|
Commit message:
Uploaded |
|
added:
paqmir_postprocess_mirdeep2/extract_seqs_by_ids.pl paqmir_postprocess_mirdeep2/postprocess_mirdeep2.xml paqmir_postprocess_mirdeep2/postprocess_mirdeep2_diff_specie.sh paqmir_postprocess_mirdeep2/postprocess_mirdeep2_same_specie.sh paqmir_postprocess_mirdeep2/test-data/.directory paqmir_postprocess_mirdeep2/test-data/Tabular_output_of_PAQmiR_MiRDeep2.tabular paqmir_postprocess_mirdeep2/test-data/hairpin_bta.fa paqmir_postprocess_mirdeep2/test-data/hairpin_bta_and_new_predicted_hairpins.fa paqmir_postprocess_mirdeep2/test-data/mature.fasta paqmir_postprocess_mirdeep2/test-data/mature_and_new_predicted_matures.fa |
| b |
| diff -r 000000000000 -r da3c91b40f61 paqmir_postprocess_mirdeep2/extract_seqs_by_ids.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/paqmir_postprocess_mirdeep2/extract_seqs_by_ids.pl Mon Mar 18 09:27:29 2019 -0400 |
| [ |
| @@ -0,0 +1,154 @@ +#! /usr/bin/perl +# +# extract_seqs_by_ids.pl +# +# Copyright 2019 Sylvain Marthey <sylvain.marthey@inra.fr> +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation; either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program; if not, see <http://www.gnu.org/licenses/>. + +use strict; +use Getopt::Long; +use Pod::Usage; +use Bio::Seq; +use Bio::SeqIO; + +my ($help,$fasta_in,$ids_file,$file_out,$inverse,$precursor_shape,@exprs,%ids_seqs,$regular_expression); + +GetOptions("help|?" => \$help, + "fasta_in:s" => \$fasta_in, + "ids_file:s" => \$ids_file, + "file_out:s" => \$file_out, + "inverse:s" => \$inverse, + "precursor_shape:s" => \$precursor_shape, + "regular_expression:s" => \$regular_expression) +or +pod2usage(-message=>"Try `$0' for more information.", -exitval => 2,-verbose=> 0); + +pod2usage(-exitval =>1, -verbose => 2) if ($help); + +if((!$fasta_in || !-f($fasta_in)) ){ + print "--fasta_in parameter missing or is not a valid file path: try extract_seqs_by_ids.pl --help\n"; + exit; +} +if((!$file_out && !-f($file_out)) ){ + print "--file_out parameter missing : try extract_seqs_by_ids.pl --help\n"; + exit; +} +if(!$ids_file || !-f($ids_file)){ + print "--ds_file parameter missing or is not a valid file path: try extract_seqs_by_ids.pl --help\n"; + exit; +} +if(uc($inverse) eq 'YES' || uc($inverse) eq 'Y'){ + $inverse = 1; +}else{ + $inverse = 0; +} +if(uc($regular_expression) eq 'YES' || uc($regular_expression) eq 'Y'){ + $regular_expression = 1; +}else{ + $regular_expression = 0; +} + + +# read the input ids file +open(IDS,$ids_file) or die "impossible d'ouvrir le fichier $ids_file\n"; + +while(<IDS>){ + chomp; + push(@exprs,qr/$_$/); + $ids_seqs{$_}++; +} +close IDS; + +my $first = Bio::SeqIO->new(-file => $fasta_in,'-format'=>'Fasta'); +my $out_fasta = Bio::SeqIO->new(-file => ">".$file_out , '-format' => 'Fasta'); + +# read the input fasta file +while (my $seq = $first->next_seq) { + my $id = $seq->id(); +# print $id."\t"; + if(uc($precursor_shape) eq 'YES' || uc($precursor_shape) eq 'Y'){ + $id =~ s/([a-zA-Z]{3}-[a-zA-Z]{3}-\w+)-(\d+)$/$1/; +# print $id."\n"; + } + my $found = 0; + if($regular_expression){ + # seach the ids_file in the identifier + foreach my $expr (@exprs){ + if($id =~ /$expr/){ + $found++; + last; + } + } + }else{ + if($ids_seqs{$id}){ + $found++; + } + } + if($found>0 && !$inverse){ + $out_fasta->write_seq($seq); + }elsif($found == 0 && $inverse){ + $out_fasta->write_seq($seq); + } +} + + +=head1 NAME + + extract_seqs_by_ids.pl + +=head1 SYNOPSIS + + extract_seqs_by_ids.pl --fasta_in <fasta file> --ids_file <string> --file_out <file_out_path> [--begining <yes|no> --inverse <yes|no>] + +=head1 OPTIONS + + --fasta_in fasta file containing sequences we want to extract + + --ids_file file containing words that will be searched in the id of the sequences we want to extract (one id peer line) + + --file_out out fasta file + + --precursor_shape searched ids doesn't contain the location tag (-1, -2, -3, -N) it will be skipped in the sequence_id research + + --inverse inverse the sequence selection (like grep -v) + + --regular_expression yes|no + + +=head1 DESCRIPTION + + This tool will read the fasta file and extract sequences where identifiers contain the searched words. + +=head1 AUTHORS + +Sylvain Marthey <sylvain.marthey@inra.fr> + +=head1 VERSION + +1.1 + +=head1 DATE + +01/01/2019 + +=head1 KEYWORDS + +fasta, identifier, filtering + +=head1 EXAMPLE + +extract_seqs_by_ids.pl --fasta_in mirbase.fa --ids_file bta --file_out mirbase_bta.fa + +=cut |
| b |
| diff -r 000000000000 -r da3c91b40f61 paqmir_postprocess_mirdeep2/postprocess_mirdeep2.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/paqmir_postprocess_mirdeep2/postprocess_mirdeep2.xml Mon Mar 18 09:27:29 2019 -0400 |
| [ |
| @@ -0,0 +1,103 @@ +<tool id="paqmir_postprocess_mirdeep2" name="PAQmiR Postprocess MiRDeep2" version="1.0.0"> + <description>filter and use the results of miRDeep2 to create new reference datasets for quantification and annotation steps</description> + <stdio> + <!-- Anything other than zero is an error --> + <exit_code range="1:" /> + <exit_code range=":-1" /> + <!-- In case the return code has not been set propery check stderr too --> + <regex match="Error:" /> + <regex match="Exception:" /> + </stdio> + + <command interpreter="bash"> + <![CDATA[ + #if $specie_choice.specie + postprocess_mirdeep2_same_specie.sh + #else + postprocess_mirdeep2_diff_specie.sh + #end if + $prediction_file + $word + $specie_choice.score_new + #if $option.choice + $option.randfold $option.exemple_mirbase $option.score_know + #else + