ --mintsize INT reject if target abundance lower\n+ --mismatch INT score for mismatch (-4)\n+ --notmatched FILENAME FASTA file for non-matching query sequences\n+ --output_no_hits output non-matching queries to output files\n+ --qmask mask query with "dust", "soft" or "none" method (dust)\n+ --query_cov REAL reject if fraction of query seq. aligned lower\n+ --rightjust reject if terminal gaps at alignment right end\n+ --rowlen INT width of alignment lines in alnout output (64)\n+ --self reject if labels identical\n+ --selfid reject if sequences identical\n+ --sizeout write abundance annotation to output\n+ --strand search "plus" or "both" strands (plus)\n+ --target_cov REAL reject if fraction of target seq. aligned lower\n+ --top_hits_only output only hits with identity equal to the best\n+ --uc FILENAME filename for UCLUST-like output\n+ --uc_allhits show all, not just top hit with uc output\n+ --usearch_global FILENAME filename of queries for global alignment search\n+ --userfields STRING fields to output in userout file\n+ --userout FILENAME filename for user-defined tab-separated output\n+ --weak_id REAL include aligned hits with >= id; continue search\n+ --wordlength INT length of words for database index 3-15 (8)\n+\n+@EXTERNAL_DOCUMENTATION@\n+\n+-------\n+\n+@REFERENCES@\n+\n+\n+]]>\n+ </help>\n+ <expand macro="citations" />\n+</tool>\n' |
| b |
| diff -r 000000000000 -r fae6527990af shuffling.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/shuffling.xml Thu May 21 03:58:09 2015 -0400 |
| [ |
| @@ -0,0 +1,59 @@ +<tool id="vsearch_shuffling" name="VSearch shuffling" version="@VERSION@.0"> + <description></description> + <macros> + <import>vsearch_macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="stdio" /> + <expand macro="version_command" /> + <command> +<![CDATA[ + vsearch + @GENERAL@ + --output $outfile + --seed $seed + --shuffle $infile + --topn $topn +]]> + </command> + <inputs> + <param name="infile" type="data" format="fasta" label="Select your FASTA file" help="(--shuffle)" /> + <param name="seed" type="integer" value="0" label="Seed" + help="Zero to use random data source. (--seed)"/> + <expand macro="topn" /> + </inputs> + <outputs> + <data name="outfile" format="fasta" label="${tool.name} on ${on_string}" /> + </outputs> + <tests> + <test> + <param name="infile" value="db.fasta" ftype="fasta" /> + <param name="seed" value="1"/> + <param name="topn" value="5"/> + <output name="outfile" file="shuffling_result1.fasta" ftype="fasta" /> + </test> + </tests> + <help> +<![CDATA[ +**What it does** + +Sequence shuffling to obtain new random sequences. + +Shuffling options + --output FILENAME output to specified FASTA file + --seed INT seed for PRNG, zero to use random data source (0) + --shuffle FILENAME shuffle order of sequences pseudo-randomly + --topn INT output just first n sequences + + +@EXTERNAL_DOCUMENTATION@ + +------- + +@REFERENCES@ + + +]]> + </help> + <expand macro="citations" /> +</tool> |
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| diff -r 000000000000 -r fae6527990af sorting.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sorting.xml Thu May 21 03:58:09 2015 -0400 |
| [ |
| @@ -0,0 +1,102 @@ +<tool id="vsearch_sorting" name="VSearch sorting" version="@VERSION@.0"> + <description></description> + <macros> + <import>vsearch_macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="stdio" /> + <expand macro="version_command" /> + <command> +<![CDATA[ + vsearch + @GENERAL@ + #if $sorting_mode.sorting_mode_select == 'sortbylength': + --sortbylength "$sorting_mode.infile" + #else: + --sortbysize "$sorting_mode.infile" + #if $sorting_mode.minsize: + --minsize $sorting_mode.minsize + #end if + #if $sorting_mode.maxsize: + --maxsize $sorting_mode.maxsize + #end if + #end if + --output $outfile + #if $sizeout: + --sizeout $sizeout + #end if + #if $topn: + --topn $topn + #end if + +]]> + </command> + <inputs> + <conditional name="sorting_mode"> + <param name="sorting_mode_select" type="select" label="Sorting by" help=""> + <option value="sortbylength">sequence length</option> + <option value="sortbyabundance">by abundance</option> + </param> + <when value="sortbylength"> + <param name="infile" type="data" format="fasta" label="Select your FASTA file" help="(--sortbylength)" /> + </when> + <when value="sortbyabundance"> + <param name="infile" type="data" format="fasta" label="Select your FASTA file" help="(--sortbysize)" /> + <param name="minsize" type="integer" value="" optional="True" label="Minimum abundance" + help="(--minsize)"/> + <param name="maxsize" type="integer" value="" optional="True" label="Maximum abundance" + help="(--maxsize)"/> + </when> + </conditional> + <expand macro="topn" /> + <param name="sizeout" type="boolean" truevalue="--sizeout" falsevalue="" checked="False" + label="Add abundance annotation to output" help="(--sizeout)"/> + </inputs> + <outputs> + <data name="outfile" format="fasta" label="${tool.name} on ${on_string}" /> + </outputs> + <tests> + <test> + <param name="sorting_mode_select" value="sortbyabundance"/> + <param name="infile" value="db.fasta" ftype="fasta" /> + <output name="outfile" file="sorting_result1.fasta" ftype="fasta" /> + </test> + <test> + <param name="sorting_mode_select" value="sortbylength"/> + <param name="infile" value="db.fasta" ftype="fasta" /> + <output name="outfile" file="sorting_result2.fasta" ftype="fasta" /> + </test> + </tests> + <help> +<![CDATA[ +**What it does** + +Fasta entries are sorted by decreasing abundance (−−sortbysize) or sequence length (−−sort- +bylength). To obtain a stable sorting order, ties are sorted by decreasing abundance and label +increasing alpha-numerical order (−−sortbylength), or just by label increasing alpha-numerical +order (−−sortbysize). Label sorting assumes that all sequences have unique labels. The same +applies to the automatic sorting performed during chimera checking (−−uchime_denovo), derepli- +cation (−−derep_fulllength), and clustering (−−cluster_fast and −−cluster_size). + +Sorting options + --maxsize INT maximum abundance for sortbysize + --minsize INT minimum abundance for sortbysize + --output FILENAME output FASTA file + --relabel STRING relabel with this prefix string after sorting + --sizeout add abundance annotation to output + --sortbylength FILENAME sort sequences by length in given FASTA file + --sortbysize FILENAME abundance sort sequences in given FASTA file + --topn INT output just top n seqs after sorting + + +@EXTERNAL_DOCUMENTATION@ + +------- + +@REFERENCES@ + + +]]> + </help> + <expand macro="citations" /> +</tool> |
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| diff -r 000000000000 -r fae6527990af test-data/BioMarKs5k.fsa.bz2 |
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| diff -r 000000000000 -r fae6527990af test-data/PR2-18S-rRNA-V4.derep.fsa.bz2 |
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| diff -r 000000000000 -r fae6527990af test-data/Rfam_11_0.repr.fasta.bz2 |
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| diff -r 000000000000 -r fae6527990af test-data/alignment_result1.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/alignment_result1.fasta Thu May 21 03:58:09 2015 -0400 |
| b |
| @@ -0,0 +1,128 @@ +vsearch --threads 1 --notrunclabels --id 0.97 --iddef 2 --allpairs_global /tmp/tmpn4c95N/files/000/dataset_1.dat --alnout /tmp/tmpn4c95N/files/000/dataset_2.dat --query_cov 0.95 +vsearch v1.1.3_linux_x86_64, 7.7GB RAM, 4 cores + +Query >RF00177;SSU_rRNA_bacteria;CP001742.1/177780-176277 666510:Acidilobus saccharovorans 345-15 + %Id TLen Target +100% 1497 RF01959;SSU_rRNA_archaea;CP001742.1/177775-176279 666510:Acidilobus saccharovorans 345-15 + + Query 1504nt >RF00177;SSU_rRNA_bacteria;CP001742.1/177780-176277 666510:Acidilobus saccharovorans 345-15 +Target 1497nt >RF01959;SSU_rRNA_archaea;CP001742.1/177775-176279 666510:Acidilobus saccharovorans 345-15 + +Qry 6 + ACUCCGGUUGAUCCUGCCGGACCCGACUGCUAUCGGGGUGAGGCUAAGCCAUGGGAGUCGCGCG 69 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Tgt 1 + ACUCCGGUUGAUCCUGCCGGACCCGACUGCUAUCGGGGUGAGGCUAAGCCAUGGGAGUCGCGCG 64 + +Qry 70 + CCCAGCCGCCGCUGGGCGCGGCGCACGGCUGAGUAACACGUAGCUAACCUACCCUCGGGACGGG 133 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Tgt 65 + CCCAGCCGCCGCUGGGCGCGGCGCACGGCUGAGUAACACGUAGCUAACCUACCCUCGGGACGGG 128 + +Qry 134 + GAUAACCCCGGGAAACUGGGGCUAAUCCCCGAUAGGCGAGGGGGCCUGGAAUGGUCCCUCGCCG 197 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Tgt 129 + GAUAACCCCGGGAAACUGGGGCUAAUCCCCGAUAGGCGAGGGGGCCUGGAAUGGUCCCUCGCCG 192 + +Qry 198 + AAAGGGACCCUGGGGGGUUAUCGCCUGGGGUCCGCCCGAGGAUGGGGCUGCGGCCCAUCAUGGU 261 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Tgt 193 + AAAGGGACCCUGGGGGGUUAUCGCCUGGGGUCCGCCCGAGGAUGGGGCUGCGGCCCAUCAUGGU 256 + +Qry 262 + AGUUGGCGGGGUAAUGGCCCGCCAAGCCGACGACGGGUAGGGGCCGUGGGAGCGGGAGCCCCCA 325 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Tgt 257 + AGUUGGCGGGGUAAUGGCCCGCCAAGCCGACGACGGGUAGGGGCCGUGGGAGCGGGAGCCCCCA 320 + +Qry 326 + GAUGGGCCCUGAGACAAGGGCCCAGGCCCUACGGGGCGCACCAGGCGCGAAACCUCCGCAAUGC 389 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Tgt 321 + GAUGGGCCCUGAGACAAGGGCCCAGGCCCUACGGGGCGCACCAGGCGCGAAACCUCCGCAAUGC 384 + +Qry 390 + GGGAAACCGUGACGGGGUCACCCCGAGUGCUCCCGUAAGGGAGCUUUUCCCCGCUGCAAGGAGG 453 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Tgt 385 + GGGAAACCGUGACGGGGUCACCCCGAGUGCUCCCGUAAGGGAGCUUUUCCCCGCUGCAAGGAGG 448 + +Qry 454 + CGGGGGAAUAAGCGGGGGGCAAGUCUGGUGUCAGCCGCCGCGGUAAUACCAGCCCCGCGAGUGG 517 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Tgt 449 + CGGGGGAAUAAGCGGGGGGCAAGUCUGGUGUCAGCCGCCGCGGUAAUACCAGCCCCGCGAGUGG 512 + +Qry 518 + UCGGGACGUCUACUGGGCCUAAAGCGCCCGUAGCCGGCCCCGUAAGUCCCUCCUGAAAGCCCUG 581 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Tgt 513 + UCGGGACGUCUACUGGGCCUAAAGCGCCCGUAGCCGGCCCCGUAAGUCCCUCCUGAAAGCCCUG 576 + +Qry 582 + GGCUCAACCCAGGGAGUGGGGGGGAUACUGCGGGGCUAGGGGGCGGGAAAGGCCGGGGGUACCC 645 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Tgt 577 + GGCUCAACCCAGGGAGUGGGGGGGAUACUGCGGGGCUAGGGGGCGGGAAAGGCCGGGGGUACCC 640 + +Qry 646 + CAGGGGUAGGGGCGAAAUCCGAUAAUCCCUGGGGGACCACCAGUGGCGAAAGCGCCCGGCUGGA 709 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Tgt 641 + CAGGGGUAGGGGCGAAAUCCGAUAAUCCCUGGGGGACCACCAGUGGCGAAAGCGCCCGGCUGGA 704 + +Qry 710 + ACGCGCCCGACGGUGAGGGGCGAAAGCCGGGGGAGCGAACCGGAUUAGAUACCCGGGUAGUCCC 773 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Tgt 705 + ACGCGCCCGACGGUGAGGGGCGAAAGCCGGGGGAGCGAACCGGAUUAGAUACCCGGGUAGUCCC 768 + +Qry 774 + GGCUGUAAACGAUGCGGGCUAGGUGUCGGGCGGGCGUUAGAGCCCGCCCGGUGCCGCAGGGAAG 837 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Tgt 769 + GGCUGUAAACGAUGCGGGCUAGGUGUCGGGCGGGCGUUAGAGCCCGCCCGGUGCCGCAGGGAAG 832 + +Qry 838 + CCGUUAAGCCCGCCGCCUGGGGAGUACGGCCGCAAGGCUGAAACUUUAAGGAAUUGGCGGGGGG 901 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Tgt 833 + CCGUUAAGCCCGCCGCCUGGGGAGUACGGCCGCAAGGCUGAAACUUUAAGGAAUUGGCGGGGGG 896 + +Qry 902 + GCACACAAGGGGUGGAGCCUGCGGCUCAAUUGGAGUCAACGCCGGGAACCUCACCGGGGGCGAC 965 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Tgt 897 + GCACACAAGGGGUGGAGCCUGCGGCUCAAUUGGAGUCAACGCCGGGAACCUCACCGGGGGCGAC 960 + +Qry 966 + AGCAGGAUGACGGCCAGGCUAACGACCUUGCCCGACGCGCUGAGGGGAGGUGCAUGGCCGUCGC 1029 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Tgt 961 + AGCAGGAUGACGGCCAGGCUAACGACCUUGCCCGACGCGCUGAGGGGAGGUGCAUGGCCGUCGC 1024 + +Qry 1030 + CAGCUCGUGCUGUGAAGUGUCCUGUUAAGUCAGGCAACGAGCGAGACCCCCGCCCCUAGUUGCG 1093 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Tgt 1025 + CAGCUCGUGCUGUGAAGUGUCCUGUUAAGUCAGGCAACGAGCGAGACCCCCGCCCCUAGUUGCG 1088 + +Qry 1094 + ACCCGGCGGGAGACCGCUGGGGCACACUAGGGGGACUGCCGCCGCUAAGGCGGAGGAAGGAGGG 1157 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Tgt 1089 + ACCCGGCGGGAGACCGCUGGGGCACACUAGGGGGACUGCCGCCGCUAAGGCGGAGGAAGGAGGG 1152 + +Qry 1158 + GGCCACGGCAGGUCAGCAUGCCCCUAAACCCCCGGGCUGCACGCGGGCUACAAUGGCGGGGACA 1221 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Tgt 1153 + GGCCACGGCAGGUCAGCAUGCCCCUAAACCCCCGGGCUGCACGCGGGCUACAAUGGCGGGGACA 1216 + +Qry 1222 + GCGGGAUCCGACCCCGAAAGGGGGAGGCAAUCCCUCAAACCCCGCCGUAGUCGGGAUUGGGGGC 1285 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Tgt 1217 + GCGGGAUCCGACCCCGAAAGGGGGAGGCAAUCCCUCAAACCCCGCCGUAGUCGGGAUUGGGGGC 1280 + +Qry 1286 + UGUAACUCGCCCCCAUGAACCUGGAAUCCCUAGUAACCGCGCGUCAACAUCGCGCGGUGAAUAC 1349 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Tgt 1281 + UGUAACUCGCCCCCAUGAACCUGGAAUCCCUAGUAACCGCGCGUCAACAUCGCGCGGUGAAUAC 1344 + +Qry 1350 + GUCCCUGCCCCUUGUACACACUGCCCGUCGCUCCACCUGAGAGAAGGAGGGGUGAGGCUUCCUC 1413 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Tgt 1345 + GUCCCUGCCCCUUGUACACACUGCCCGUCGCUCCACCUGAGAGAAGGAGGGGUGAGGCUUCCUC 1408 + +Qry 1414 + CUUCGGGAGGGAGUCGAACCCCUCCUUCUCGAGGGGGGAGAAGUCGUAACAAGGUAGCCGUAGG 1477 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Tgt 1409 + CUUCGGGAGGGAGUCGAACCCCUCCUUCUCGAGGGGGGAGAAGUCGUAACAAGGUAGCCGUAGG 1472 + +Qry 1478 + GGAACCUGCGGCUGGAUCACCUCUC 1502 + ||||||||||||||||||||||||| +Tgt 1473 + GGAACCUGCGGCUGGAUCACCUCUC 1497 + +1497 cols, 1497 ids (100.0%), 0 gaps (0.0%) + +Query >RF00423;SCARNA4;AAVX01260432.1/2253-2118 7868:Callorhinchus milii (ghost shark) + %Id TLen Target +100% 134 RF00426;SCARNA15;AAVX01260432.1/2252-2119 7868:Callorhinchus milii (ghost shark) + + Query 136nt >RF00423;SCARNA4;AAVX01260432.1/2253-2118 7868:Callorhinchus milii (ghost shark) +Target 134nt >RF00426;SCARNA15;AAVX01260432.1/2252-2119 7868:Callorhinchus milii (ghost shark) + +Qry 2 + UCGGAGGAAUAAGAAAGCACAGUCUCGAGAGUGUCCAUGACUUUGCUGAUACUCUCCUCCUAUA 65 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Tgt 1 + UCGGAGGAAUAAGAAAGCACAGUCUCGAGAGUGUCCAUGACUUUGCUGAUACUCUCCUCCUAUA 64 + +Qry 66 + GAAAAGUGGUGGAAGAACAGGUCUUCUCUUGUGGCUGUGGAGUUCUGACCUACUUAAUCCACUC 129 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Tgt 65 + GAAAAGUGGUGGAAGAACAGGUCUUCUCUUGUGGCUGUGGAGUUCUGACCUACUUAAUCCACUC 128 + +Qry 130 + ACAAGU 135 + |||||| +Tgt 129 + ACAAGU 134 + +134 cols, 134 ids (100.0%), 0 gaps (0.0%) |
| b |
| diff -r 000000000000 -r fae6527990af test-data/chimera_result1.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/chimera_result1.fasta Thu May 21 03:58:09 2015 -0400 |
| b |
| b'@@ -0,0 +1,958 @@\n+>AF281177.1.2172_G|AF281177|R|||11|Eukaryota|Opisthokonta|Fungi|Ascomycota|Pezizomycotina|Sordariomycetes|Claviceps|Claviceps+sorghicola|Claviceps|Claviceps+sorghicola;size=10\n+AGCTCCAATAGCGTATATTAAAGTTGTTGTGGTTAAAAAGCTCGTAGTTGAACCTTGGGCCTGGCTGGCCGGTCCGCCTC\n+ACCGCGAGTACTGGTCCGGCCGGGCCTTTCCCTCTGTGGAACCCCATGCCCTTCACTGGGCGTGGCGGGGAAACAGGACT\n+TTTACTTTGAAAAAATTAGAGTGCTCCAGGCAGGCCTATGCTCGAATACATTAGCATGGAATAATGAAATAGGACGCGCG\n+GTTCTATTTTGTTGGTTTCTAGGACCGCCGTAATGATTAATAGGGACAGTCGGGGGCATCAGTATTCAATTGTCAGAGGT\n+GAAATTCTTGGATTTATTGAAGACTAACTACTGCGAAAGCATTTGCCAAGGATGTTTTCA\n+>DQ514862.1.1735_U|DQ514862|U|||11|Eukaryota|Stramenopiles|Ochrophyta|Bacillariophyta|Bacillariophyta_X|Polar-centric-Mediophyceae|Thalassiosira|Thalassiosira+pseudonana|Thalassiosira|Thalassiosira+pseudonana;size=10\n+AGCTCCAATAGCGTATATTAAAGTTGTTGCAGTTAAAAAGCTCGTAGTTGGATTTCTGGCAGGAGCGACCGGTCTCACAC\n+TCAGTGCGAGAACTCGTGTTGTCTCTGGCCATCCTTGGGGATATCCTGTTTGGCATTAAGTTGTCGGGCAGGGGATACCC\n+ATCGTTTACTGTGAAAAAATTAGAGTGTTTAAAGCAGGCTTATGCCGTTGAATATATTAGCATGGAATAATAAGATAGGA\n+CCCTGGTACTATTTTGTTGGTTTGCGCACCGAGGTAATGATTAAAAGAGACAGGCGGGGCTATTCGTATTGCATTGTCAG\n+AGGTGAAATTCTTGGATTTCTGCAAGACGAACTACTGCGAAAGCATTTAGCAAGGATGTTTTCA\n+>CK269001.1.1038_U|CK269001|U|||11|Eukaryota|Archaeplastida|Streptophyta|Embryophyceae|Embryophyceae_X|Embryophyceae_XX|Solanum|Solanum+tuberosum|Solanum|Solanum+tuberosum;size=9\n+AGCTCCAATAGCGTATATTTAAGTTGTTGCAGTTAAAAAGCTCGTAGTTGGACTTTGGGATGGGCCGGCCGGTCCGCCCT\n+AGGTGTGCACCGGTCGTCTCGTCCCTTCTGTCGGCGATGCGCTCCTGGCCTTAATTGGCCGGGTCGTGCCTCCGGCGCTG\n+TTACTTTGAAGAAATTAGAGTGCTCAAAGCAAGCCTACGCTCTGTATACATTAGCATGGGATAACATTATAGGATTTCGG\n+TCCTATTACGTTGGCCTTCGGGATCGGAGTAATGATTAACAGGGACAGTCGGGGGCATTCGTATTTCATAGTCAGAGGTG\n+AAATTCTTGGATTTATGAAAGACGAACAACTGCGAAAGCATTTGCCAAGGATGTTTTCA\n+>AJ972856.1.1760_UC|AJ972856|U||Reference|11|Eukaryota|Opisthokonta|Fungi|Ascomycota|Pezizomycotina|Dothideomycetes|Capnobotryella|Capnobotryella+sp.|Capnobotryella|Capnobotryella+sp.;size=8\n+AGCTCCAGTAGCGTATATTAAAGTTGTTGCAGTTAAAAAGCTCGTAGTTGAACCTTGGGTCTGGCTGGCCGGTCCGCCTC\n+ACCGCGTGTTACTGGTCCGGCCGGGTGAAATTCTTGGATTTATTGAAGACAAACTACTGCGAAAGCATTTGCCAAGGATG\n+TTTTCA\n+>AM236073.1.1638_U|AM236073|U|||11|Eukaryota|Stramenopiles|Ochrophyta|Bacillariophyta|Bacillariophyta_X|Polar-centric-Mediophyceae|Cyclotella|Cyclotella+meneghiniana|Cyclotella|Cyclotella+meneghiniana;size=8\n+AGCTCCAATAGCGTATATTAAAGTTGTTGCAGTTAAAAAGCTCGTAGTTGGATTTCTGGCAGGAGCGTCTGGTCTCACAC\n+TCTGTGCGGGAACTTGGATGTCTCTGGCCATCTTTGGGGATATCCTGTTTGGCATTAAGTTGTCGGGCAGGGGATACCCA\n+TCGTTTACTGTGAAAAAATTAGAGTGTTTAAAGCAGGCTTATGCCGTTGAATATATTAGCATGGAATAATAAGATAGGAC\n+CCTGGTACTATTTTGTTGGTTTGCGCACCTGGGTAATGATTAATAGAGACAGGCGGGGCTATTCGTATTGCATTGTCAGA\n+GGTGAAATTCTTGGATTTCTGCAAGACGAACTACTGCGAAAGCATTTAGCAAGGATGTTTTCA\n+>EF526943.1.1394_U|EF526943|U|||11|Eukaryota|Stramenopiles|Ochrophyta|Bacillariophyta|Bacillariophyta_X|Polar-centric-Mediophyceae|Cyclotella|Cyclotella+sp.|uncultured|uncultured+marine;size=8\n+AGCTCCAATAGCGTATATTAAAGTTGTTGCAGTTAAAAAGCTCGTAGTTGGATTTCTGGCAGGAGCGTCCGGTCTCACAC\n+TCAGTGCGGGAACTTGGATGTCTCTGGCCATCTTTGGGGATATCCTGTTTGGCATTAAGTTGTCGGGCAGGGGACACCCA\n+TCGTTTACTGTGAAAAAATTAGAGTGTTTAAAGCAGGCTTATGCCGTTGAATATATTAGCATGGAATAATAAGATAGGAC\n+GTAGGTACTATTTTGTTGGTTTGCGCACCCACGTAATGATTAATAGAGACAGGCGGGGCTATTCGTATTGCATTGTCAGA\n+GGTGAAATTCTTGGATTTCTGCAAGACGAACTACTGCGAAAGCATTTAGCAAGGATGTTTTCA\n+>HQ680491.1.1812_U|HQ680491|U|||11|Eukaryota|Stramenopiles|Ochrophyta|Bacillariophyta|Bacillariophyta_X|Raphid-pennate|Cymbella|Cymbella+hebridica|Cymbella|Cymbella+hebridica;size=8\n+AGCTCCAATAGCGTATATTAAAGTTGTTGCAGTTAAAAAGCTCGTAGTTGGATTTGTGGTTGGAGCAACGTGCCCTTCAC\n+TTGTGTTGGTGCTTGTTTGTCTCCGTCCATCCTTGGGTGGAACCTGTGTGGCATTAAGTTGTCGTGCAGGGGATGCCCAT\n+CTTTTACTGTGAAAAAATTAGAGTGTTCAAAGCAGGCTTACGCCGTTGAATATATTAGCATGGAATAATGAGATAGGACC\n+TGGGTACTATTTTGTTGGTTTGCGCACCGAGGTAATGATTAATAGGGACAGTTGGGGGTATTCGTATTCCATTGTCAGAG\n+GTGAAATTCTTGGATTTTTGGAAGACGAACTACTGCGAAAGCATTTACCAAGGATGTTTTCA\n+>AB594350.1.1721_U|AB594350|U|||11|Eukaryota|Opisthokonta|Metazoa|Mollusca|Bivalvia|Pterioida-Pinnidae|P'..b'0-28//12-20|Eukaryota|Stramenopiles|Stramenopiles_X|MAST|MAST-12|MAST-12B|MAST-12B_X|MAST-12B_X+sp.|uncultured|uncultured+eukaryote;size=1\n+AGCTCCAATAGCGTATACTAATGTTGTTGCAGTTAAAAAGCTCGTAGTTGAATTTCTGGTTGTCGACTTATGGTCCTGCG\n+CCTCGTGCGTTTTGGTACCGTTTTTGTCGACGCCATCTTAGTCGTGATTGCTTCTGGCATTAGGTTGTCGGTTTTAGGAG\n+CGGCTTCGTTTACTGTGATAACAAATAGAGTGTTCAAAGCAGACATTACGTCTTGAATGCTTCAGCATGGAATAAAAAGA\n+TAGGACAGCGGTACTATTTTATTGGTATGTATACCGTAGTAATGATTAATAGGGATAGTTGGGGGTATTCATATTTGATT\n+GTCAGAGGTGAAATTCTTGGATTTATGAAAGATGAACAACTGCGAAAGCATTTACCAAGGATGTTTTCA\n+>HQ867242.1.872_U|HQ867242|U|||11|Eukaryota|Hacrobia|Cryptophyta|Cryptophyceae|Cryptophyceae_X|Cryptomonadales|Cryptomonadales_X|Cryptomonadales_X+sp.|uncultured|uncultured+eukaryote;size=1\n+AGCTCTAATAGCGTATATTAAAGTTGTTGCAGTCAAAAAGCTCGTAGTCGGATGTCGGGCTCGGGCAAGCTGTCGGCCTT\n+TGGTCGGACGGCAGGCTCGGGTCTTTCTGCCTGAGGAACCCGGTTGCTTTAACGAGCTGCCGGTGGACGCAGGTCGTTTA\n+CTTTGAAAAAATTAGAGTGTTCAAAGCAGGCTAGCGCTTGAATACATTAGCATGGAATAATGGAATAGGACTTTGGTCCT\n+ATTTTGTTGGTTTTCGGGACCGAAGTAATGATTAATAGGGACAGTTGGGGGCATTCGTATTTAATTGTCAGAGGTGAAAT\n+TCTTGGATTTATGAAAGACGAACTTCTGCGAAAGCATCTGCCAAGGATGTTTTCA\n+>JN832714.1.1689_U|JN832714|U|||gb_191-cc|Eukaryota|Alveolata|Dinophyta|Dinophyceae|Dinophyceae_X|Dinophyceae_XX|Dinophyceae_XXX|Dinophyceae_XXX+sp.|environmental_samples|uncultured+eukaryote;size=1\n+AGCTCCAATAGCGTATACTAACGTTGTTGCAGTTAAAAAGCTCGTAGTTGGATTTCTGTAGTGGGATGCCGGCCGGGTTC\n+TCTGAACTTGTAGCTAGGTTATCTTGCTGCATCTTGTCGTAATTCTCACTGGCATTCATTTGTTGGTGTAGAGGACCGAC\n+TCGTTTACTTTGAGAAAATTAGAGTGTTTAAAGCAGGCATACGCCTTGAATACATTAGCATGGAATAATAAGATAGGACC\n+TCGGTTCTATTTTGTTGGTTTCTAGAGCTGAGGTAATGATTAATAGGGATAGTTGGGGGCATTCGTATTTAACTGTCAGA\n+GGTGAAATTCTTGGATTTGTTAAAGACGGACTACTGCGAAAGCATTTGCCAAGGATGTTTTCA\n+>KC674974.1.1781_U|KC674974|U||gb197A|cc_2n|Eukaryota|Opisthokonta|Fungi|Ascomycota|Pezizomycotina|Sordariomycetes|Sordariomycetes_X|Sordariomycetes_X+sp.|environmental_samples|uncultured+fungus;size=1\n+AGCTCCAATAGCGTATATTAAAGTTGTTGCAGTTAAAAAGCTCGTAGTTGGACCTTGGACCTGGACAGGCGGTCCGCCTC\n+ACGGCGAGTACTGTCTTGCTGGGTCTTTCCTCTTGGTGATCTGTTGTTTCGGCAGCAGGGAACCAGGACCTTTACTTTGA\n+AAAAATTAGAGTGCTCCAGGCAGGCCTATGCTCGAATACATTAGCATGGAATAATAGAATAGGACGTGTGGTTCTATTTT\n+GTTGGTTTCTAGGACCGCCGTAATGATTAATAGGGACAGTCGGGGGCATCAGTATTCAATTGTCAGAGGTGAAATTCTTG\n+GATTTATTGAAGACTAACTACTGCGAAAGCATTTGCCAAGGATGTTTCA\n+>U32401.1.1034_U|U32401|U|||11|Eukaryota|Opisthokonta|Fungi|Ascomycota|Pezizomycotina|Sordariomycetes|Claviceps|Claviceps+paspali|Claviceps|Claviceps+paspali;size=1\n+AGCTCCAATAGCGTATATTAAAGTTGTTGTGGTTAAAAAGCTCGTAGTTGAACCTTGGGCCTGGCTGGCCGGTCCGCCTC\n+ACCGCGTGTACTGGTCCGGCCGGGCCTTTCCCTCTGTGGAACCCCATGCCCTTCACTGGGCGTGGCGGGGAAACAGGACT\n+TTTACTTTGAAAAAATTAGAGTGCTCCAGGCAGGCCTATGCTCGAATACATTAGCATGGAATAATGAAATAGGACGCGCG\n+GTTCTATTTTGTTGGTTTCTAGGACCGCCGTAATGATTAATAGGGACAGTCGGGGGCATCAGTATTCAATTGTCAGAGGT\n+GAAATTCTTGGATTTATTGAAGACTAACTACNGCGAAAGCATTTGCCAAGGATGTTTTCA\n+>U83122.1.1738_U|U83122|U||Reference|11|Eukaryota|Archaeplastida|Chlorophyta|Chlorophyceae|Chlorophyceae_X|CW-Chlamydomonadales|Gloeococcus|Gloeococcus+maximus|Gloeococcus|Gloeococcus+maximus;size=1\n+AGCTCCAATAGCGTATATTTAAGTTGTTGCAGTTAAAAAGCTCGTAGTTGGATTTCGTGTGGGTTGGCGCGGTCCGCTCT\n+GGTGTGCACTGCGCCGGTCCACCTTCCAGCCGGGGACGGGCTCCTGGGCTTCACTGTCTGGGACTCGGAGTCGACGATGT\n+TACTTTGAGAAAATTAGAGTGTTCAAAGCAAGCCTACGCTCTGAATAGTTTAGCATGGAATAACGCGATAGGACTCTGGC\n+CTATCCCGTTGGTCTGTGGGACCGGAGTAATGATTAAGAGGGACAGTCGGGGGCATTCGTATTTCATTGTCAGAGGTGAA\n+ATTCTTGGATTTATGAAAGACGAACTTCTGCGAAAGCATTTGCCAAGGATGTTTTCA\n+>Z83751.1.1890_U|Z83751|U||Reference|11|Eukaryota|Opisthokonta|Metazoa|Annelida|Annelida_X|Annelida_XX|Glossiphonia|Glossiphonia+sp.|Glossiphonia|Glossiphonia+sp.;size=1\n+AGCTCCAATAGCGTATGTTATAGTTGTTGCAGTTAAAAAGCTCGTAGTTGGATCTCGGGTTCGGACTGGTTGCAACCTCG\n+CGGCGTAGCGACCCGCTCCGACCTGTTTTCGGTTCTGCGCCCGGTTCTTCTTAACCGAGTGCCGGGTGCGGCCGAGACGT\n+TTACTTTGAAAAAATTAAAGTGCTTAAAGCAGGCTCGACAGCCTGAATAGTAGCGCATGGAATAATAGAATAGGACCTCG\n+GTTCTATTTTGTTGGTTTTCGGAGCTCGAGGTAATGATTAAGAGGGACAGTTGGGGGTCATTGCGGTTATTTCGATTGTC\n+AGAGGTGAAATTCTTGGATTTGCGAAAGACGAACTAATGCGAAAGCATTTGCCAAGAATGTTTTCA\n' |
| b |
| diff -r 000000000000 -r fae6527990af test-data/chimera_uchimeout_result1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/chimera_uchimeout_result1.tabular Thu May 21 03:58:09 2015 -0400 |
| b |
| b'@@ -0,0 +1,13060 @@\n+0.0000\tKC487520.1.1651_U|KC487520|U||gb197A|cc_2n|Eukaryota|Alveolata|Apicomplexa|Apicomplexa_X|Colpodellidae|Colpodellidae_X|Colpodellidae_XX|Colpodellidae_XX+sp.|environmental_samples|uncultured+Colpodellidae;size=914\t*\t*\t*\t*\t*\t*\t*\t*\t0\t0\t0\t0\t0\t0\t*\tN\n+0.0000\tEU175348.1.814_U|EU175348|U|||11|Eukaryota|Opisthokonta|Fungi|Ascomycota|Pezizomycotina|Sordariomycetes|Sordariomycetes_X|Sordariomycetes_X+sp.|uncultured|uncultured+fungus;size=485\t*\t*\t*\t*\t*\t*\t*\t*\t0\t0\t0\t0\t0\t0\t*\tN\n+0.0000\tGU971995.1.816_U|GU971995|U|||11|Eukaryota|Opisthokonta|Fungi|Basidiomycota|Ustilaginomycotina|Exobasidiomycetes|Exobasidiomycetes_X|Exobasidiomycetes_X+sp.|uncultured|uncultured+organism;size=424\t*\t*\t*\t*\t*\t*\t*\t*\t0\t0\t0\t0\t0\t0\t*\tN\n+0.0000\tKC672135.1.1740_U|KC672135|U||gb197A|cc_2n|Eukaryota|Opisthokonta|Fungi|Basidiomycota|Ustilaginomycotina|Exobasidiomycetes|Malassezia|Malassezia+globosa|environmental_samples|uncultured+fungus;size=356\t*\t*\t*\t*\t*\t*\t*\t*\t0\t0\t0\t0\t0\t0\t*\tN\n+0.0000\tDQ680046.1.1088_UC|DQ680046|UC|||11|Eukaryota|Opisthokonta|Fungi|Ascomycota|Pezizomycotina|Sordariomycetes|Stachybotrys|Stachybotrys+chartarum|Stachybotrys|Stachybotrys+chartarum;size=315\t*\t*\t*\t*\t*\t*\t*\t*\t0\t0\t0\t0\t0\t0\t*\tN\n+0.0000\tHQ865593.1.872_U|HQ865593|U|||11|Eukaryota|Stramenopiles|Stramenopiles_X|Bicoecea|Bicoecea_X|Bicoecea_XX|Bicoecea_XXX|Bicoecea_XXX+sp.|uncultured|uncultured+eukaryote;size=265\t*\t*\t*\t*\t*\t*\t*\t*\t0\t0\t0\t0\t0\t0\t*\tN\n+0.0627\tAC193417.150218.152027_U|AC193417|U|||11|Eukaryota|Archaeplastida|Streptophyta|Embryophyceae|Embryophyceae_X|Embryophyceae_XX|Zea|Zea+mays|Zea|Zea+mays;size=228\tEU175348.1.814_U|EU175348|U|||11|Eukaryota|Opisthokonta|Fungi|Ascomycota|Pezizomycotina|Sordariomycetes|Sordariomycetes_X|Sordariomycetes_X+sp.|uncultured|uncultured+fungus;size=485\tKC487520.1.1651_U|KC487520|U||gb197A|cc_2n|Eukaryota|Alveolata|Apicomplexa|Apicomplexa_X|Colpodellidae|Colpodellidae_X|Colpodellidae_XX|Colpodellidae_XX+sp.|environmental_samples|uncultured+Colpodellidae;size=914\tEU175348.1.814_U|EU175348|U|||11|Eukaryota|Opisthokonta|Fungi|Ascomycota|Pezizomycotina|Sordariomycetes|Sordariomycetes_X|Sordariomycetes_X+sp.|uncultured|uncultured+fungus;size=485\t80.1\t78.2\t76.3\t77.1\t78.2\t39\t25\t42\t7\t0\t6\t1.9\tN\n+0.0590\tHQ870089.1.881_U|HQ870089|U|||11|Eukaryota|Archaeplastida|Streptophyta|Embryophyceae|Embryophyceae_X|Embryophyceae_XX|Embryophyceae_XXX|Embryophyceae_XXX+sp.|uncultured|uncultured+eukaryote;size=194\tGU971995.1.816_U|GU971995|U|||11|Eukaryota|Opisthokonta|Fungi|Basidiomycota|Ustilaginomycotina|Exobasidiomycetes|Exobasidiomycetes_X|Exobasidiomycetes_X+sp.|uncultured|uncultured+organism;size=424\tKC487520.1.1651_U|KC487520|U||gb197A|cc_2n|Eukaryota|Alveolata|Apicomplexa|Apicomplexa_X|Colpodellidae|Colpodellidae_X|Colpodellidae_XX|Colpodellidae_XX+sp.|environmental_samples|uncultured+Colpodellidae;size=914\tKC487520.1.1651_U|KC487520|U||gb197A|cc_2n|Eukaryota|Alveolata|Apicomplexa|Apicomplexa_X|Colpodellidae|Colpodellidae_X|Colpodellidae_XX|Colpodellidae_XX+sp.|environmental_samples|uncultured+Colpodellidae;size=914\t77.5\t74.7\t77.0\t77.2\t77.0\t25\t23\t51\t10\t0\t6\t0.6\tN\n+0.0000\tAAPE02054660.131.1675_U|AAPE02054660|U|||11|Eukaryota|Opisthokonta|Metazoa|Craniata|Craniata_X|Craniata_XX|Myotis|Myotis+lucifugus|Myotis|Myotis+lucifugus;size=172\t*\t*\t*\t*\t*\t*\t*\t*\t0\t0\t0\t0\t0\t0\t*\tN\n+0.1149\tABXC01010957.1335.3144_U|ABXC01010957|U|||11|Eukaryota|Archaeplastida|Streptophyta|Embryophyceae|Embryophyceae_X|Embryophyceae_XX|Sorghum|Sorghum+bicolor|Sorghum|Sorghum+bicolor;size=170\tKC672135.1.1740_U|KC672135|U||gb197A|cc_2n|Eukaryota|Opisthokonta|Fungi|Basidiomycota|Ustilaginomycotina|Exobasidiomycetes|Malassezia|Malassezia+globosa|environmental_samples|uncultured+fungus;size=356\tKC487520.1.1651_U|KC487520|U||gb197A|cc_2n|Eukaryota|Alveolata|Apicomplexa|Apicomplexa_X|Colpodellidae|Colpodellidae_X|Colpodellidae_XX|Colpodellidae_XX+sp.|environmental_samples|uncultured+Colpodellidae;size=914\tKC672135.1.1740_U|KC672135|U||gb197A|cc_2n|Eukaryota|Opisthokonta|Fungi|Basidiomycota|Ustilaginomy'..b'vata|Metamonada|Parabasalia|Cristamonadida|Calonymphidae-Devescovinidae|Metadevescovina|Metadevescovina+modica|Metadevescovina|Metadevescovina+modica;size=3\tAB326380.1.1525_U|AB326380|U||Reference|11|Eukaryota|Excavata|Metamonada|Parabasalia|Cristamonadida|Calonymphidae-Devescovinidae|Deltotrichonympha|Deltotrichonympha+operculata|Deltotrichonympha|Deltotrichonympha+operculata;size=3\t91.2\t90.1\t88.5\t89.3\t90.1\t8\t1\t11\t7\t4\t7\t1.1\tN\n+0.0039\tX98829.1.1811_U|X98829|U|||11|Eukaryota|Opisthokonta|Metazoa|Mollusca|Polyplacophora|Polyplacophora_X|Lepidozona|Lepidozona+coreanica|Lepidozona|Lepidozona+coreanica;size=1\tHQ907767.1.1726_U|HQ907767|U|||11|Eukaryota|Opisthokonta|Metazoa|Mollusca|Polyplacophora|Polyplacophora_X|Leptochiton|Leptochiton+sp.|Leptochiton|Leptochiton+sp.;size=19\tHQ907736.1.1742_U|HQ907736|U|||11|Eukaryota|Opisthokonta|Metazoa|Mollusca|Polyplacophora|Polyplacophora_X|Acanthochitona|Acanthochitona+rhodea|Acanthochitona|Acanthochitona+rhodea;size=2\tHQ907767.1.1726_U|HQ907767|U|||11|Eukaryota|Opisthokonta|Metazoa|Mollusca|Polyplacophora|Polyplacophora_X|Leptochiton|Leptochiton+sp.|Leptochiton|Leptochiton+sp.;size=19\t97.3\t97.1\t97.1\t99.5\t97.1\t1\t0\t2\t1\t0\t8\t0.3\tN\n+0.0000\tY17633.1.1768_U|Y17633|U||Reference|11|Eukaryota|Opisthokonta|Fungi|Glomeromycota|Glomeromycotina|Glomeromycotina_X|Acaulospora|Acaulospora+laevis|Acaulospora|Acaulospora+laevis;size=1\t*\t*\t*\t*\t*\t*\t*\t*\t0\t0\t0\t0\t0\t0\t*\tN\n+0.0000\tY17636.1.1698_U|Y17636|U|||11|Eukaryota|Opisthokonta|Fungi|Glomeromycota|Glomeromycotina|Glomeromycetes|Claroideoglomus|Claroideoglomus+claroideum|Claroideoglomus|Claroideoglomus+claroideum;size=1\t*\t*\t*\t*\t*\t*\t*\t*\t0\t0\t0\t0\t0\t0\t*\tN\n+0.0000\tZ11590.1.1648_U|Z11590|U||Reference|11|Eukaryota|Opisthokonta|Metazoa|Platyhelminthes|Trematoda|Digenea|Schistosoma|Schistosoma+japonicum|Schistosoma|Schistosoma+japonicum;size=1\t*\t*\t*\t*\t*\t*\t*\t*\t0\t0\t0\t0\t0\t0\t*\tN\n+1.9127\tZ83751.1.1890_U|Z83751|U||Reference|11|Eukaryota|Opisthokonta|Metazoa|Annelida|Annelida_X|Annelida_XX|Glossiphonia|Glossiphonia+sp.|Glossiphonia|Glossiphonia+sp.;size=1\tGQ368792.1.1765_U|GQ368792|U|||11|Eukaryota|Opisthokonta|Metazoa|Annelida|Annelida_X|Annelida_XX|Hirudo|Hirudo+orientalis|Hirudo|Hirudo+orientalis;size=5\tJN227970.1.1297_U|JN227970|U|||gb_191-cc|Eukaryota|Opisthokonta|Metazoa|Cnidaria|Cnidaria_X|Anthozoa|Trichogorgia|Trichogorgia+capensis|Trichogorgia|Trichogorgia+capensis;size=2\tGQ368792.1.1765_U|GQ368792|U|||11|Eukaryota|Opisthokonta|Metazoa|Annelida|Annelida_X|Annelida_XX|Hirudo|Hirudo+orientalis|Hirudo|Hirudo+orientalis;size=5\t97.7\t95.4\t81.9\t81.7\t95.4\t55\t0\t3\t8\t0\t5\t2.3\tY\n+0.0395\tZ97583.1.1876_U|Z97583|U|||11|Eukaryota|Opisthokonta|Metazoa|Arthropoda|Hexapoda|Insecta|Stiphra|Stiphra+robusta|Stiphra|Stiphra+robusta;size=1\tAY121146.1.1811_U|AY121146|U|||11|Eukaryota|Opisthokonta|Metazoa|Arthropoda|Hexapoda|Insecta|Melanoplus|Melanoplus+sp.|Melanoplus|Melanoplus+sp.;size=3\tEU364522.1.1748_U|EU364522|U||Reference|11|Eukaryota|Opisthokonta|Metazoa|Arthropoda|Hexapoda|Insecta|Euparatettix|Euparatettix+erythronotus|Euparatettix|Euparatettix+erythronotus;size=2\tAY121146.1.1811_U|AY121146|U|||11|Eukaryota|Opisthokonta|Metazoa|Arthropoda|Hexapoda|Insecta|Melanoplus|Melanoplus+sp.|Melanoplus|Melanoplus+sp.;size=3\t95.7\t95.5\t94.0\t93.1\t95.5\t9\t1\t7\t9\t8\t3\t0.2\tN\n+0.0246\tZ99946.1.1790_U|Z99946|U||Reference|11|Eukaryota|Opisthokonta|Metazoa|Platyhelminthes|Turbellaria|Seriata|Baikalobia|Baikalobia+guttata|Baikalobia|Baikalobia+guttata;size=1\tAJ287559.1.1759_U|AJ287559|U||Reference|11|Eukaryota|Opisthokonta|Metazoa|Platyhelminthes|Turbellaria|Seriata|Phagocata|Phagocata+sibirica|Phagocata|Phagocata+sibirica;size=2\tZ99949.1.1760_U|Z99949|U||Reference|11|Eukaryota|Opisthokonta|Metazoa|Platyhelminthes|Turbellaria|Seriata|Polycelis|Polycelis+tenuis|Polycelis|Polycelis+tenuis;size=2\tAJ287559.1.1759_U|AJ287559|U||Reference|11|Eukaryota|Opisthokonta|Metazoa|Platyhelminthes|Turbellaria|Seriata|Phagocata|Phagocata+sibirica|Phagocata|Phagocata+sibirica;size=2\t92.6\t92.3\t90.4\t90.4\t92.3\t11\t3\t8\t6\t5\t11\t0.3\tN\n' |
| b |
| diff -r 000000000000 -r fae6527990af test-data/clustering_blast6out_result1.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/clustering_blast6out_result1.tab Thu May 21 03:58:09 2015 -0400 |
| b |
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|
| b |
| diff -r 000000000000 -r fae6527990af test-data/clustering_centroids_result1.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/clustering_centroids_result1.fasta Thu May 21 03:58:09 2015 -0400 |
| b |
| b'@@ -0,0 +1,9698 @@\n+>5b3bd3d89041bf6676e95510f0b0b8e6;size=32\n+AGCTCCAATAGCGTATATTAAAGTTGTTGCGGTTAAAAAGCTCGTAGTTGGATTTCTGTCTTCGGCCGGGCGGTGCCGCC\n+TGATAATCAAGGGCGCGCACTGCTTTGGGAGCGTTGGTGTCAAAGCCGCGCTCTTTTAACGGTCGGACAATACCACCGGA\n+GTGGTGACGGGTCGGCGGGGTTGGCTTTTATCGGCCTTCACTGTCGGCTCCCACCCGTAATCGTCCGAGGTGCTCTTAAC\n+CGAGTGTCTCGGGCGGCCGGTAACGTTTACTTTGAACAAATTAGAGTGCTCAAAGCAGGTGCTTGCTCGCCTGAATATCA\n+CAGCATGGAATGATGGAATAGGACCTCGGTCTTATTTTGTTGGTTTTCTTCTAGACCCGAGGTAATGGTTAATAGAGACA\n+GACGGGGGCATTCGTACTGCGACGCTAGAGGTGAAATTCTTGGACCGTCGCAAGACGAACAACTGCGAAAGCATTTGCCA\n+AGAATGTTTTCA\n+>dd9c9696486e4c8e44f64040bfd68af0;size=43\n+AGCTCCAATAGCGTATATTAAAGTTGTTGCGGTTAAAAAGCTCGTAGTTGGATTCCTGTCTTCGGCCGGGCGGTGCCGCC\n+CGATCAAAGGGCGTCGCACTGCTTTGGGTCGGCGGTGTCAAAGCCGTCGACTTTTAACGGTCGGACAATACCACCGGAGC\n+GGTCGCGTCGGTCCGTCGGGCCTCAGGGTTCGGCGGTCGCCGGCGCGGCCCGTAATCGTCCGAGGTGCCCTTAACAAGGT\n+GTCTCGGGCGGCCGGTAACGTTTACTTTGAACAAATTAGAGTGCTCCAAGCAGGTGCATACCTTCGCCTGAATAGTACAG\n+CATGGAATGATGGAATAGGACCTCGGTCTTATTTTGTTGGTTTTTCTAGACCCGAGGTAATGGTTAATAGAGACGGACGG\n+GGGCATTCGTACTGCGACGCTAGAGGTGAAATTCTTGGACCGTCGCAAGACGAACGACTGCGAAAGCATTTGCCAAGAAT\n+GTTTTCA\n+>fc137ae3d4f5eb20104e5d3f1490201c;size=75\n+AGCTCCAATAGCGTATATTAAAGTTGTTGCGGTTAAAAAGCTCGTAGTTGGATTTCTGTCTTCGGCCGGGCGGTGCCGCC\n+TGATAATCAAGGGCGCGCACTGCTTTGGGAGCGTCGGTGTCAAAGCCGCGCTCTTTTAACGGTCGGACAATACCACCGGA\n+GTGGCGGACGGAGGGGTGTCGAGCTCTCGGGCTTTTCGCTTCTCTCCCGCCCGTAATCGTCCGAGGTGCTCTTAACCGAG\n+TGTCTCGGGCGGCCGGTAACGTTTACTTTGAACAAATTAGAGTGCTCAAAGCAGGTGCTTATCGCCTGAATATCACAGCA\n+TGGAATGATGGAATAGGACCTCGGTCTTATTTTGTTGGTTTTCTCTAGACCCGAGGTAATGGTTAATAGAGACAGACGGG\n+GGCATTCGTACTGCGGCGCTAGAGGTGAAATTCTTGGACCGCCGCAAGACGAACAACTGCGAAAGCATTTGCCAAGAATG\n+TTTTCA\n+>d9dd80f66077bd29d1569180753d1ea6;size=30\n+AGCTCCAATAGCGTATATTAAAGTTGTTGCGGTTAAAAAGCTCGTAGTTGGATTTCTGTCTTCGGCCGGGCGGTGCCGCC\n+TGATAATCAAGGGCGCGCACTGCTTTGGGAGCGCCGGTGTCAAAGCCGCGCTCTTTTAACGGTCGGACAATACCACCGGA\n+GTGGTGACGGGCCGGCGGGGTTGGTTCGCCCTTCACCGTCGGTCCCCACCCGTAATCGTCCGAGGTGCTCTTAACCGAGT\n+GTCTCGGGCGGCCGGTAACGTTTACTTTGAACAAATTAGAGTGCTCAAAGCAGGTGCTTGCTCGCCTGAATATCACAGCA\n+TGGAATGATGGAATAGGACCTCGGTCTTATTTTGTTGGTTTTCTCTAGACCCGAGGTAATGGTTAATAGAGACAGACGGG\n+GGCATTCGTACTGCGACGCTAGAGGTGAAATTCTTGGACCGTCGCAAGACGAACAACTGCGAAAGCATTTGCCAAGAATG\n+TTTTCA\n+>54b9859f6c86ac8d2736e3fa4d13ba87;size=95\n+AGCTCCACTAGCGTATATTAAAGTTGCTGCAGTTAAAAAGCTCGTAGTCGGATCTCGGGATCGTATCTCGTCGGTGTCGT\n+TGGGTCATGCCTCGAAAGGGGTTGTGGTCTTTCGGCGTCTTCGGGGTCTCATCCGGAGGGTCTCTGGCTTCACGCCGGGG\n+TTTCACCTTCCGCGATGGCCCGCCGTCGCGTTTGGGTGGGTGTCCTTAATTGGATGCCCGCCGTCGAACGTGACCATTTT\n+ACCTTGAACAAATCGGAGTGCTCAACGCAGGCTCCACCACGCTCGAACGGTAGCGCATGGAATAATGGAAGAGGACCAGC\n+TTCCGCTTCTATTGGTCTCACGGAGGCAGGTAATGATCAAGAGGAACGGATGGGGGGCAGAGGTATGGCTCGGCGAGAGG\n+TGAAATTCTTGGACCCTAGCCAGACCCTCGAGAGCGAAAGCATCTGCCAAAGATGTTTTCA\n+>1fcfe9045f0bc00da82d03df44a48394;size=53\n+AGCTCCACTAGCGTATATTAAAGTTGCTGCAGTTAAAAAGCTCGTAGTCGGATCTCGGGATCGTGTCGGCGTTCTCGTGG\n+TTTCTCCTGCGGTTCTGCCGTTGGGAGTTTCCGCGGGTCGTCGGCCCTGGCGGCTAGGTCCCCACCTGATGGTGGGGTTC\n+CACCTGGCTCGTCCAGCCCGCCGTCGCGTTTGGGCGGGTGTCCTTAATTGGATGCCCGCTCTCGAACGTGGCCCGTTTAC\n+CTTGAACAAATCGGAGTGCTCAAAGCAGGCTCTACGTCGCTCGAACGGTAGCGCATGGAATAATGGAAGAGGGACCGGGC\n+TTCCGCTTTCTGTTGGTCTCACGGAGGCAGGTAATGATCAAGAGGGACGGACGGGGGCGGAGGTATGGCTCGGCGAGAGG\n+TGAAATTCTTGGACCCTAGCCAGACCCTCGAGAGCGAAAGCATCCGCCAAGGATGTTTCCA\n+>3b5b50289fa657be02f8223db1ceecc1;size=38\n+AGCTCCACTAGCGTATATTAAAGTTGCTGCAGTTAAAAAGCTCGTAGTCGGATCTCGGGATCGTACCCCCTCGGTTTTCG\n+TTGGGCCATGCCTCGCAAGGGGTTGTGGACTCGCGGGGCCGTTGGGGTCTCATCCAGAGGGTCTCTGGTATTTCGCCGGG\n+GTTTTACCTTCTGCGATGGCCCGCCGTTGTGTTTGGGTGGGTGTCCTTAATTGGATGCCCGCTTTCGAACGCGACCATTT\n+TACCTTGAACAAATCGGAGTGCTTAAAGCAGGCTCCACCACGCTCGTACGGTAGCGCATGGAATAATGGAAGAGGACCCG\n+CTTCCGCTTCTGTTGGTCTCACGGAGGCAGGTAATGATCAAGAGGAACGGACGGGGGCGGAGGTATGGCTCGGCGAGAGG\n+TGAAATTCTTGGACCCCAGCCAGACCTACGAGAGCGAAAGCATCCGCCAAGGATGTTTCCA\n+>8cf694bf5517e02fc09302d0c222f492;size=32\n+AGCTCCACTAGCGTATATTAAAGTTGCTGCAGTTAAAAAGCTCGTAGTCGGATCTCGGGATCGTGTCGGCGTTCTCGTGG\n+TTTCTCCTGCGGTTCTGCCGTTGGGAGTTTCCGCGGGTCGTCGGCCCTGGCGGCTAGGTCCCCACCTGATGGTGGGGTTC\n+CACCTGGCTCGTCCAGCCCGCCGTCGCGTTTGGGCGGGTGTCCTT'..b'GTTGCAGTTAAAAAGCTCGTAGTTGAATTTAGGAGAAAGAATTCTCCTGTCTGCA\n+CTCTTCAGGGCAAATGATATTGCTCTGGAGAACAGACTTTTACTGTGAGAAAACTAAAGTGCTCAAAGCAGGCTAACGCT\n+TGAATATTAAAGCATGGAATAATAAAATAGGACTTTATTCTATTATTGGTCATTGGATAAAGTAATGATTAACAGAAACA\n+GTTGGGGGCATTCGTATTTAATTGTCAGAGGTGAAATTCTTGGATTAATTAAAGACGAACTAGTGCGAAAGCATTTGCCA\n+AGGATGTTTTCA\n+>96a9caaafe30428b70835b5d473865f4;size=78\n+AGCTCCAATAGCGTATATTAAAGTTGTTGCAGTTAAAAAGCTCGTAGTTGGATCTCGGGAGCAGGCCGGCGGTCCGCCTC\n+GCGGCGGTTACTGCCTGTCCTGCCCTACCTGCCGGTTTTCCCCCGGTGCTCTTCATTGAGTGCCTCGGGTGGCCGGAACG\n+TTTACTTTGACCATTATGGAATAATGGAATAGGACCTCGGTTCTATTTTGTTGGTCTCGATGTTGGATTAAGAGGGACAG\n+ACGGGGGCATTCGTATTACACTGTTAGAGGTGAAATTCTTGGATCGGTGTAAGACGAACTACTGCGAAAGCATTTGCCAA\n+GAATGTTTTCA\n+>6e693c587ce4656374be43a0c5a0e0f1;size=33\n+AGCTCCAGTAGCGTATATTAAAGTTGTTGCAGTTAAAAAGCTCGTAGTTGGACTTGCACTCCTTTTGGAGCAGCCTAGCA\n+ACTCCGCATGTCCTTAATTGGATGGCGGAGACCTGCGGGCCCTTTACCTTGAGAAAATTAGAGTGTTTAAGGCAGGCCAC\n+GCCTGAATACTGCAGCTGGGAATAATGCATCACGACTGTCTTGGCGAGGCAGCTCTACACTTTTAATAGGAACGGTTGGG\n+GGCATTCGTACTCAGCAGTCAGAGGTGAAATTCTTGGATTTGCTGAAGACGGACTAGTGCGAAAGCATTTGCCAAGGATG\n+TTTTCA\n+>6d23e3b9b8db42f3ee64c4b8b3b3e016;size=71\n+AGCTCCAATAGCGTATATTAAAGTTGTTGTGGTTAAAAAGCTCGTAGTTTTGCCAGAGGTTTCGGGGTGCTCTTAATCGA\n+GTGTCCCGGGATGCTGGCAGGTTTACTTTGAAAAAATTAGAGTGCTCAAAGCAGGCTATTACGCCTGAATATTCGTGCAT\n+GGAATAATAGAATAGGAAGTCGTTTCTATTTTGTTGGTTTTCGGAAATCGACTTAATGATTAATAGGGACAGTCGGGGGC\n+ATTTGTATTCAAACGACAGAGGTGAAATTCTTGGACCGTTTGAAGACAAACTACTGCGAAAGCATTTGCCAAGAATGTTT\n+TCA\n+>ea0e653d3c6c63a34d2fd51697955280;size=56\n+AGCTCCAATAGCGTATATTAAAGTTGTTGCAGTTAAAAAGCTCGTAGTTGGATTTCAAGGTGGAGATGGGGTTTACTCCG\n+TTGAAGCTTATCAGTCCGAAAGGACTGTTACTGTGAGAAAATTAGAGTGTTTCAAGCAGGCAATTGCAGGAATACATTAG\n+CATGGAATAACGAATGTGTCTAGAATCTTGGTTAATTCTAGATTACGATTAATAGGGACAGTTGGGGGCATTAGTATTTA\n+ATTGTCAGAGGTGAAATTCTTGGATTTGTTAAAGACTAACCTATGCGAAAGCATTTGCCAAGGATGTTTTCA\n+>90ded2932eac98a8cb2a92bf4d04e0bf;size=120\n+AGCTCCAATAGCGTATATTAAAGTTGTTGCAGTTAAAAAGCTCGTAGTTGGATTTCTAGATAAGTGGGTACTTGTACTTT\n+GCTTGTCTACCAGTCTTAGACTGTTACTGTGAGAAAAATTAGAGTGTTTCAAGCAGGCTGTTGCAGGAATACATTAGCAT\n+GGAATAACGAATGTGTCTGGAATATTGGTTAATTCTAGATTACGATTAATAGGGACAGTTGGGGGCATTAGTATTTAATT\n+GTCAGAGGTGAAATTCTTGGATTTATTAAAGACTAACGTATGCGAAAGCATTTGCCAAGGATGTTTTCA\n+>b858b313f1df62306272d6837665a1ff;size=65\n+AGCTCCAATAGCGTATATTAAAGTTGTTGCAGTTAAAAAGCTCGTAGTTGGATTTCAAGGATCTCAGCGTGGATACACGT\n+TTGAATCCTACCAGTCTTTGACTGTTACTGTGAGAAAATTAGAGTGTTTCAAGCAGGCTGTTGCAGGAATACATTAGCAT\n+GGAATAACGAATGTGTCTAGAATCTTGGTTAATTCTAGAATACGATTAATAGGGACAGTTGGGGGCATTAGTATTTAATT\n+GTCAGAGGTGAAATTCTTGGATTTATTAAAGACTAACGTATGCGAAAGCATTTGCCAAGGATGTTTTCA\n+>46c166a8a872048e3b43afc09a7ff4e4;size=64\n+AGCTCCAATAGCGTATATTAAAGTTGTTGCAGTTAAAAAGCTCGTAGTTGGATTTCTAGATAAGTGGGTACTTGTACTTT\n+GCTTGTCTACCAGTCATAGACTGTTACTGTGAGAAAATTAGAGTGTTTCAAGCAGGCTGTTGCAGGAATACATTAGCATG\n+GAATAACGAATGTGTCTGGAATATTGGTTAATTCTAGATTACGATTAATAGGGACAGTTGGGGGCATTAGTATTTAATTG\n+TCAGAGGTGAAATTCTTGGATTTATTAAAGACTAACGTATGCGAAAGCATTTGCCAAGGATGTTTTTCA\n+>5f6b41eee25b85749d6079c416331706;size=52\n+AGCTCCAATAGCGTATATTAAAGTTGTTGCAGTTAAAAAGCTCGTAGTTGGATTTCAAGAGACGCATCTGGGGATACCGG\n+TATGCTCTCTACGGTCTCAGGACTGTTACTGTGAGAAAATTAGAGTGTTCAAAGCAGGCTATTGCAGGAATATATTAGCA\n+TGGAATAACGAATGTGTTTACAATTTGGTTAATTGTAGATTTCAATTAATAGGGACAGTTGGGGGCATTAGTATTTAATT\n+GTCAGAGGTGAAATTCTTGGATTAGTTAAAGACTAACGTATGCGAAAGCATTTGCCAAGGATGTTTTCA\n+>8eece1bfb387537588b482297f3a3861;size=61\n+AGCTCTTTTTGTGTACTTTAAAGTTACTTTGTTTGAAAAGTTCGTCGTCTGTGTTGTTGTTTGAGTTGATTTTTCGAAAG\n+AAAGTAGTACTGTGAGAAAATGGGTTTGTTTCAGATGACTTGTTAGCATGGTATATTTGTGTGTATGTTTAGCGATTGTT\n+TTGTTAAAAATAAGACAAGAAGAGTGGTCGGGGGTGCTCGTATTTGTGGGCCAGAGGTGAAATTCTTGGATTCCACAAGG\n+ACGTCCAATCGCGCAAGCATTCGCCCAGGACACGTCTG\n+>cbd30db2f4ec28a4d991954efbe58ec7;size=43\n+ATACCCCTTTATGGAGATGGATTAAACATCCGCGATTGGCTTTATGTTGAAGACCATGTGGATGCATTACTCCTAGCAGC\n+CTGTCGAGGAACATCTGGACGCAGCTATTGCGTTGGTGGCCATGGTGAAAAAACGAATCAAGAGGTGGTCAATGCAATCT\n+GCCATCAGT\n+>ddc6ea88330faf28ef92ee4e8b1380cf;size=38\n+AGCTCCAATAGCGTATATTAAAGTTGTTGTGGTTAAAAAGCTCGTAGTTTTCA\n+>ce291c2620b3cd6a0b627ca586ddd4e9;size=40\n+TAAAGTAGCAACTGAACGTAGAATAGGGAAGAAGCTACGAAGAGAGAATA\n' |
| b |
| diff -r 000000000000 -r fae6527990af test-data/clustering_notmatched_result1.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/clustering_notmatched_result1.fasta Thu May 21 03:58:09 2015 -0400 |
| b |
| b'@@ -0,0 +1,9698 @@\n+>5b3bd3d89041bf6676e95510f0b0b8e6;size=32\n+AGCTCCAATAGCGTATATTAAAGTTGTTGCGGTTAAAAAGCTCGTAGTTGGATTTCTGTCTTCGGCCGGGCGGTGCCGCC\n+TGATAATCAAGGGCGCGCACTGCTTTGGGAGCGTTGGTGTCAAAGCCGCGCTCTTTTAACGGTCGGACAATACCACCGGA\n+GTGGTGACGGGTCGGCGGGGTTGGCTTTTATCGGCCTTCACTGTCGGCTCCCACCCGTAATCGTCCGAGGTGCTCTTAAC\n+CGAGTGTCTCGGGCGGCCGGTAACGTTTACTTTGAACAAATTAGAGTGCTCAAAGCAGGTGCTTGCTCGCCTGAATATCA\n+CAGCATGGAATGATGGAATAGGACCTCGGTCTTATTTTGTTGGTTTTCTTCTAGACCCGAGGTAATGGTTAATAGAGACA\n+GACGGGGGCATTCGTACTGCGACGCTAGAGGTGAAATTCTTGGACCGTCGCAAGACGAACAACTGCGAAAGCATTTGCCA\n+AGAATGTTTTCA\n+>dd9c9696486e4c8e44f64040bfd68af0;size=43\n+AGCTCCAATAGCGTATATTAAAGTTGTTGCGGTTAAAAAGCTCGTAGTTGGATTCCTGTCTTCGGCCGGGCGGTGCCGCC\n+CGATCAAAGGGCGTCGCACTGCTTTGGGTCGGCGGTGTCAAAGCCGTCGACTTTTAACGGTCGGACAATACCACCGGAGC\n+GGTCGCGTCGGTCCGTCGGGCCTCAGGGTTCGGCGGTCGCCGGCGCGGCCCGTAATCGTCCGAGGTGCCCTTAACAAGGT\n+GTCTCGGGCGGCCGGTAACGTTTACTTTGAACAAATTAGAGTGCTCCAAGCAGGTGCATACCTTCGCCTGAATAGTACAG\n+CATGGAATGATGGAATAGGACCTCGGTCTTATTTTGTTGGTTTTTCTAGACCCGAGGTAATGGTTAATAGAGACGGACGG\n+GGGCATTCGTACTGCGACGCTAGAGGTGAAATTCTTGGACCGTCGCAAGACGAACGACTGCGAAAGCATTTGCCAAGAAT\n+GTTTTCA\n+>fc137ae3d4f5eb20104e5d3f1490201c;size=75\n+AGCTCCAATAGCGTATATTAAAGTTGTTGCGGTTAAAAAGCTCGTAGTTGGATTTCTGTCTTCGGCCGGGCGGTGCCGCC\n+TGATAATCAAGGGCGCGCACTGCTTTGGGAGCGTCGGTGTCAAAGCCGCGCTCTTTTAACGGTCGGACAATACCACCGGA\n+GTGGCGGACGGAGGGGTGTCGAGCTCTCGGGCTTTTCGCTTCTCTCCCGCCCGTAATCGTCCGAGGTGCTCTTAACCGAG\n+TGTCTCGGGCGGCCGGTAACGTTTACTTTGAACAAATTAGAGTGCTCAAAGCAGGTGCTTATCGCCTGAATATCACAGCA\n+TGGAATGATGGAATAGGACCTCGGTCTTATTTTGTTGGTTTTCTCTAGACCCGAGGTAATGGTTAATAGAGACAGACGGG\n+GGCATTCGTACTGCGGCGCTAGAGGTGAAATTCTTGGACCGCCGCAAGACGAACAACTGCGAAAGCATTTGCCAAGAATG\n+TTTTCA\n+>d9dd80f66077bd29d1569180753d1ea6;size=30\n+AGCTCCAATAGCGTATATTAAAGTTGTTGCGGTTAAAAAGCTCGTAGTTGGATTTCTGTCTTCGGCCGGGCGGTGCCGCC\n+TGATAATCAAGGGCGCGCACTGCTTTGGGAGCGCCGGTGTCAAAGCCGCGCTCTTTTAACGGTCGGACAATACCACCGGA\n+GTGGTGACGGGCCGGCGGGGTTGGTTCGCCCTTCACCGTCGGTCCCCACCCGTAATCGTCCGAGGTGCTCTTAACCGAGT\n+GTCTCGGGCGGCCGGTAACGTTTACTTTGAACAAATTAGAGTGCTCAAAGCAGGTGCTTGCTCGCCTGAATATCACAGCA\n+TGGAATGATGGAATAGGACCTCGGTCTTATTTTGTTGGTTTTCTCTAGACCCGAGGTAATGGTTAATAGAGACAGACGGG\n+GGCATTCGTACTGCGACGCTAGAGGTGAAATTCTTGGACCGTCGCAAGACGAACAACTGCGAAAGCATTTGCCAAGAATG\n+TTTTCA\n+>54b9859f6c86ac8d2736e3fa4d13ba87;size=95\n+AGCTCCACTAGCGTATATTAAAGTTGCTGCAGTTAAAAAGCTCGTAGTCGGATCTCGGGATCGTATCTCGTCGGTGTCGT\n+TGGGTCATGCCTCGAAAGGGGTTGTGGTCTTTCGGCGTCTTCGGGGTCTCATCCGGAGGGTCTCTGGCTTCACGCCGGGG\n+TTTCACCTTCCGCGATGGCCCGCCGTCGCGTTTGGGTGGGTGTCCTTAATTGGATGCCCGCCGTCGAACGTGACCATTTT\n+ACCTTGAACAAATCGGAGTGCTCAACGCAGGCTCCACCACGCTCGAACGGTAGCGCATGGAATAATGGAAGAGGACCAGC\n+TTCCGCTTCTATTGGTCTCACGGAGGCAGGTAATGATCAAGAGGAACGGATGGGGGGCAGAGGTATGGCTCGGCGAGAGG\n+TGAAATTCTTGGACCCTAGCCAGACCCTCGAGAGCGAAAGCATCTGCCAAAGATGTTTTCA\n+>1fcfe9045f0bc00da82d03df44a48394;size=53\n+AGCTCCACTAGCGTATATTAAAGTTGCTGCAGTTAAAAAGCTCGTAGTCGGATCTCGGGATCGTGTCGGCGTTCTCGTGG\n+TTTCTCCTGCGGTTCTGCCGTTGGGAGTTTCCGCGGGTCGTCGGCCCTGGCGGCTAGGTCCCCACCTGATGGTGGGGTTC\n+CACCTGGCTCGTCCAGCCCGCCGTCGCGTTTGGGCGGGTGTCCTTAATTGGATGCCCGCTCTCGAACGTGGCCCGTTTAC\n+CTTGAACAAATCGGAGTGCTCAAAGCAGGCTCTACGTCGCTCGAACGGTAGCGCATGGAATAATGGAAGAGGGACCGGGC\n+TTCCGCTTTCTGTTGGTCTCACGGAGGCAGGTAATGATCAAGAGGGACGGACGGGGGCGGAGGTATGGCTCGGCGAGAGG\n+TGAAATTCTTGGACCCTAGCCAGACCCTCGAGAGCGAAAGCATCCGCCAAGGATGTTTCCA\n+>3b5b50289fa657be02f8223db1ceecc1;size=38\n+AGCTCCACTAGCGTATATTAAAGTTGCTGCAGTTAAAAAGCTCGTAGTCGGATCTCGGGATCGTACCCCCTCGGTTTTCG\n+TTGGGCCATGCCTCGCAAGGGGTTGTGGACTCGCGGGGCCGTTGGGGTCTCATCCAGAGGGTCTCTGGTATTTCGCCGGG\n+GTTTTACCTTCTGCGATGGCCCGCCGTTGTGTTTGGGTGGGTGTCCTTAATTGGATGCCCGCTTTCGAACGCGACCATTT\n+TACCTTGAACAAATCGGAGTGCTTAAAGCAGGCTCCACCACGCTCGTACGGTAGCGCATGGAATAATGGAAGAGGACCCG\n+CTTCCGCTTCTGTTGGTCTCACGGAGGCAGGTAATGATCAAGAGGAACGGACGGGGGCGGAGGTATGGCTCGGCGAGAGG\n+TGAAATTCTTGGACCCCAGCCAGACCTACGAGAGCGAAAGCATCCGCCAAGGATGTTTCCA\n+>8cf694bf5517e02fc09302d0c222f492;size=32\n+AGCTCCACTAGCGTATATTAAAGTTGCTGCAGTTAAAAAGCTCGTAGTCGGATCTCGGGATCGTGTCGGCGTTCTCGTGG\n+TTTCTCCTGCGGTTCTGCCGTTGGGAGTTTCCGCGGGTCGTCGGCCCTGGCGGCTAGGTCCCCACCTGATGGTGGGGTTC\n+CACCTGGCTCGTCCAGCCCGCCGTCGCGTTTGGGCGGGTGTCCTT'..b'GTTGCAGTTAAAAAGCTCGTAGTTGAATTTAGGAGAAAGAATTCTCCTGTCTGCA\n+CTCTTCAGGGCAAATGATATTGCTCTGGAGAACAGACTTTTACTGTGAGAAAACTAAAGTGCTCAAAGCAGGCTAACGCT\n+TGAATATTAAAGCATGGAATAATAAAATAGGACTTTATTCTATTATTGGTCATTGGATAAAGTAATGATTAACAGAAACA\n+GTTGGGGGCATTCGTATTTAATTGTCAGAGGTGAAATTCTTGGATTAATTAAAGACGAACTAGTGCGAAAGCATTTGCCA\n+AGGATGTTTTCA\n+>96a9caaafe30428b70835b5d473865f4;size=78\n+AGCTCCAATAGCGTATATTAAAGTTGTTGCAGTTAAAAAGCTCGTAGTTGGATCTCGGGAGCAGGCCGGCGGTCCGCCTC\n+GCGGCGGTTACTGCCTGTCCTGCCCTACCTGCCGGTTTTCCCCCGGTGCTCTTCATTGAGTGCCTCGGGTGGCCGGAACG\n+TTTACTTTGACCATTATGGAATAATGGAATAGGACCTCGGTTCTATTTTGTTGGTCTCGATGTTGGATTAAGAGGGACAG\n+ACGGGGGCATTCGTATTACACTGTTAGAGGTGAAATTCTTGGATCGGTGTAAGACGAACTACTGCGAAAGCATTTGCCAA\n+GAATGTTTTCA\n+>6e693c587ce4656374be43a0c5a0e0f1;size=33\n+AGCTCCAGTAGCGTATATTAAAGTTGTTGCAGTTAAAAAGCTCGTAGTTGGACTTGCACTCCTTTTGGAGCAGCCTAGCA\n+ACTCCGCATGTCCTTAATTGGATGGCGGAGACCTGCGGGCCCTTTACCTTGAGAAAATTAGAGTGTTTAAGGCAGGCCAC\n+GCCTGAATACTGCAGCTGGGAATAATGCATCACGACTGTCTTGGCGAGGCAGCTCTACACTTTTAATAGGAACGGTTGGG\n+GGCATTCGTACTCAGCAGTCAGAGGTGAAATTCTTGGATTTGCTGAAGACGGACTAGTGCGAAAGCATTTGCCAAGGATG\n+TTTTCA\n+>6d23e3b9b8db42f3ee64c4b8b3b3e016;size=71\n+AGCTCCAATAGCGTATATTAAAGTTGTTGTGGTTAAAAAGCTCGTAGTTTTGCCAGAGGTTTCGGGGTGCTCTTAATCGA\n+GTGTCCCGGGATGCTGGCAGGTTTACTTTGAAAAAATTAGAGTGCTCAAAGCAGGCTATTACGCCTGAATATTCGTGCAT\n+GGAATAATAGAATAGGAAGTCGTTTCTATTTTGTTGGTTTTCGGAAATCGACTTAATGATTAATAGGGACAGTCGGGGGC\n+ATTTGTATTCAAACGACAGAGGTGAAATTCTTGGACCGTTTGAAGACAAACTACTGCGAAAGCATTTGCCAAGAATGTTT\n+TCA\n+>ea0e653d3c6c63a34d2fd51697955280;size=56\n+AGCTCCAATAGCGTATATTAAAGTTGTTGCAGTTAAAAAGCTCGTAGTTGGATTTCAAGGTGGAGATGGGGTTTACTCCG\n+TTGAAGCTTATCAGTCCGAAAGGACTGTTACTGTGAGAAAATTAGAGTGTTTCAAGCAGGCAATTGCAGGAATACATTAG\n+CATGGAATAACGAATGTGTCTAGAATCTTGGTTAATTCTAGATTACGATTAATAGGGACAGTTGGGGGCATTAGTATTTA\n+ATTGTCAGAGGTGAAATTCTTGGATTTGTTAAAGACTAACCTATGCGAAAGCATTTGCCAAGGATGTTTTCA\n+>90ded2932eac98a8cb2a92bf4d04e0bf;size=120\n+AGCTCCAATAGCGTATATTAAAGTTGTTGCAGTTAAAAAGCTCGTAGTTGGATTTCTAGATAAGTGGGTACTTGTACTTT\n+GCTTGTCTACCAGTCTTAGACTGTTACTGTGAGAAAAATTAGAGTGTTTCAAGCAGGCTGTTGCAGGAATACATTAGCAT\n+GGAATAACGAATGTGTCTGGAATATTGGTTAATTCTAGATTACGATTAATAGGGACAGTTGGGGGCATTAGTATTTAATT\n+GTCAGAGGTGAAATTCTTGGATTTATTAAAGACTAACGTATGCGAAAGCATTTGCCAAGGATGTTTTCA\n+>b858b313f1df62306272d6837665a1ff;size=65\n+AGCTCCAATAGCGTATATTAAAGTTGTTGCAGTTAAAAAGCTCGTAGTTGGATTTCAAGGATCTCAGCGTGGATACACGT\n+TTGAATCCTACCAGTCTTTGACTGTTACTGTGAGAAAATTAGAGTGTTTCAAGCAGGCTGTTGCAGGAATACATTAGCAT\n+GGAATAACGAATGTGTCTAGAATCTTGGTTAATTCTAGAATACGATTAATAGGGACAGTTGGGGGCATTAGTATTTAATT\n+GTCAGAGGTGAAATTCTTGGATTTATTAAAGACTAACGTATGCGAAAGCATTTGCCAAGGATGTTTTCA\n+>46c166a8a872048e3b43afc09a7ff4e4;size=64\n+AGCTCCAATAGCGTATATTAAAGTTGTTGCAGTTAAAAAGCTCGTAGTTGGATTTCTAGATAAGTGGGTACTTGTACTTT\n+GCTTGTCTACCAGTCATAGACTGTTACTGTGAGAAAATTAGAGTGTTTCAAGCAGGCTGTTGCAGGAATACATTAGCATG\n+GAATAACGAATGTGTCTGGAATATTGGTTAATTCTAGATTACGATTAATAGGGACAGTTGGGGGCATTAGTATTTAATTG\n+TCAGAGGTGAAATTCTTGGATTTATTAAAGACTAACGTATGCGAAAGCATTTGCCAAGGATGTTTTTCA\n+>5f6b41eee25b85749d6079c416331706;size=52\n+AGCTCCAATAGCGTATATTAAAGTTGTTGCAGTTAAAAAGCTCGTAGTTGGATTTCAAGAGACGCATCTGGGGATACCGG\n+TATGCTCTCTACGGTCTCAGGACTGTTACTGTGAGAAAATTAGAGTGTTCAAAGCAGGCTATTGCAGGAATATATTAGCA\n+TGGAATAACGAATGTGTTTACAATTTGGTTAATTGTAGATTTCAATTAATAGGGACAGTTGGGGGCATTAGTATTTAATT\n+GTCAGAGGTGAAATTCTTGGATTAGTTAAAGACTAACGTATGCGAAAGCATTTGCCAAGGATGTTTTCA\n+>8eece1bfb387537588b482297f3a3861;size=61\n+AGCTCTTTTTGTGTACTTTAAAGTTACTTTGTTTGAAAAGTTCGTCGTCTGTGTTGTTGTTTGAGTTGATTTTTCGAAAG\n+AAAGTAGTACTGTGAGAAAATGGGTTTGTTTCAGATGACTTGTTAGCATGGTATATTTGTGTGTATGTTTAGCGATTGTT\n+TTGTTAAAAATAAGACAAGAAGAGTGGTCGGGGGTGCTCGTATTTGTGGGCCAGAGGTGAAATTCTTGGATTCCACAAGG\n+ACGTCCAATCGCGCAAGCATTCGCCCAGGACACGTCTG\n+>cbd30db2f4ec28a4d991954efbe58ec7;size=43\n+ATACCCCTTTATGGAGATGGATTAAACATCCGCGATTGGCTTTATGTTGAAGACCATGTGGATGCATTACTCCTAGCAGC\n+CTGTCGAGGAACATCTGGACGCAGCTATTGCGTTGGTGGCCATGGTGAAAAAACGAATCAAGAGGTGGTCAATGCAATCT\n+GCCATCAGT\n+>ddc6ea88330faf28ef92ee4e8b1380cf;size=38\n+AGCTCCAATAGCGTATATTAAAGTTGTTGTGGTTAAAAAGCTCGTAGTTTTCA\n+>ce291c2620b3cd6a0b627ca586ddd4e9;size=40\n+TAAAGTAGCAACTGAACGTAGAATAGGGAAGAAGCTACGAAGAGAGAATA\n' |
| b |
| diff -r 000000000000 -r fae6527990af test-data/db.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/db.fasta Thu May 21 03:58:09 2015 -0400 |
| b |
| @@ -0,0 +1,54 @@ +>tr|M0F5C2|M0F5C2_9EURY 30S ribosomal protein S14 type Z OS=Halorubrum hochstenium ATCC 700873 GN=rps14P PE=3 SV=1 +MSEANNDTGEHAAKRTDSRHTCRRCDREQGLVGKYDINLCRQCFREVARDMGFEKYS +>tr|M0KT65|M0KT65_9EURY 50S ribosomal protein L37e OS=Haloarcula amylolytica JCM 13557 GN=rpl37e PE=3 SV=1 +MTGAGTPSQGKKNTTTHTKCRRCGEKSYHTKKKVCSSCGFGKSAKRRDYEWQSKAGE +>tr|M0KH83|M0KH83_9EURY 50S ribosomal protein L18Ae OS=Haloarcula amylolytica JCM 13557 GN=rplX PE=3 SV=1 +MSTYTVRGSFPARDGPQQFEKEVDAPNENVAEERVYSDFGSQHNLKRTQITIEEVAA +>tr|M0PIT7|M0PIT7_9EURY 30S ribosomal protein S14 type Z OS=Halorubrum arcis JCM 13916 GN=rps14P PE=3 SV=1 +MSEANNDTGEHAAKRTDSRHTCRRCDREQGLVGKYDINLCRQCFREVARDMGFEKYS +>tr|M0MK44|M0MK44_9EURY 50S ribosomal protein L37e OS=Halococcus saccharolyticus DSM 5350 GN=rpl37e PE=3 SV=1 +MTGSGTPSQGKKNKTVHVKCRRCGEASYHKTKKVCASCGFGKSAKRRDYAWQEKAGE +>tr|M0MEH5|M0MEH5_9EURY 30S ribosomal protein S14 type Z OS=Halococcus saccharolyticus DSM 5350 GN=rps14P PE=3 SV=1 +MSESETDTGEHATKRTGQLEDCQRCGRKQGLVGKYDIWLCRQCFREIARGMGFRKYK +>tr|M0D8K9|M0D8K9_9EURY 30S ribosomal protein S14 type Z OS=Halorubrum terrestre JCM 10247 GN=rps14P PE=3 SV=1 +MSEANNDTGEHAAKRTDSRHTCRRCDREQGLVGKYDINLCRQCFREVARDMGFEKYS +>tr|L9WBT3|L9WBT3_9EURY 50S ribosomal protein L18Ae OS=Natronorubrum sulfidifaciens JCM 14089 GN=rplX PE=3 SV=1 +MSQFTVTGQFKSRDGYAPFETTIDAENENVAREHVLSQLGSQHGLKRTEIDLEEVSE +>tr|M0NIQ6|M0NIQ6_9EURY 30S ribosomal protein S14 type Z OS=Halorubrum lipolyticum DSM 21995 GN=rps14P PE=3 SV=1 +MSEANNDTGEHAAKRTDSRHTCRRCDREQGLVGKYDINLCRQCFREVARDMGFEKYS +>tr|L9WHT8|L9WHT8_9EURY 50S ribosomal protein L18Ae OS=Natronorubrum bangense JCM 10635 GN=rplX PE=3 SV=1 +MSQFTVTGQFKSRDGYSPFETTIDAENENVAREHVYSQLGSQHGLKRSEIELDEVSA +>sp|Q91G65|032R_IIV6 Uncharacterized protein 032R OS=Invertebrate iridescent virus 6 GN=IIV6-032R PE=4 SV=1 +MGVYKFCYNKKKEVGQVAVLQKERLIFYIVTKEKSYLKPTLANFSNAIDSLYNECLLRKC +CKLAIPKIGCCLDRLYWKTVKNIIIDKLCKKGIEVVVYYI +>sp|Q66125|2B_CMVQ Suppressor of silencing 2b OS=Cucumber mosaic virus (strain Q) GN=ORF2b PE=1 SV=1 +MDVLTVVVSTADLHLANLQEVKRRRRRSHVRNRRARGYKSPSERARSIARLFQMLPFHGV +DPVDWFPDVVRSPSVTSLVSYESFDDTDWFAGNEWAEGSF +>sp|P20194|A100_SSV1 Uncharacterized protein A-100 OS=Sulfolobus spindle-shape virus 1 GN=a100 PE=1 SV=1 +MVSPQTRKEEELLEKQNSVFYLLTLGRKPYGSYLHIKIELDEDEKLEKEIYADNIKLENE +LRQLKRLYEVYQSVEIDDAQKAIQKEALLTIAKILSVFDF +>sp|P0DMP9|APOC3_PANTA Apolipoprotein C-III OS=Panthera tigris altaica GN=APOC3 PE=3 SV=1 +MQSRVLLVTALLVLLASARATEGEDPSLLGLMQGYVQHATKTAQDTLTTMREFPVAQQAR +DWVTGRFSSLKDYWSTLTGKFSGFWDSTFAVTPTPASEAK +>sp|Q89681|DR4_HHV6U Uncharacterized protein DR4 OS=Human herpesvirus 6A (strain Uganda-1102) GN=DR4L PE=4 SV=1 +MRGTRRGPSGGWSPLGLALPRYPAGSVAASDPRSDTPPPRAPPPPPPLTTSAYRPHTHPA +AESGARTRAEHARQHARHRPPEVTEPVHVPVLAGVCARVP +>sp|B3MQ24|ENY2_DROAN Enhancer of yellow 2 transcription factor OS=Drosophila ananassae GN=e(y)2 PE=3 SV=1 +MTVSNTVDQYTVLSGDRSKIKDLLCNRLTECGWRDEVRLLCRTILLEKGTGNSFTVEQLI +TEVTPKARTLVPDAVKKELLMKIRTILTENESEIEDAEEP +>tr|H0ACG9|H0ACG9_HALSG Uncharacterized protein OS=Haloredivivus sp. (strain G17) GN=HRED_08116 PE=4 SV=1 +MREVRVPEDRVGVVIGEGGETKKRXEEGFV +>tr|N6VV02|N6VV02_9EURY Uncharacterized protein (Fragment) OS=Thermoplasmatales archaeon SCGC AB-539-C06 GN=MBGDC06_00209 PE=4 SV=1 +KRLEGALEHGKMNIGSVFIKTTMGPSGRIL +>tr|X0LYM3|X0LYM3_FUSOX Uncharacterized protein OS=Fusarium oxysporum f. sp. vasinfectum 25433 GN=FOTG_17987 PE=4 SV=1 +MTNAPGRPSKACDICKRQKVGCSPFLERYK +>tr|V9H0X7|V9H0X7_NEUCS Neurospora crassa DNA for RNA polymerase I second-largest subunit OS=Neurospora crassa PE=4 SV=1 +MPPAHISDNRPDTQPADYEGIIQGALHFAA +>tr|W9PMP6|W9PMP6_FUSOX Uncharacterized protein OS=Fusarium oxysporum f. sp. pisi HDV247 GN=FOVG_07074 PE=4 SV=1 +MTNAPGRPSKACDICKRQKVGCSPFLERYK +>tr|H3BPV3|H3BPV3_HUMAN ATP-dependent RNA helicase DDX19B OS=Homo sapiens GN=DDX19B PE=4 SV=1 +MATDSWALAVDEQEAAAESRTELPSPYSTS +>tr|Q53RS6|Q53RS6_HUMAN Putative uncharacterized protein ALS2CR3 (Fragment) OS=Homo sapiens GN=ALS2CR3 PE=4 SV=1 +MSQSQNAIFTSPTGEENLMNSNHRDSESIT +>tr|Q9BZF8|Q9BZF8_HUMAN NF-E2-related factor 2 (Fragment) OS=Homo sapiens PE=2 SV=1 +MMDLELPPPGLPSQQDMDLIDILWRQDIDL |
| b |
| diff -r 000000000000 -r fae6527990af test-data/dereplication_result1.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dereplication_result1.fasta Thu May 21 03:58:09 2015 -0400 |
| b |
| @@ -0,0 +1,3 @@ +>97485665bcded44c4d86c131ca714848 +gtcgctcctaccgattgaatacgttggtgattgaattggataaagagatatcatcttaaatgatagcaaagcggtaaaca +tttgtaaactagattatttagaggaaggagaagtcgtaacaaggtttcc |
| b |
| diff -r 000000000000 -r fae6527990af test-data/masking_result1.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/masking_result1.fasta Thu May 21 03:58:09 2015 -0400 |
| b |
| @@ -0,0 +1,48 @@ +>tr|M0F5C2|M0F5C2_9EURY 30S ribosomal protein S14 type Z OS=Halorubrum hochstenium ATCC 700873 GN=rps14P PE=3 SV=1 +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +>tr|M0KT65|M0KT65_9EURY 50S ribosomal protein L37e OS=Haloarcula amylolytica JCM 13557 GN=rpl37e PE=3 SV=1 +MTGAGTSGKKNTTTHTKCRRCGKSYHTKKKVCSSCGGNNNNNNNNNNNNG +>tr|M0KH83|M0KH83_9EURY 50S ribosomal protein L18Ae OS=Haloarcula amylolytica JCM 13557 GN=rplX PE=3 SV=1 +MSTYTVRGNNNNNNNNNNNNNNNNNNNNNNNNTTVAA +>tr|M0PIT7|M0PIT7_9EURY 30S ribosomal protein S14 type Z OS=Halorubrum arcis JCM 13916 GN=rps14P PE=3 SV=1 +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +>tr|M0MK44|M0MK44_9EURY 50S ribosomal protein L37e OS=Halococcus saccharolyticus DSM 5350 GN=rpl37e PE=3 SV=1 +MTGSGTSGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNG +>tr|M0MEH5|M0MEH5_9EURY 30S ribosomal protein S14 type Z OS=Halococcus saccharolyticus DSM 5350 GN=rps14P PE=3 SV=1 +MSSTDTGHATKRTGDCRCGRKGVGKYDWCRCRARGMGRKYK +>tr|M0D8K9|M0D8K9_9EURY 30S ribosomal protein S14 type Z OS=Halorubrum terrestre JCM 10247 GN=rps14P PE=3 SV=1 +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +>tr|L9WBT3|L9WBT3_9EURY 50S ribosomal protein L18Ae OS=Natronorubrum sulfidifaciens JCM 14089 GN=rplX PE=3 SV=1 +MSTVTGKSRDGYATTNNNNNNNNNNGSHGKRTDVS +>tr|M0NIQ6|M0NIQ6_9EURY 30S ribosomal protein S14 type Z OS=Halorubrum lipolyticum DSM 21995 GN=rps14P PE=3 SV=1 +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +>tr|L9WHT8|L9WHT8_9EURY 50S ribosomal protein L18Ae OS=Natronorubrum bangense JCM 10635 GN=rplX PE=3 SV=1 +MSTVTGKSRDGYSTTNNNNNNNNNNNNNNNNNNNNNN +>sp|Q91G65|032R_IIV6 Uncharacterized protein 032R OS=Invertebrate iridescent virus 6 GN=IIV6-032R PE=4 SV=1 +MGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +>sp|Q66125|2B_CMVQ Suppressor of silencing 2b OS=Cucumber mosaic virus (strain Q) GN=ORF2b PE=1 SV=1 +MDVTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTDWAGNWAGS +>sp|P20194|A100_SSV1 Uncharacterized protein A-100 OS=Sulfolobus spindle-shape virus 1 GN=a100 PE=1 SV=1 +MVSTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +>sp|P0DMP9|APOC3_PANTA Apolipoprotein C-III OS=Panthera tigris altaica GN=APOC3 PE=3 SV=1 +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTGKSGWDSTAVTTASAK +>sp|Q89681|DR4_HHV6U Uncharacterized protein DR4 OS=Human herpesvirus 6A (strain Uganda-1102) GN=DR4L PE=4 SV=1 +MRGTRRGSGGWSGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGVCARV +>sp|B3MQ24|ENY2_DROAN Enhancer of yellow 2 transcription factor OS=Drosophila ananassae GN=e(y)2 PE=3 SV=1 +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +>tr|H0ACG9|H0ACG9_HALSG Uncharacterized protein OS=Haloredivivus sp. (strain G17) GN=HRED_08116 PE=4 SV=1 +NNNNNNNNGVVGGGTKKRGV +>tr|N6VV02|N6VV02_9EURY Uncharacterized protein (Fragment) OS=Thermoplasmatales archaeon SCGC AB-539-C06 GN=MBGDC06_00209 PE=4 SV=1 +KRGAHGKMNGSVKTTMGSGR +>tr|X0LYM3|X0LYM3_FUSOX Uncharacterized protein OS=Fusarium oxysporum f. sp. vasinfectum 25433 GN=FOTG_17987 PE=4 SV=1 +MTNAGRSKACDCKRKVGCSRYK +>tr|V9H0X7|V9H0X7_NEUCS Neurospora crassa DNA for RNA polymerase I second-largest subunit OS=Neurospora crassa PE=4 SV=1 +NNNNNNNNTADYGGAHAA +>tr|W9PMP6|W9PMP6_FUSOX Uncharacterized protein OS=Fusarium oxysporum f. sp. pisi HDV247 GN=FOVG_07074 PE=4 SV=1 +MTNAGRSKACDCKRKVGCSRYK +>tr|H3BPV3|H3BPV3_HUMAN ATP-dependent RNA helicase DDX19B OS=Homo sapiens GN=DDX19B PE=4 SV=1 +MATNNNNNNNNNNNNTSYSTS +>tr|Q53RS6|Q53RS6_HUMAN Putative uncharacterized protein ALS2CR3 (Fragment) OS=Homo sapiens GN=ALS2CR3 PE=4 SV=1 +MSSNATSTGNNNNNNNNNNT +>tr|Q9BZF8|Q9BZF8_HUMAN NF-E2-related factor 2 (Fragment) OS=Homo sapiens PE=2 SV=1 +MMDGNNNNNNNNN |
| b |
| diff -r 000000000000 -r fae6527990af test-data/masking_result2.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/masking_result2.fasta Thu May 21 03:58:09 2015 -0400 |
| b |
| @@ -0,0 +1,48 @@ +>tr|M0F5C2|M0F5C2_9EURY 30S ribosomal protein S14 type Z OS=Halorubrum hochstenium ATCC 700873 GN=rps14P PE=3 SV=1 +MSANNDTGHAAKRTDSRHTCRRCDRGVGKYDNCRCRVARDMGKYS +>tr|M0KT65|M0KT65_9EURY 50S ribosomal protein L37e OS=Haloarcula amylolytica JCM 13557 GN=rpl37e PE=3 SV=1 +MTGAGTSGKKNTTTHTKCRRCGKSYHTKKKVCSSCGGKSAKRRDYWSKAG +>tr|M0KH83|M0KH83_9EURY 50S ribosomal protein L18Ae OS=Haloarcula amylolytica JCM 13557 GN=rplX PE=3 SV=1 +MSTYTVRGSARDGKVDANNVARVYSDGSHNKRTTVAA +>tr|M0PIT7|M0PIT7_9EURY 30S ribosomal protein S14 type Z OS=Halorubrum arcis JCM 13916 GN=rps14P PE=3 SV=1 +MSANNDTGHAAKRTDSRHTCRRCDRGVGKYDNCRCRVARDMGKYS +>tr|M0MK44|M0MK44_9EURY 50S ribosomal protein L37e OS=Halococcus saccharolyticus DSM 5350 GN=rpl37e PE=3 SV=1 +MTGSGTSGKKNKTVHVKCRRCGASYHKTKKVCASCGGKSAKRRDYAWKAG +>tr|M0MEH5|M0MEH5_9EURY 30S ribosomal protein S14 type Z OS=Halococcus saccharolyticus DSM 5350 GN=rps14P PE=3 SV=1 +MSSTDTGHATKRTGDCRCGRKGVGKYDWCRCRARGMGRKYK +>tr|M0D8K9|M0D8K9_9EURY 30S ribosomal protein S14 type Z OS=Halorubrum terrestre JCM 10247 GN=rps14P PE=3 SV=1 +MSANNDTGHAAKRTDSRHTCRRCDRGVGKYDNCRCRVARDMGKYS +>tr|L9WBT3|L9WBT3_9EURY 50S ribosomal protein L18Ae OS=Natronorubrum sulfidifaciens JCM 14089 GN=rplX PE=3 SV=1 +MSTVTGKSRDGYATTDANNVARHVSGSHGKRTDVS +>tr|M0NIQ6|M0NIQ6_9EURY 30S ribosomal protein S14 type Z OS=Halorubrum lipolyticum DSM 21995 GN=rps14P PE=3 SV=1 +MSANNDTGHAAKRTDSRHTCRRCDRGVGKYDNCRCRVARDMGKYS +>tr|L9WHT8|L9WHT8_9EURY 50S ribosomal protein L18Ae OS=Natronorubrum bangense JCM 10635 GN=rplX PE=3 SV=1 +MSTVTGKSRDGYSTTDANNVARHVYSGSHGKRSDVSA +>sp|Q91G65|032R_IIV6 Uncharacterized protein 032R OS=Invertebrate iridescent virus 6 GN=IIV6-032R PE=4 SV=1 +MGVYKCYNKKKVGVAVKRYVTKKSYKTANSNADSYNCRKCCKAKGCCDRYWKTVKNDKCKKGVVVYY +>sp|Q66125|2B_CMVQ Suppressor of silencing 2b OS=Cucumber mosaic virus (strain Q) GN=ORF2b PE=1 SV=1 +MDVTVVVSTADHANVKRRRRRSHVRNRRARGYKSSRARSARMHGVDVDWDVVRSSVTSVSYSDDTDWAGNWAGS +>sp|P20194|A100_SSV1 Uncharacterized protein A-100 OS=Sulfolobus spindle-shape virus 1 GN=a100 PE=1 SV=1 +MVSTRKKNSVYTGRKYGSYHKDDKKYADNKNRKRYVYSVDDAKAKATAKSVD +>sp|P0DMP9|APOC3_PANTA Apolipoprotein C-III OS=Panthera tigris altaica GN=APOC3 PE=3 SV=1 +MSRVVTAVASARATGDSGMGYVHATKTADTTTMRVAARDWVTGRSSKDYWSTTGKSGWDSTAVTTASAK +>sp|Q89681|DR4_HHV6U Uncharacterized protein DR4 OS=Human herpesvirus 6A (strain Uganda-1102) GN=DR4L PE=4 SV=1 +MRGTRRGSGGWSGARYAGSVAASDRSDTRATTSAYRHTHAASGARTRAHARHARHRVTVHVVAGVCARV +>sp|B3MQ24|ENY2_DROAN Enhancer of yellow 2 transcription factor OS=Drosophila ananassae GN=e(y)2 PE=3 SV=1 +MTVSNTVDYTVSGDRSKKDCNRTCGWRDVRCRTKGTGNSTVTVTKARTVDAVKKMKRTTNSDA +>tr|H0ACG9|H0ACG9_HALSG Uncharacterized protein OS=Haloredivivus sp. (strain G17) GN=HRED_08116 PE=4 SV=1 +MRVRVDRVGVVGGGTKKRGV +>tr|N6VV02|N6VV02_9EURY Uncharacterized protein (Fragment) OS=Thermoplasmatales archaeon SCGC AB-539-C06 GN=MBGDC06_00209 PE=4 SV=1 +KRGAHGKMNGSVKTTMGSGR +>tr|X0LYM3|X0LYM3_FUSOX Uncharacterized protein OS=Fusarium oxysporum f. sp. vasinfectum 25433 GN=FOTG_17987 PE=4 SV=1 +MTNAGRSKACDCKRKVGCSRYK +>tr|V9H0X7|V9H0X7_NEUCS Neurospora crassa DNA for RNA polymerase I second-largest subunit OS=Neurospora crassa PE=4 SV=1 +MAHSDNRDTADYGGAHAA +>tr|W9PMP6|W9PMP6_FUSOX Uncharacterized protein OS=Fusarium oxysporum f. sp. pisi HDV247 GN=FOVG_07074 PE=4 SV=1 +MTNAGRSKACDCKRKVGCSRYK +>tr|H3BPV3|H3BPV3_HUMAN ATP-dependent RNA helicase DDX19B OS=Homo sapiens GN=DDX19B PE=4 SV=1 +MATDSWAAVDAAASRTSYSTS +>tr|Q53RS6|Q53RS6_HUMAN Putative uncharacterized protein ALS2CR3 (Fragment) OS=Homo sapiens GN=ALS2CR3 PE=4 SV=1 +MSSNATSTGNMNSNHRDSST +>tr|Q9BZF8|Q9BZF8_HUMAN NF-E2-related factor 2 (Fragment) OS=Homo sapiens PE=2 SV=1 +MMDGSDMDDWRDD |
| b |
| diff -r 000000000000 -r fae6527990af test-data/query.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/query.fasta Thu May 21 03:58:09 2015 -0400 |
| b |
| @@ -0,0 +1,26 @@ +>ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds. +GAGAGGACGAGGTGCCGCTGCCTGGAGAATCCTCCGCTGCCGTCGGCTCCCGGAGCCCAG +CCCTTTCCTAACCCAACCCAACCTAGCCCAGTCCCAGCCGCCAGCGCCTGTCCCTGTCAC +GGACCCCAGCGTTACCATGCATCCTGCCGTCTTCCTATCCTTACCCGACCTCAGATGCTC +CCTTCTGCTCCTGGTAACTTGGGTTTTTACTCCTGTAACAACTGAAATAACAAGTCTTGA +TACAGAGAATATAGATGAAATTTTAAACAATGCTGATGTTGCTTTAGTAAATTTTTATGC +TGACTGGTGTCGTTTCAGTCAGATGTTGCATCCAATTTTTGAGGAAGCTTCCGATGTCAT +TAAGGAAGAATTTCCAAATGAAAATCAAGTAGTGTTTGCCAGAGTTGATTGTGATCAGCA +CTCTGACATAGCCCAGAGATACAGGATAAGCAAATACCCAACCCTCAAATTGTTTCGTAA +TGGGATGATGATGAAGAGAGAATACAGGGGTCAGCGATCAGTGAAAGCATTGGCAGATTA +CATCAGGCAACAAAAAAGTGACCCCATTCAAGAAATTCGGGACTTAGCAGAAATCACCAC +TCTTGATCGCAGCAAAAGAAATATCATTGGATATTTTGAGCAAAAGGACTCGGACAACTA +TAGAGTTTTTGAACGAGTAGCGAATATTTTGCATGATGACTGTGCCTTTCTTTCTGCATT +TGGGGATGTTTCAAAACCGGAAAGATATAGTGGCGACAACATAATCTACAAACCACCAGG +GCATTCTGCTCCGGATATGGTGTACTTGGGAGCTATGACAAATTTTGATGTGACTTACAA +TTGGATTCAAGATAAATGTGTTCCTCTTGTCCGAGAAATAACATTTGAAAATGGAGAGGA +ATTGACAGAAGAAGGACTGCCTTTTCTCATACTCTTTCACATGAAAGAAGATACAGAAAG +TTTAGAAATATTCCAGAATGAAGTAGCTCGGCAATTAATAAGTGAAAAAGGTACAATAAA +CTTTTTACATGCCGATTGTGACAAATTTAGACATCCTCTTCTGCACATACAGAAAACTCC +AGCAGATTGTCCTGTAATCGCTATTGACAGCTTTAGGCATATGTATGTGTTTGGAGACTT +CAAAGATGTATTAATTCCTGGAAAACTCAAGCAATTCGTATTTGACTTACATTCTGGAAA +ACTGCACAGAGAATTCCATCATGGACCTGACCCAACTGATACAGCCCCAGGAGAGCAAGC +CCAAGATGTAGCAAGCAGTCCACCTGAGAGCTCCTTCCAGAAACTAGCACCCAGTGAATA +TAGGTATACTCTATTGAGGGATCGAGATGAGCTTTAAAAACTTGAAAAACAGTTTGTAAG +CCTTTCAACAGCAGCATCAACCTACGTGGTGGAAATAGTAAACCTATATTTTCATAATTC +TATGTGTATTTTTATTTTGAATAAACAGAAAGAAATTTTGGGTTTTTAATTTTTTTCTCC |
| b |
| diff -r 000000000000 -r fae6527990af test-data/search_blast6out_result1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/search_blast6out_result1.tabular Thu May 21 03:58:09 2015 -0400 |
| b |
| @@ -0,0 +1,1 @@ +ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds. ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds. 100.0 1500 0 0 1 1500 1 4796 -1 0 |
| b |
| diff -r 000000000000 -r fae6527990af test-data/search_dbmatched_result1.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/search_dbmatched_result1.fasta Thu May 21 03:58:09 2015 -0400 |
| b |
| @@ -0,0 +1,61 @@ +>ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds. +GAGAGGACGAGGTGCCGCTGCCTGGAGAATCCTCCGCTGCCGTCGGCTCCCGGAGCCCAGCCCTTTCCTAACCCAACCCA +ACCTAGCCCAGTCCCAGCCGCCAGCGCCTGTCCCTGTCACGGACCCCAGCGTTACCATGCATCCTGCCGTCTTCCTATCC +TTACCCGACCTCAGATGCTCCCTTCTGCTCCTGGTAACTTGGGTTTTTACTCCTGTAACAACTGAAATAACAAGTCTTGA +TACAGAGAATATAGATGAAATTTTAAACAATGCTGATGTTGCTTTAGTAAATTTTTATGCTGACTGGTGTCGTTTCAGTC +AGATGTTGCATCCAATTTTTGAGGAAGCTTCCGATGTCATTAAGGAAGAATTTCCAAATGAAAATCAAGTAGTGTTTGCC +AGAGTTGATTGTGATCAGCACTCTGACATAGCCCAGAGATACAGGATAAGCAAATACCCAACCCTCAAATTGTTTCGTAA +TGGGATGATGATGAAGAGAGAATACAGGGGTCAGCGATCAGTGAAAGCATTGGCAGATTACATCAGGCAACAAAAAAGTG +ACCCCATTCAAGAAATTCGGGACTTAGCAGAAATCACCACTCTTGATCGCAGCAAAAGAAATATCATTGGATATTTTGAG +CAAAAGGACTCGGACAACTATAGAGTTTTTGAACGAGTAGCGAATATTTTGCATGATGACTGTGCCTTTCTTTCTGCATT +TGGGGATGTTTCAAAACCGGAAAGATATAGTGGCGACAACATAATCTACAAACCACCAGGGCATTCTGCTCCGGATATGG +TGTACTTGGGAGCTATGACAAATTTTGATGTGACTTACAATTGGATTCAAGATAAATGTGTTCCTCTTGTCCGAGAAATA +ACATTTGAAAATGGAGAGGAATTGACAGAAGAAGGACTGCCTTTTCTCATACTCTTTCACATGAAAGAAGATACAGAAAG +TTTAGAAATATTCCAGAATGAAGTAGCTCGGCAATTAATAAGTGAAAAAGGTACAATAAACTTTTTACATGCCGATTGTG +ACAAATTTAGACATCCTCTTCTGCACATACAGAAAACTCCAGCAGATTGTCCTGTAATCGCTATTGACAGCTTTAGGCAT +ATGTATGTGTTTGGAGACTTCAAAGATGTATTAATTCCTGGAAAACTCAAGCAATTCGTATTTGACTTACATTCTGGAAA +ACTGCACAGAGAATTCCATCATGGACCTGACCCAACTGATACAGCCCCAGGAGAGCAAGCCCAAGATGTAGCAAGCAGTC +CACCTGAGAGCTCCTTCCAGAAACTAGCACCCAGTGAATATAGGTATACTCTATTGAGGGATCGAGATGAGCTTTAAAAA +CTTGAAAAACAGTTTGTAAGCCTTTCAACAGCAGCATCAACCTACGTGGTGGAAATAGTAAACCTATATTTTCATAATTC +TATGTGTATTTTTATTTTGAATAAACAGAAAGAAATTTTGGGTTTTTAATTTTTTTCTCCCCGACTCAAAATGCATTGTC +ATTTAATATAGTAGCCTCTTAAAAAAAAAAAAACCTGCTAGGATTTAAAAATAAAAATCAGAGGCCTATCTCCACTTTAA +ATCTGTCCTGTAAAAGTTTTATAAATCAAATGAAAGGTGACATTGCCAGAAACTTACCATTAACTTGCACTACTAGGGTA +GGGAGGACTTAGGATGTTTCCTGTGTCGTATGTGCTTTTCTTTCTTTCATATGATCAATTCTGTTGGTATTTTCAGTATC +TCATTTCTCAAAGCTAAAGAGATATACATTCTGGATACTTGGGAGGGGAATAAATTAAAGTTTTCACACTGTGTACTGTG +TTTTACTGATTGGTTGGATATTGCTTATGAAAATTCCATAGTGGTATTTTTTTGGATTCTTAATGTGTAACTTAAACATA +CTTTGAAGTGGAGGAGAGTCATAAGACAGAACATTTGGCAGGAATTGTCCTTATGAAACAAGAAAAAGAAAATGAAAAGT +ATTATTAAGCTTCTGTGTTTGTCTAAAAATGTGGCATATGGATGGCATTTAAAACTTTGAATGAATTATACCTAAATCTG +GGACAGGGAGGTGACAGTGGAACAGGCTACCAATCAGAACTAGATGACTTTTAAGGCTCCTCCTATTATGAGACTTCAAT +TTCCAAAGAGAAGAACTAGCAGAGAAATTGTATTTCAGTAATTTTAAGCTCCTTCTGTCTTGTAGAGTCTTGTTATAGTT +GTATAAATCAAAAACACAGAATAAGGAACATATTTAACTTTTTTTCATTATAAAATGGTTAGAGGACCCTACCCCCTCTA +GATTCCCTGATTTCCCCAGGCCTGCAGCATACAGTAAGATGGGTCCCTGTGCCAGGCCTCAATACTGCCAGGGAATAAAA +CCAGAGGGAGAGGACCCTCAGTGTCATATCAGGAAGCCCAGTGCCAGAGGACAGACAGGTTCAAAACTGGCTTTTCCTCT +GGGCCTGGGTTGGTGCTATAGGCCAAGGGTCATTTTATACTTGGGTATAAATCAATCCCAGTTTGGGAAAAGATTATTTT +TAAGCTTAAAAGGCTGACATGTGCCATTATATGTAGTATGTAATATATGTAACATCTTCCAATTCTTTTAAAATAAAATT +AATATTTATAATGGATATTTAATGATTGTTATTTTTAAAAACCAGCTTATAATTCCTCGTTATGCATGATTTATCCAAAG +TTTCCATAGTTTTATTCAAAATAATAAATGTTAATAAGGTGATAAGGGGTATATTTAATGTATTGTATCAAATTGTGAAT +AAGAAAGTAGGATGGAGCTTTCTAGAGGTTGGGCCTTAGTTCTGTTATCCTCATTGCTTTTAACCAATAAGTTAAATGAA +GTTAGAGTTATGGTCTTCAGGTTAGATTATGGACCAGATCTGTGAGGGTCAGCATGGAAATTCACATTCAACAAGGTAGC +ACACAGGACCAAGAGCAGCACATGCAATCAACTGGAATAATATAGTAATCCTGTAACTGGGTTTGAAAAAATAATCAACA +AAAGATACAATTCAAGGGTTAGGTTGCAGAGAGCTGGCTTGAGAGTAGTTATTATGAAAAAGGCCTCAAGGAGTACGTGT +TCAGTATGCTCTAAGATGATAAAGTGGCTGTTAAAAAGGGAGTTGATTTGAGGAAGTATTACTTAGCATTCATGCATATT +GGGCTTAGGCTCTAGCCCTGCCACTATCATTGTCTTCTCTGGACTGTGAAGTCACTGAGGACAAGGAAACTAAATTTAAT +GTCTGTATCACTAGTGCCTAGAATTTCTGGACACTTAGTAGTCACCATCAGGCGTTTATTTAATGAATGAGAAGCAAAGT +GACCTTGGTTACTTTTTTACCCTGAGGGGCTCAGCACTCATTAGGACTTGGTGCCTAATTTTATAAAAAGTCACTAAGCT +CAAGTGCTTGGATGAAAGGACAGCGTGGATAAAAAGGTTTTTAAAACATGGATGTTAAGGCTGTTTTGCTTGGAGAAGAC +TTGGGACTGGGACAGTCTTTAGATATTATTTGAAATGCTGGCACTGTCTATCTGGATCCCAGGGCTTGAACTAGGATTTG +AGGAAGTCACAGGGAAGCAGATTTCAGTCTGACATTTATTCAGTGCAAGTTTTTTGGTGCTGTAGTATATGATGAAAGAT +GTAAAGCTGAATAAAGCATTATTTCTGCCCTAGAGTTGTTCACAGCCTAGTCAGGCATATGGATATGTAAACAATGACTG +TAACGTGTTATAGATGTAAAGACAAAATAAAGGTTAAAGAGGGCATAAAGGAGCACTCAATTGCAGAGATTTGAGGACAT +TATTTTTATTTTGAGCTTTAAAAAGATGAATAGGTGTTCTCAGGAGGTAGGGATCTGGCTGAGAGGGAATAATCTGAGCA +AAGGTATGAAACAGCCTAATGCATTAGAGAAAAAAGTTCTTTTAGTAAGGCATTTGGGGTTGGGGAAGCTAGAAAAAGAA +ATGGGAGCTGGTCACACAGGGCCTTGTGTGCCAGACTAAGGGGTTTGTAGTATATATTGTAGGCAGAAGAGATCCATCAA +CAGATTGCAAGCAAGGAAGTATGTTCACTTTAAAGTTTGAGAAAGAATAGTGTGGAAGCACGTCTCAAATTTAGACTTAC +TTGTTCCCCCTCTGAACCGTGAATCAGACCATTTCAGGTAGAAGTCTTCCCCGGTTTATCTGATCTACTCGGGGCCTCAG +GCTTCTCAGCTGGGAAGAGAGGATGCAAGACCAGACTGAAGAACACGGTTGAGTCCCCAGAACCAAAAGGGGGCCTTTCT +GCTTCTTAGCCAGCTACCTCTTCGAGTTTTTCAAATTGTGAGGGGGACCATAAAAGGATGGAAACTTTTAGATGACATTC +TACAAATTATTTTTTTCTTTAAATTAAAAGAACCTAGCCAATAAGATAGAGAATGGGCATCTAAGGCATCTCAGAGCTCT +CTGATGAAGCCAGGTTGTCAAAGATCATTTGCAAAAGAAGGGAAAACTGGCATGACAAAAGCTACAGAGAGGAGAGTGAA +ATATAGAAGTGTTTGAAATGTTCAAGCTCACAATAAGCTTAAATTTATAGAAAATGCTAAGGTTGTCAAGAAGGCTTTTT +TTTTTTTCTTTTTTAAACCTGAGGGCAAAAAGGAATGGATAAAGTAGTGTAATGGATTGACAATCAGGAAGAACAGAATA +ACTCAGTTTTTTTTTCTCCTACAAGGAGATATGGCTGGACCAAAATAAAATGACATGAAATTGCAAAAATGAAAAT |
| b |
| diff -r 000000000000 -r fae6527990af test-data/search_fastapairs_result2.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/search_fastapairs_result2.fasta Thu May 21 03:58:09 2015 -0400 |
| b |
| @@ -0,0 +1,5 @@ +>ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds. +GAGAGGACGAGGTGCCGCTGCCTGGAGAATCCTCCGCTGCCGTCGGCTCCCGGAGCCCAGCCCTTTCCTAACCCAACCCAACCTAGCCCAGTCCCAGCCGCCAGCGCCTGTCCCTGTCACGGACCCCAGCGTTACCATGCATCCTGCCGTCTTCCTATCCTTACCCGACCTCAGATGCTCCCTTCTGCTCCTGGTAACTTGGGTTTTTACTCCTGTAACAACTGAAATAACAAGTCTTGATACAGAGAATATAGATGAAATTTTAAACAATGCTGATGTTGCTTTAGTAAATTTTTATGCTGACTGGTGTCGTTTCAGTCAGATGTTGCATCCAATTTTTGAGGAAGCTTCCGATGTCATTAAGGAAGAATTTCCAAATGAAAATCAAGTAGTGTTTGCCAGAGTTGATTGTGATCAGCACTCTGACATAGCCCAGAGATACAGGATAAGCAAATACCCAACCCTCAAATTGTTTCGTAATGGGATGATGATGAAGAGAGAATACAGGGGTCAGCGATCAGTGAAAGCATTGGCAGATTACATCAGGCAACAAAAAAGTGACCCCATTCAAGAAATTCGGGACTTAGCAGAAATCACCACTCTTGATCGCAGCAAAAGAAATATCATTGGATATTTTGAGCAAAAGGACTCGGACAACTATAGAGTTTTTGAACGAGTAGCGAATATTTTGCATGATGACTGTGCCTTTCTTTCTGCATTTGGGGATGTTTCAAAACCGGAAAGATATAGTGGCGACAACATAATCTACAAACCACCAGGGCATTCTGCTCCGGATATGGTGTACTTGGGAGCTATGACAAATTTTGATGTGACTTACAATTGGATTCAAGATAAATGTGTTCCTCTTGTCCGAGAAATAACATTTGAAAATGGAGAGGAATTGACAGAAGAAGGACTGCCTTTTCTCATACTCTTTCACATGAAAGAAGATACAGAAAGTTTAGAAATATTCCAGAATGAAGTAGCTCGGCAATTAATAAGTGAAAAAGGTACAATAAACTTTTTACATGCCGATTGTGACAAATTTAGACATCCTCTTCTGCACATACAGAAAACTCCAGCAGATTGTCCTGTAATCGCTATTGACAGCTTTAGGCATATGTATGTGTTTGGAGACTTCAAAGATGTATTAATTCCTGGAAAACTCAAGCAATTCGTATTTGACTTACATTCTGGAAAACTGCACAGAGAATTCCATCATGGACCTGACCCAACTGATACAGCCCCAGGAGAGCAAGCCCAAGATGTAGCAAGCAGTCCACCTGAGAGCTCCTTCCAGAAACTAGCACCCAGTGAATATAGGTATACTCTATTGAGGGATCGAGATGAGCTTTAAAAACTTGAAAAACAGTTTGTAAGCCTTTCAACAGCAGCATCAACCTACGTGGTGGAAATAGTAAACCTATATTTTCATAATTCTATGTgtatttttattttgaataaacagaaagaaattttgggtttttaatttttttCTCC +>ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds. +GAGAGGACGAGGTGCCGCTGCCTGGAGAATCCTCCGCTGCCGTCGGCTCCCGGAGCCCAGCCCTTTCCTAACCCAACCCAACCTAGCCCAGTCCCAGCCGCCAGCGCCTGTCCCTGTCACGGACCCCAGCGTTACCATGCATCCTGCCGTCTTCCTATCCTTACCCGACCTCAGATGCTCCCTTCTGCTCCTGGTAACTTGGGTTTTTACTCCTGTAACAACTGAAATAACAAGTCTTGATACAGAGAATATAGATGAAATTTTAAACAATGCTGATGTTGCTTTAGTAAATTTTTATGCTGACTGGTGTCGTTTCAGTCAGATGTTGCATCCAATTTTTGAGGAAGCTTCCGATGTCATTAAGGAAGAATTTCCAAATGAAAATCAAGTAGTGTTTGCCAGAGTTGATTGTGATCAGCACTCTGACATAGCCCAGAGATACAGGATAAGCAAATACCCAACCCTCAAATTGTTTCGTAATGGGATGATGATGAAGAGAGAATACAGGGGTCAGCGATCAGTGAAAGCATTGGCAGATTACATCAGGCAACAAAAAAGTGACCCCATTCAAGAAATTCGGGACTTAGCAGAAATCACCACTCTTGATCGCAGCAAAAGAAATATCATTGGATATTTTGAGCAAAAGGACTCGGACAACTATAGAGTTTTTGAACGAGTAGCGAATATTTTGCATGATGACTGTGCCTTTCTTTCTGCATTTGGGGATGTTTCAAAACCGGAAAGATATAGTGGCGACAACATAATCTACAAACCACCAGGGCATTCTGCTCCGGATATGGTGTACTTGGGAGCTATGACAAATTTTGATGTGACTTACAATTGGATTCAAGATAAATGTGTTCCTCTTGTCCGAGAAATAACATTTGAAAATGGAGAGGAATTGACAGAAGAAGGACTGCCTTTTCTCATACTCTTTCACATGAAAGAAGATACAGAAAGTTTAGAAATATTCCAGAATGAAGTAGCTCGGCAATTAATAAGTGAAAAAGGTACAATAAACTTTTTACATGCCGATTGTGACAAATTTAGACATCCTCTTCTGCACATACAGAAAACTCCAGCAGATTGTCCTGTAATCGCTATTGACAGCTTTAGGCATATGTATGTGTTTGGAGACTTCAAAGATGTATTAATTCCTGGAAAACTCAAGCAATTCGTATTTGACTTACATTCTGGAAAACTGCACAGAGAATTCCATCATGGACCTGACCCAACTGATACAGCCCCAGGAGAGCAAGCCCAAGATGTAGCAAGCAGTCCACCTGAGAGCTCCTTCCAGAAACTAGCACCCAGTGAATATAGGTATACTCTATTGAGGGATCGAGATGAGCTTTAAAAACTTGAAAAACAGTTTGTAAGCCTTTCAACAGCAGCATCAACCTACGTGGTGGAAATAGTAAACCTATATTTTCATAATTCTATGTGTATTTTTATTTTGAATAAACAGAAAGAAATTTTGGGTTTTTAATTTTTTTCTCC + |
| b |
| diff -r 000000000000 -r fae6527990af test-data/search_matched_result2.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/search_matched_result2.fasta Thu May 21 03:58:09 2015 -0400 |
| b |
| @@ -0,0 +1,20 @@ +>ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds. +GAGAGGACGAGGTGCCGCTGCCTGGAGAATCCTCCGCTGCCGTCGGCTCCCGGAGCCCAGCCCTTTCCTAACCCAACCCA +ACCTAGCCCAGTCCCAGCCGCCAGCGCCTGTCCCTGTCACGGACCCCAGCGTTACCATGCATCCTGCCGTCTTCCTATCC +TTACCCGACCTCAGATGCTCCCTTCTGCTCCTGGTAACTTGGGTTTTTACTCCTGTAACAACTGAAATAACAAGTCTTGA +TACAGAGAATATAGATGAAATTTTAAACAATGCTGATGTTGCTTTAGTAAATTTTTATGCTGACTGGTGTCGTTTCAGTC +AGATGTTGCATCCAATTTTTGAGGAAGCTTCCGATGTCATTAAGGAAGAATTTCCAAATGAAAATCAAGTAGTGTTTGCC +AGAGTTGATTGTGATCAGCACTCTGACATAGCCCAGAGATACAGGATAAGCAAATACCCAACCCTCAAATTGTTTCGTAA +TGGGATGATGATGAAGAGAGAATACAGGGGTCAGCGATCAGTGAAAGCATTGGCAGATTACATCAGGCAACAAAAAAGTG +ACCCCATTCAAGAAATTCGGGACTTAGCAGAAATCACCACTCTTGATCGCAGCAAAAGAAATATCATTGGATATTTTGAG +CAAAAGGACTCGGACAACTATAGAGTTTTTGAACGAGTAGCGAATATTTTGCATGATGACTGTGCCTTTCTTTCTGCATT +TGGGGATGTTTCAAAACCGGAAAGATATAGTGGCGACAACATAATCTACAAACCACCAGGGCATTCTGCTCCGGATATGG +TGTACTTGGGAGCTATGACAAATTTTGATGTGACTTACAATTGGATTCAAGATAAATGTGTTCCTCTTGTCCGAGAAATA +ACATTTGAAAATGGAGAGGAATTGACAGAAGAAGGACTGCCTTTTCTCATACTCTTTCACATGAAAGAAGATACAGAAAG +TTTAGAAATATTCCAGAATGAAGTAGCTCGGCAATTAATAAGTGAAAAAGGTACAATAAACTTTTTACATGCCGATTGTG +ACAAATTTAGACATCCTCTTCTGCACATACAGAAAACTCCAGCAGATTGTCCTGTAATCGCTATTGACAGCTTTAGGCAT +ATGTATGTGTTTGGAGACTTCAAAGATGTATTAATTCCTGGAAAACTCAAGCAATTCGTATTTGACTTACATTCTGGAAA +ACTGCACAGAGAATTCCATCATGGACCTGACCCAACTGATACAGCCCCAGGAGAGCAAGCCCAAGATGTAGCAAGCAGTC +CACCTGAGAGCTCCTTCCAGAAACTAGCACCCAGTGAATATAGGTATACTCTATTGAGGGATCGAGATGAGCTTTAAAAA +CTTGAAAAACAGTTTGTAAGCCTTTCAACAGCAGCATCAACCTACGTGGTGGAAATAGTAAACCTATATTTTCATAATTC +TATGTgtatttttattttgaataaacagaaagaaattttgggtttttaatttttttCTCC |
| b |
| diff -r 000000000000 -r fae6527990af test-data/search_userfields_result2.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/search_userfields_result2.tabular Thu May 21 03:58:09 2015 -0400 |
| b |
| @@ -0,0 +1,1 @@ +ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds. ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds. -1 |
| b |
| diff -r 000000000000 -r fae6527990af test-data/shuffling_result1.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/shuffling_result1.fasta Thu May 21 03:58:09 2015 -0400 |
| b |
| @@ -0,0 +1,10 @@ +>tr|Q53RS6|Q53RS6_HUMAN Putative uncharacterized protein ALS2CR3 (Fragment) OS=Homo sapiens GN=ALS2CR3 PE=4 SV=1 +MSSNATSTGNMNSNHRDSST +>tr|M0MEH5|M0MEH5_9EURY 30S ribosomal protein S14 type Z OS=Halococcus saccharolyticus DSM 5350 GN=rps14P PE=3 SV=1 +MSSTDTGHATKRTGDCRCGRKGVGKYDWCRCRARGMGRKYK +>sp|Q66125|2B_CMVQ Suppressor of silencing 2b OS=Cucumber mosaic virus (strain Q) GN=ORF2b PE=1 SV=1 +MDVTVVVSTADHANVKRRRRRSHVRNRRARGYKSSRARSARMHGVDVDWDVVRSSVTSVSYSDDTDWAGNWAGS +>sp|B3MQ24|ENY2_DROAN Enhancer of yellow 2 transcription factor OS=Drosophila ananassae GN=e(y)2 PE=3 SV=1 +MTVSNTVDYTVSGDRSKKDCNRTCGWRDVRCRTKGTGNSTVTVTKARTVDAVKKMKRTTNSDA +>tr|M0D8K9|M0D8K9_9EURY 30S ribosomal protein S14 type Z OS=Halorubrum terrestre JCM 10247 GN=rps14P PE=3 SV=1 +MSANNDTGHAAKRTDSRHTCRRCDRGVGKYDNCRCRVARDMGKYS |
| b |
| diff -r 000000000000 -r fae6527990af test-data/sorting_result1.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sorting_result1.fasta Thu May 21 03:58:09 2015 -0400 |
| b |
| @@ -0,0 +1,48 @@ +>sp|B3MQ24|ENY2_DROAN Enhancer of yellow 2 transcription factor OS=Drosophila ananassae GN=e(y)2 PE=3 SV=1 +MTVSNTVDYTVSGDRSKKDCNRTCGWRDVRCRTKGTGNSTVTVTKARTVDAVKKMKRTTNSDA +>sp|P0DMP9|APOC3_PANTA Apolipoprotein C-III OS=Panthera tigris altaica GN=APOC3 PE=3 SV=1 +MSRVVTAVASARATGDSGMGYVHATKTADTTTMRVAARDWVTGRSSKDYWSTTGKSGWDSTAVTTASAK +>sp|P20194|A100_SSV1 Uncharacterized protein A-100 OS=Sulfolobus spindle-shape virus 1 GN=a100 PE=1 SV=1 +MVSTRKKNSVYTGRKYGSYHKDDKKYADNKNRKRYVYSVDDAKAKATAKSVD +>sp|Q66125|2B_CMVQ Suppressor of silencing 2b OS=Cucumber mosaic virus (strain Q) GN=ORF2b PE=1 SV=1 +MDVTVVVSTADHANVKRRRRRSHVRNRRARGYKSSRARSARMHGVDVDWDVVRSSVTSVSYSDDTDWAGNWAGS +>sp|Q89681|DR4_HHV6U Uncharacterized protein DR4 OS=Human herpesvirus 6A (strain Uganda-1102) GN=DR4L PE=4 SV=1 +MRGTRRGSGGWSGARYAGSVAASDRSDTRATTSAYRHTHAASGARTRAHARHARHRVTVHVVAGVCARV +>sp|Q91G65|032R_IIV6 Uncharacterized protein 032R OS=Invertebrate iridescent virus 6 GN=IIV6-032R PE=4 SV=1 +MGVYKCYNKKKVGVAVKRYVTKKSYKTANSNADSYNCRKCCKAKGCCDRYWKTVKNDKCKKGVVVYY +>tr|H0ACG9|H0ACG9_HALSG Uncharacterized protein OS=Haloredivivus sp. (strain G17) GN=HRED_08116 PE=4 SV=1 +MRVRVDRVGVVGGGTKKRGV +>tr|H3BPV3|H3BPV3_HUMAN ATP-dependent RNA helicase DDX19B OS=Homo sapiens GN=DDX19B PE=4 SV=1 +MATDSWAAVDAAASRTSYSTS +>tr|L9WBT3|L9WBT3_9EURY 50S ribosomal protein L18Ae OS=Natronorubrum sulfidifaciens JCM 14089 GN=rplX PE=3 SV=1 +MSTVTGKSRDGYATTDANNVARHVSGSHGKRTDVS +>tr|L9WHT8|L9WHT8_9EURY 50S ribosomal protein L18Ae OS=Natronorubrum bangense JCM 10635 GN=rplX PE=3 SV=1 +MSTVTGKSRDGYSTTDANNVARHVYSGSHGKRSDVSA +>tr|M0D8K9|M0D8K9_9EURY 30S ribosomal protein S14 type Z OS=Halorubrum terrestre JCM 10247 GN=rps14P PE=3 SV=1 +MSANNDTGHAAKRTDSRHTCRRCDRGVGKYDNCRCRVARDMGKYS +>tr|M0F5C2|M0F5C2_9EURY 30S ribosomal protein S14 type Z OS=Halorubrum hochstenium ATCC 700873 GN=rps14P PE=3 SV=1 +MSANNDTGHAAKRTDSRHTCRRCDRGVGKYDNCRCRVARDMGKYS +>tr|M0KH83|M0KH83_9EURY 50S ribosomal protein L18Ae OS=Haloarcula amylolytica JCM 13557 GN=rplX PE=3 SV=1 +MSTYTVRGSARDGKVDANNVARVYSDGSHNKRTTVAA +>tr|M0KT65|M0KT65_9EURY 50S ribosomal protein L37e OS=Haloarcula amylolytica JCM 13557 GN=rpl37e PE=3 SV=1 +MTGAGTSGKKNTTTHTKCRRCGKSYHTKKKVCSSCGGKSAKRRDYWSKAG +>tr|M0MEH5|M0MEH5_9EURY 30S ribosomal protein S14 type Z OS=Halococcus saccharolyticus DSM 5350 GN=rps14P PE=3 SV=1 +MSSTDTGHATKRTGDCRCGRKGVGKYDWCRCRARGMGRKYK +>tr|M0MK44|M0MK44_9EURY 50S ribosomal protein L37e OS=Halococcus saccharolyticus DSM 5350 GN=rpl37e PE=3 SV=1 +MTGSGTSGKKNKTVHVKCRRCGASYHKTKKVCASCGGKSAKRRDYAWKAG +>tr|M0NIQ6|M0NIQ6_9EURY 30S ribosomal protein S14 type Z OS=Halorubrum lipolyticum DSM 21995 GN=rps14P PE=3 SV=1 +MSANNDTGHAAKRTDSRHTCRRCDRGVGKYDNCRCRVARDMGKYS +>tr|M0PIT7|M0PIT7_9EURY 30S ribosomal protein S14 type Z OS=Halorubrum arcis JCM 13916 GN=rps14P PE=3 SV=1 +MSANNDTGHAAKRTDSRHTCRRCDRGVGKYDNCRCRVARDMGKYS +>tr|N6VV02|N6VV02_9EURY Uncharacterized protein (Fragment) OS=Thermoplasmatales archaeon SCGC AB-539-C06 GN=MBGDC06_00209 PE=4 SV=1 +KRGAHGKMNGSVKTTMGSGR +>tr|Q53RS6|Q53RS6_HUMAN Putative uncharacterized protein ALS2CR3 (Fragment) OS=Homo sapiens GN=ALS2CR3 PE=4 SV=1 +MSSNATSTGNMNSNHRDSST +>tr|Q9BZF8|Q9BZF8_HUMAN NF-E2-related factor 2 (Fragment) OS=Homo sapiens PE=2 SV=1 +MMDGSDMDDWRDD +>tr|V9H0X7|V9H0X7_NEUCS Neurospora crassa DNA for RNA polymerase I second-largest subunit OS=Neurospora crassa PE=4 SV=1 +MAHSDNRDTADYGGAHAA +>tr|W9PMP6|W9PMP6_FUSOX Uncharacterized protein OS=Fusarium oxysporum f. sp. pisi HDV247 GN=FOVG_07074 PE=4 SV=1 +MTNAGRSKACDCKRKVGCSRYK +>tr|X0LYM3|X0LYM3_FUSOX Uncharacterized protein OS=Fusarium oxysporum f. sp. vasinfectum 25433 GN=FOTG_17987 PE=4 SV=1 +MTNAGRSKACDCKRKVGCSRYK |
| b |
| diff -r 000000000000 -r fae6527990af test-data/sorting_result2.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sorting_result2.fasta Thu May 21 03:58:09 2015 -0400 |
| b |
| @@ -0,0 +1,48 @@ +>sp|Q66125|2B_CMVQ Suppressor of silencing 2b OS=Cucumber mosaic virus (strain Q) GN=ORF2b PE=1 SV=1 +MDVTVVVSTADHANVKRRRRRSHVRNRRARGYKSSRARSARMHGVDVDWDVVRSSVTSVSYSDDTDWAGNWAGS +>sp|P0DMP9|APOC3_PANTA Apolipoprotein C-III OS=Panthera tigris altaica GN=APOC3 PE=3 SV=1 +MSRVVTAVASARATGDSGMGYVHATKTADTTTMRVAARDWVTGRSSKDYWSTTGKSGWDSTAVTTASAK +>sp|Q89681|DR4_HHV6U Uncharacterized protein DR4 OS=Human herpesvirus 6A (strain Uganda-1102) GN=DR4L PE=4 SV=1 +MRGTRRGSGGWSGARYAGSVAASDRSDTRATTSAYRHTHAASGARTRAHARHARHRVTVHVVAGVCARV +>sp|Q91G65|032R_IIV6 Uncharacterized protein 032R OS=Invertebrate iridescent virus 6 GN=IIV6-032R PE=4 SV=1 +MGVYKCYNKKKVGVAVKRYVTKKSYKTANSNADSYNCRKCCKAKGCCDRYWKTVKNDKCKKGVVVYY +>sp|B3MQ24|ENY2_DROAN Enhancer of yellow 2 transcription factor OS=Drosophila ananassae GN=e(y)2 PE=3 SV=1 +MTVSNTVDYTVSGDRSKKDCNRTCGWRDVRCRTKGTGNSTVTVTKARTVDAVKKMKRTTNSDA +>sp|P20194|A100_SSV1 Uncharacterized protein A-100 OS=Sulfolobus spindle-shape virus 1 GN=a100 PE=1 SV=1 +MVSTRKKNSVYTGRKYGSYHKDDKKYADNKNRKRYVYSVDDAKAKATAKSVD +>tr|M0KT65|M0KT65_9EURY 50S ribosomal protein L37e OS=Haloarcula amylolytica JCM 13557 GN=rpl37e PE=3 SV=1 +MTGAGTSGKKNTTTHTKCRRCGKSYHTKKKVCSSCGGKSAKRRDYWSKAG +>tr|M0MK44|M0MK44_9EURY 50S ribosomal protein L37e OS=Halococcus saccharolyticus DSM 5350 GN=rpl37e PE=3 SV=1 +MTGSGTSGKKNKTVHVKCRRCGASYHKTKKVCASCGGKSAKRRDYAWKAG +>tr|M0D8K9|M0D8K9_9EURY 30S ribosomal protein S14 type Z OS=Halorubrum terrestre JCM 10247 GN=rps14P PE=3 SV=1 +MSANNDTGHAAKRTDSRHTCRRCDRGVGKYDNCRCRVARDMGKYS +>tr|M0F5C2|M0F5C2_9EURY 30S ribosomal protein S14 type Z OS=Halorubrum hochstenium ATCC 700873 GN=rps14P PE=3 SV=1 +MSANNDTGHAAKRTDSRHTCRRCDRGVGKYDNCRCRVARDMGKYS +>tr|M0NIQ6|M0NIQ6_9EURY 30S ribosomal protein S14 type Z OS=Halorubrum lipolyticum DSM 21995 GN=rps14P PE=3 SV=1 +MSANNDTGHAAKRTDSRHTCRRCDRGVGKYDNCRCRVARDMGKYS +>tr|M0PIT7|M0PIT7_9EURY 30S ribosomal protein S14 type Z OS=Halorubrum arcis JCM 13916 GN=rps14P PE=3 SV=1 +MSANNDTGHAAKRTDSRHTCRRCDRGVGKYDNCRCRVARDMGKYS +>tr|M0MEH5|M0MEH5_9EURY 30S ribosomal protein S14 type Z OS=Halococcus saccharolyticus DSM 5350 GN=rps14P PE=3 SV=1 +MSSTDTGHATKRTGDCRCGRKGVGKYDWCRCRARGMGRKYK +>tr|L9WHT8|L9WHT8_9EURY 50S ribosomal protein L18Ae OS=Natronorubrum bangense JCM 10635 GN=rplX PE=3 SV=1 +MSTVTGKSRDGYSTTDANNVARHVYSGSHGKRSDVSA +>tr|M0KH83|M0KH83_9EURY 50S ribosomal protein L18Ae OS=Haloarcula amylolytica JCM 13557 GN=rplX PE=3 SV=1 +MSTYTVRGSARDGKVDANNVARVYSDGSHNKRTTVAA +>tr|L9WBT3|L9WBT3_9EURY 50S ribosomal protein L18Ae OS=Natronorubrum sulfidifaciens JCM 14089 GN=rplX PE=3 SV=1 +MSTVTGKSRDGYATTDANNVARHVSGSHGKRTDVS +>tr|W9PMP6|W9PMP6_FUSOX Uncharacterized protein OS=Fusarium oxysporum f. sp. pisi HDV247 GN=FOVG_07074 PE=4 SV=1 +MTNAGRSKACDCKRKVGCSRYK +>tr|X0LYM3|X0LYM3_FUSOX Uncharacterized protein OS=Fusarium oxysporum f. sp. vasinfectum 25433 GN=FOTG_17987 PE=4 SV=1 +MTNAGRSKACDCKRKVGCSRYK +>tr|H3BPV3|H3BPV3_HUMAN ATP-dependent RNA helicase DDX19B OS=Homo sapiens GN=DDX19B PE=4 SV=1 +MATDSWAAVDAAASRTSYSTS +>tr|H0ACG9|H0ACG9_HALSG Uncharacterized protein OS=Haloredivivus sp. (strain G17) GN=HRED_08116 PE=4 SV=1 +MRVRVDRVGVVGGGTKKRGV +>tr|N6VV02|N6VV02_9EURY Uncharacterized protein (Fragment) OS=Thermoplasmatales archaeon SCGC AB-539-C06 GN=MBGDC06_00209 PE=4 SV=1 +KRGAHGKMNGSVKTTMGSGR +>tr|Q53RS6|Q53RS6_HUMAN Putative uncharacterized protein ALS2CR3 (Fragment) OS=Homo sapiens GN=ALS2CR3 PE=4 SV=1 +MSSNATSTGNMNSNHRDSST +>tr|V9H0X7|V9H0X7_NEUCS Neurospora crassa DNA for RNA polymerase I second-largest subunit OS=Neurospora crassa PE=4 SV=1 +MAHSDNRDTADYGGAHAA +>tr|Q9BZF8|Q9BZF8_HUMAN NF-E2-related factor 2 (Fragment) OS=Homo sapiens PE=2 SV=1 +MMDGSDMDDWRDD |
| b |
| diff -r 000000000000 -r fae6527990af test-data/three_human_mRNA.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/three_human_mRNA.fasta Thu May 21 03:58:09 2015 -0400 |
| b |
| b'@@ -0,0 +1,183 @@\n+>ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.\n+GAGAGGACGAGGTGCCGCTGCCTGGAGAATCCTCCGCTGCCGTCGGCTCCCGGAGCCCAG\n+CCCTTTCCTAACCCAACCCAACCTAGCCCAGTCCCAGCCGCCAGCGCCTGTCCCTGTCAC\n+GGACCCCAGCGTTACCATGCATCCTGCCGTCTTCCTATCCTTACCCGACCTCAGATGCTC\n+CCTTCTGCTCCTGGTAACTTGGGTTTTTACTCCTGTAACAACTGAAATAACAAGTCTTGA\n+TACAGAGAATATAGATGAAATTTTAAACAATGCTGATGTTGCTTTAGTAAATTTTTATGC\n+TGACTGGTGTCGTTTCAGTCAGATGTTGCATCCAATTTTTGAGGAAGCTTCCGATGTCAT\n+TAAGGAAGAATTTCCAAATGAAAATCAAGTAGTGTTTGCCAGAGTTGATTGTGATCAGCA\n+CTCTGACATAGCCCAGAGATACAGGATAAGCAAATACCCAACCCTCAAATTGTTTCGTAA\n+TGGGATGATGATGAAGAGAGAATACAGGGGTCAGCGATCAGTGAAAGCATTGGCAGATTA\n+CATCAGGCAACAAAAAAGTGACCCCATTCAAGAAATTCGGGACTTAGCAGAAATCACCAC\n+TCTTGATCGCAGCAAAAGAAATATCATTGGATATTTTGAGCAAAAGGACTCGGACAACTA\n+TAGAGTTTTTGAACGAGTAGCGAATATTTTGCATGATGACTGTGCCTTTCTTTCTGCATT\n+TGGGGATGTTTCAAAACCGGAAAGATATAGTGGCGACAACATAATCTACAAACCACCAGG\n+GCATTCTGCTCCGGATATGGTGTACTTGGGAGCTATGACAAATTTTGATGTGACTTACAA\n+TTGGATTCAAGATAAATGTGTTCCTCTTGTCCGAGAAATAACATTTGAAAATGGAGAGGA\n+ATTGACAGAAGAAGGACTGCCTTTTCTCATACTCTTTCACATGAAAGAAGATACAGAAAG\n+TTTAGAAATATTCCAGAATGAAGTAGCTCGGCAATTAATAAGTGAAAAAGGTACAATAAA\n+CTTTTTACATGCCGATTGTGACAAATTTAGACATCCTCTTCTGCACATACAGAAAACTCC\n+AGCAGATTGTCCTGTAATCGCTATTGACAGCTTTAGGCATATGTATGTGTTTGGAGACTT\n+CAAAGATGTATTAATTCCTGGAAAACTCAAGCAATTCGTATTTGACTTACATTCTGGAAA\n+ACTGCACAGAGAATTCCATCATGGACCTGACCCAACTGATACAGCCCCAGGAGAGCAAGC\n+CCAAGATGTAGCAAGCAGTCCACCTGAGAGCTCCTTCCAGAAACTAGCACCCAGTGAATA\n+TAGGTATACTCTATTGAGGGATCGAGATGAGCTTTAAAAACTTGAAAAACAGTTTGTAAG\n+CCTTTCAACAGCAGCATCAACCTACGTGGTGGAAATAGTAAACCTATATTTTCATAATTC\n+TATGTGTATTTTTATTTTGAATAAACAGAAAGAAATTTTGGGTTTTTAATTTTTTTCTCC\n+CCGACTCAAAATGCATTGTCATTTAATATAGTAGCCTCTTAAAAAAAAAAAAACCTGCTA\n+GGATTTAAAAATAAAAATCAGAGGCCTATCTCCACTTTAAATCTGTCCTGTAAAAGTTTT\n+ATAAATCAAATGAAAGGTGACATTGCCAGAAACTTACCATTAACTTGCACTACTAGGGTA\n+GGGAGGACTTAGGATGTTTCCTGTGTCGTATGTGCTTTTCTTTCTTTCATATGATCAATT\n+CTGTTGGTATTTTCAGTATCTCATTTCTCAAAGCTAAAGAGATATACATTCTGGATACTT\n+GGGAGGGGAATAAATTAAAGTTTTCACACTGTGTACTGTGTTTTACTGATTGGTTGGATA\n+TTGCTTATGAAAATTCCATAGTGGTATTTTTTTGGATTCTTAATGTGTAACTTAAACATA\n+CTTTGAAGTGGAGGAGAGTCATAAGACAGAACATTTGGCAGGAATTGTCCTTATGAAACA\n+AGAAAAAGAAAATGAAAAGTATTATTAAGCTTCTGTGTTTGTCTAAAAATGTGGCATATG\n+GATGGCATTTAAAACTTTGAATGAATTATACCTAAATCTGGGACAGGGAGGTGACAGTGG\n+AACAGGCTACCAATCAGAACTAGATGACTTTTAAGGCTCCTCCTATTATGAGACTTCAAT\n+TTCCAAAGAGAAGAACTAGCAGAGAAATTGTATTTCAGTAATTTTAAGCTCCTTCTGTCT\n+TGTAGAGTCTTGTTATAGTTGTATAAATCAAAAACACAGAATAAGGAACATATTTAACTT\n+TTTTTCATTATAAAATGGTTAGAGGACCCTACCCCCTCTAGATTCCCTGATTTCCCCAGG\n+CCTGCAGCATACAGTAAGATGGGTCCCTGTGCCAGGCCTCAATACTGCCAGGGAATAAAA\n+CCAGAGGGAGAGGACCCTCAGTGTCATATCAGGAAGCCCAGTGCCAGAGGACAGACAGGT\n+TCAAAACTGGCTTTTCCTCTGGGCCTGGGTTGGTGCTATAGGCCAAGGGTCATTTTATAC\n+TTGGGTATAAATCAATCCCAGTTTGGGAAAAGATTATTTTTAAGCTTAAAAGGCTGACAT\n+GTGCCATTATATGTAGTATGTAATATATGTAACATCTTCCAATTCTTTTAAAATAAAATT\n+AATATTTATAATGGATATTTAATGATTGTTATTTTTAAAAACCAGCTTATAATTCCTCGT\n+TATGCATGATTTATCCAAAGTTTCCATAGTTTTATTCAAAATAATAAATGTTAATAAGGT\n+GATAAGGGGTATATTTAATGTATTGTATCAAATTGTGAATAAGAAAGTAGGATGGAGCTT\n+TCTAGAGGTTGGGCCTTAGTTCTGTTATCCTCATTGCTTTTAACCAATAAGTTAAATGAA\n+GTTAGAGTTATGGTCTTCAGGTTAGATTATGGACCAGATCTGTGAGGGTCAGCATGGAAA\n+TTCACATTCAACAAGGTAGCACACAGGACCAAGAGCAGCACATGCAATCAACTGGAATAA\n+TATAGTAATCCTGTAACTGGGTTTGAAAAAATAATCAACAAAAGATACAATTCAAGGGTT\n+AGGTTGCAGAGAGCTGGCTTGAGAGTAGTTATTATGAAAAAGGCCTCAAGGAGTACGTGT\n+TCAGTATGCTCTAAGATGATAAAGTGGCTGTTAAAAAGGGAGTTGATTTGAGGAAGTATT\n+ACTTAGCATTCATGCATATTGGGCTTAGGCTCTAGCCCTGCCACTATCATTGTCTTCTCT\n+GGACTGTGAAGTCACTGAGGACAAGGAAACTAAATTTAATGTCTGTATCACTAGTGCCTA\n+GAATTTCTGGACACTTAGTAGTCACCATCAGGCGTTTATTTAATGAATGAGAAGCAAAGT\n+GACCTTGGTTACTTTTTTACCCTGAGGGGCTCAGCACTCATTAGGACTTGGTGCCTAATT\n+TTATAAAAAGTCACTAAGCTCAAGTGCTTGGATGAAAGGACAGCGTGGATAAAAAGGTTT\n+TTAAAACATGGATGTTAAGGCTGTTTTGCTTGGAGAAGACTTGGGACTGGGACAGTCTTT\n+AGATATTATTTGAAATGCTGGCACTGTCTATCTGGATCCCAGGGCTTGAACTAGGATTTG\n+AGGAAGTCACAGGGAAGCAGATTTCAGTCTGACATTTATTCAGTGCAAGTTTTTTGGTGC\n+TGTAGTATATGATGAAAGATGTAAAGCTGAATAAAGCATTATTTCTGCCCTAGAGTTGTT\n+CACAGCCTAGTCAGGCATATGGATATGTAAACAATGACTGTAACGTGTTATAGATGT'..b'AAGCTGCCCTCGAGGACCTGGTCTCCACCATTCGAGTCTGAAGATTCT\n+CAGAAGCACAACCAGAGTGAGTATGAGGATTCGGCCGGCGAATGCTGCTCCTGTCCAAAG\n+ACAGACTCTCAGATCCTGAAGGAGCTGGAGGAGTCCTCGTTTAGGAAGACGTTTGAGGAT\n+TACCTGCACAACGTGGTTTTCGTCCCCAGAAAAACCTCTTCAGGCACTGGTGCCGAGGAC\n+CCTAGGCCATCTCGGAAACGCAGGTCCCTTGGCGATGTTGGGAATGTGACGGTGGCCGTG\n+CCCACGGTGGCAGCTTTCCCCAACACTTCCTCGACCAGCGTGCCCACGAGTCCGGAGGAG\n+CACAGGCCTTTTGAGAAGGTGGTGAACAAGGAGTCGCTGGTCATCTCCGGCTTGCGACAC\n+TTCACGGGCTATCGCATCGAGCTGCAGGCTTGCAACCAGGACACCCCTGAGGAACGGTGC\n+AGTGTGGCAGCCTACGTCAGTGCGAGGACCATGCCTGAAGCCAAGGCTGATGACATTGTT\n+GGCCCTGTGACGCATGAAATCTTTGAGAACAACGTCGTCCACTTGATGTGGCAGGAGCCG\n+AAGGAGCCCAATGGTCTGATCGTGCTGTATGAAGTGAGTTATCGGCGATATGGTGATGAG\n+GAGCTGCATCTCTGCGTCTCCCGCAAGCACTTCGCTCTGGAACGGGGCTGCAGGCTGCGT\n+GGGCTGTCACCGGGGAACTACAGCGTGCGAATCCGGGCCACCTCCCTTGCGGGCAACGGC\n+TCTTGGACGGAACCCACCTATTTCTACGTGACAGACTATTTAGACGTCCCGTCAAATATT\n+GCAAAAATTATCATCGGCCCCCTCATCTTTGTCTTTCTCTTCAGTGTTGTGATTGGAAGT\n+ATTTATCTATTCCTGAGAAAGAGGCAGCCAGATGGGCCGCTGGGACCGCTTTACGCTTCT\n+TCAAACCCTGAGTATCTCAGTGCCAGTGATGTGTTTCCATGCTCTGTGTACGTGCCGGAC\n+GAGTGGGAGGTGTCTCGAGAGAAGATCACCCTCCTTCGAGAGCTGGGGCAGGGCTCCTTC\n+GGCATGGTGTATGAGGGCAATGCCAGGGACATCATCAAGGGTGAGGCAGAGACCCGCGTG\n+GCGGTGAAGACGGTCAACGAGTCAGCCAGTCTCCGAGAGCGGATTGAGTTCCTCAATGAG\n+GCCTCGGTCATGAAGGGCTTCACCTGCCATCACGTGGTGCGCCTCCTGGGAGTGGTGTCC\n+AAGGGCCAGCCCACGCTGGTGGTGATGGAGCTGATGGCTCACGGAGACCTGAAGAGCTAC\n+CTCCGTTCTCTGCGGCCAGAGGCTGAGAATAATCCTGGCCGCCCTCCCCCTACCCTTCAA\n+GAGATGATTCAGATGGCGGCAGAGATTGCTGACGGGATGGCCTACCTGAACGCCAAGAAG\n+TTTGTGCATCGGGACCTGGCAGCGAGAAACTGCATGGTCGCCCATGATTTTACTGTCAAA\n+ATTGGAGACTTTGGAATGACCAGAGACATCTATGAAACGGATTACTACCGGAAAGGGGGC\n+AAGGGTCTGCTCCCTGTACGGTGGATGGCACCGGAGTCCCTGAAGGATGGGGTCTTCACC\n+ACTTCTTCTGACATGTGGTCCTTTGGCGTGGTCCTTTGGGAAATCACCAGCTTGGCAGAA\n+CAGCCTTACCAAGGCCTGTCTAATGAACAGGTGTTGAAATTTGTCATGGATGGAGGGTAT\n+CTGGATCAACCCGACAACTGTCCAGAGAGAGTCACTGACCTCATGCGCATGTGCTGGCAA\n+TTCAACCCCAAGATGAGGCCAACCTTCCTGGAGATTGTCAACCTGCTCAAGGACGACCTG\n+CACCCCAGCTTTCCAGAGGTGTCGTTCTTCCACAGCGAGGAGAACAAGGCTCCCGAGAGT\n+GAGGAGCTGGAGATGGAGTTTGAGGACATGGAGAATGTGCCCCTGGACCGTTCCTCGCAC\n+TGTCAGAGGGAGGAGGCGGGGGGCCGGGATGGAGGGTCCTCGCTGGGTTTCAAGCGGAGC\n+TACGAGGAACACATCCCTTACACACACATGAACGGAGGCAAGAAAAACGGGCGGATTCTG\n+ACCTTGCCTCGGTCCAATCCTTCCTAACAGTGCCTACCGTGGCGGGGGCGGGCAGGGGTT\n+CCCATTTTCGCTTTCCTCTGGTTTGAAAGCCTCTGGAAAACTCAGGATTCTCACGACTCT\n+ACCATGTCCAGTGGAGTTCAGAGATCGTTCCTATACATTTCTGTTCATCTTAAGGTGGAC\n+TCGTTTGGTTACCAATTTAACTAGTCCTGCAGAGGATTTAACTGTGAACCTGGAGGGCAA\n+GGGGTTTCCACAGTTGCTGCTCCTTTGGGGCAACGACGGTTTCAAACCAGGATTTTGTGT\n+TTTTTCGTTCCCCCCACCCGCCCCCAGCAGATGGAAAGAAAGCACCTGTTTTTACAAATT\n+CTTTTTTTTTTTTTTTTTTTTTTTTTTTTGCTGGTGTCTGAGCTTCAGTATAAAAGACAA\n+AACTTCCTGTTTGTGGAACAAAATTTCGAAAGAAAAAACCAAA\n+>ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds.\n+CCAGCTGGAGCCCTGAGTGGCTGAGCTCAGGCCTTCGCAGCATTCTTGGGTGGGAGCAGC\n+CACGGGTCAGCCACAAGGGCCACAGCCATGAATGGCACAGAAGGCCCTAACTTCTACGTG\n+CCCTTCTCCAATGCGACGGGTGTGGTACGCAGCCCCTTCGAGTACCCACAGTACTACCTG\n+GCTGAGCCATGGCAGTTCTCCATGCTGGCCGCCTACATGTTTCTGCTGATCGTGCTGGGC\n+TTCCCCATCAACTTCCTCACGCTCTACGTCACCGTCCAGCACAAGAAGCTGCGCACGCCT\n+CTCAACTACATCCTGCTCAACCTAGCCGTGGCTGACCTCTTCATGGTCCTAGGTGGCTTC\n+ACCAGCACCCTCTACACCTCTCTGCATGGATACTTCGTCTTCGGGCCCACAGGATGCAAT\n+TTGGAGGGCTTCTTTGCCACCCTGGGCGGTGAAATTGCCCTGTGGTCCTTGGTGGTCCTG\n+GCCATCGAGCGGTACGTGGTGGTGTGTAAGCCCATGAGCAACTTCCGCTTCGGGGAGAAC\n+CATGCCATCATGGGCGTTGCCTTCACCTGGGTCATGGCGCTGGCCTGCGCCGCACCCCCA\n+CTCGCCGGCTGGTCCAGGTACATCCCCGAGGGCCTGCAGTGCTCGTGTGGAATCGACTAC\n+TACACGCTCAAGCCGGAGGTCAACAACGAGTCTTTTGTCATCTACATGTTCGTGGTCCAC\n+TTCACCATCCCCATGATTATCATCTTTTTCTGCTATGGGCAGCTCGTCTTCACCGTCAAG\n+GAGGCCGCTGCCCAGCAGCAGGAGTCAGCCACCACACAGAAGGCAGAGAAGGAGGTCACC\n+CGCATGGTCATCATCATGGTCATCGCTTTCCTGATCTGCTGGGTGCCCTACGCCAGCGTG\n+GCATTCTACATCTTCACCCACCAGGGCTCCAACTTCGGTCCCATCTTCATGACCATCCCA\n+GCGTTCTTTGCCAAGAGCGCCGCCATCTACAACCCTGTCATCTATATCATGATGAACAAG\n+CAGTTCCGGAACTGCATGCTCACCACCATCTGCTGCGGCAAGAACCCACTGGGTGACGAT\n+GAGGCCTCTGCTACCGTGTCCAAGACGGAGACGAGCCAGGTGGCCCCGGCCTAAGACCTG\n+CCTAGGACTCTGTGGCCGACTATAGGCGTCTCCCATCCCCTACACCTTCCCCCAGCCACA\n+GCCATCCCACCAG\n' |
| b |
| diff -r 000000000000 -r fae6527990af tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Thu May 21 03:58:09 2015 -0400 |
| b |
| @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="vsearch" version="1.1.3"> + <repository changeset_revision="c1fc77fac9fb" name="package_vsearch_1_1_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |
| b |
| diff -r 000000000000 -r fae6527990af vsearch_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/vsearch_macros.xml Thu May 21 03:58:09 2015 -0400 |
| b |
| b'@@ -0,0 +1,237 @@\n+<macros>\n+ <xml name="requirements">\n+ <requirements>\n+ <requirement type="package" version="1.1.3">vsearch</requirement>\n+ </requirements>\n+ </xml>\n+ <xml name="version_command">\n+ <version_command>vsearch --version | head -n 1 | awk \'{print $2}\' | sed \'s/,//\'</version_command>\n+ </xml>\n+ <xml name="stdio">\n+ <stdio>\n+ <exit_code range="1:" />\n+ <exit_code range=":-1" />\n+ <regex match="Error:" />\n+ <regex match="Exception:" />\n+ </stdio>\n+ </xml>\n+\n+ <xml name="topn">\n+ <param name="topn" type="integer" value="" optional="True" label="Output just first n sequences"\n+ help="(--topn)"/>\n+ </xml>\n+\n+ <xml name="maxaccepts">\n+ <param name="maxaccepts" type="integer" value="1" label="Number of hits to accept and show per strand"\n+ help="(--maxaccepts)"/>\n+ </xml>\n+ <xml name="maxrejects">\n+ <param name="maxrejects" type="integer" value="32" label="Number of non-matching hits to consider"\n+ help="(--maxrejects)"/>\n+ </xml>\n+ <xml name="qmask">\n+ <param name="qmask" type="select" label="Mask sequences" help="(--qmask)">\n+ <option value="no">No masking</option>\n+ <option value="dust" selected="True">dust</option>\n+ <option value="soft">soft</option>\n+ </param>\n+ </xml>\n+\n+ <xml name="hardmask">\n+ <param name="hardmask" type="boolean" truevalue="--hardmask" falsevalue="" checked="False" \n+ label="Mask by replacing with N instead of lower case" help="(--hardmask)"/>\n+ </xml>\n+\n+ <xml name="id_and_iddef">\n+ <param name="iddef" type="select" label="ID definition" help="(--iddef)">\n+ <option value="0">CD-HIT</option>\n+ <option value="1">all</option>\n+ <option value="2" selected="True">int</option>\n+ <option value="3">MBL</option>\n+ <option value="4">BLAST</option>\n+ </param>\n+ <param name="id" type="float" value="" optional="True" label="Reject hit if identity is lower than this value"\n+ help="(--id)"/>\n+ </xml>\n+\n+ <xml name="self_and_selfid">\n+ <param name="self_param" type="boolean" truevalue="--self" falsevalue="" checked="False" \n+ label="Exclude identical labels for --uchime_ref" help="(--self)"/>\n+ <param name="selfid_param" type="boolean" truevalue="--selfid" falsevalue="" checked="False" \n+ label="Exclude identical sequences for --uchime_ref" help="(--selfid)"/>\n+ </xml>\n+\n+ <xml name="strand">\n+ <param name="strand" type="select" label="Strand specific clustering" help="(--strand)">\n+ <option value="plus" selected="True">Plus strand</option>\n+ <option value="both">Both strands</option>\n+ </param>\n+ </xml>\n+\n+ <xml name="sizein">\n+ <param name="sizein" type="boolean" truevalue="--sizein" falsevalue="" checked="False" \n+ label="Read abundance annotation from input" help="(--sizein)"/>\n+ </xml>\n+\n+ <xml name="sizeout">\n+ <param name="sizeout" type="boolean" truevalue="--sizeout" falsevalue="" checked="False" \n+ label="Write cluster abundances to centroid file" help="(--sizeout)"/>\n+ </xml>\n+\n+ <xml name="uclust_like_output">\n+ <param name="uc" type="boolean" truevalue="--uc" falsevalue="" checked="False" \n+ label="UCLUST-like output" help="(--uc)"/>\n+ </xml>\n+\n+ <token name="@GENERAL@">\n+ --threads "\\${GALAXY_SLOTS:-4}"\n+ --notrunclabels\n+ </token>\n+ <token name="@USERFIELDS@">\n+ #if $userfields_output.userfields_output_select == \'yes\':\n+ --userfields \'#echo \'+\'.join( str($userfields_output.userfields).split(\',\') )#\'\n+ --userout $userout\n+ #end if\n+ </token>\n+ <xml name="userfields_output">\n+ <data name="userout" format="tabular" label="${tool.'..b'ences, this is equivalent to the percentage of matches (real value ranging from 0.0 to 100.0).\n+pv Number of positive columns. When working with nucleotide sequences, this is equivalent to the number of matches (zero or positive integer value).\n+qcov Fraction of the query sequence that is aligned with the target sequence (real value ranging from 0.0 to 100.0). The query coverage is computed as 100.0 * (matches + mismatches) / query sequence length. Internal or terminal gaps are not taken into account. The field is set to 0.0 if there is no alignment.\n+qframe Query frame (-3 to +3). That field only concerns coding sequences and is not computed by vsearch. Always set to +0.\n+qhi Last nucleotide of the query aligned with the target. Always equal to the length of the pairwise alignment. The field is set to 0 if there is no alignment.\n+qihi Last nucleotide of the query aligned with the target (ignoring terminal gaps). Nucleotide numbering starts from 1. The field is set to 0 if there is no alignment.\n+qilo First nucleotide of the query aligned with the target (ignoring initial gaps). Nucleotide numbering starts from 1. The field is set to 0 if there is no alignment.\n+ql Query sequence length (positive integer value). The field is set to 0 if there is no alignment.\n+qlo First nucleotide of the query aligned with the target. Always equal to 1 if there is an alignment, 0 otherwise.\n+qrow Print the sequence of the query segment as seen in the pairwise alignment (i.e. with gap insertions if need be). Empty field if there is no alignment.\n+qs Query segment length. Always equal to query sequence length.\n+qstrand Query strand orientation (+ or - for nucleotide sequences). Empty field if there is no alignment.\n+query Query label.\n+raw Raw alignment score (negative, null or positive integer value). The score is the sum of match rewards minus mismatch penalties, gap openings and gap extensions. The field is set to 0 if there is no alignment.\n+target Target label. The field is set to "*" if there is no alignment.\n+tcov Fraction of the target sequence that is aligned with the query sequence (real value rang-ing from 0.0 to 100.0). The target coverage is computed as 100.0 * (matches + mis-matches) / target sequence length. Internal or terminal gaps are not taken into account. The field is set to 0.0 if there is no alignment.\n+tframe Target frame (-3 to +3). That field only concerns coding sequences and is not computed by vsearch. Always set to +0.\n+thi Last nucleotide of the target aligned with the query. Always equal to the length of the pairwise alignment. The field is set to 0 if there is no alignment.\n+tihi Last nucleotide of the target aligned with the query (ignoring terminal gaps). Nucleotide numbering starts from 1. The field is set to 0 if there is no alignment.\n+tilo First nucleotide of the target aligned with the query (ignoring initial gaps). Nucleotide numbering starts from 1. The field is set to 0 if there is no alignment.\n+tl Target sequence length (positive integer value). The field is set to 0 if there is no alignment.\n+tlo First nucleotide of the target aligned with the query. Always equal to 1 if there is an alignment, 0 otherwise.\n+trow Print the sequence of the target segment as seen in the pairwise alignment (i.e. with gap insertions if need be). Empty field if there is no alignment.\n+ts Target segment length. Always equal to target sequence length. The field is set to 0 if there is no alignment.\n+tstrand Target strand orientation (+ or - for nucleotide sequences). Always set to "+", so reverse strand matches have tstrand "+" and qstrand "-". Empty field if there is no alignment.\n+========= ================\n+\n+ </token>\n+ <xml name="citations">\n+ <citations>\n+ <citation type="doi">10.5281/zenodo.15524</citation>\n+ <yield />\n+ </citations>\n+ </xml>\n+</macros>\n' |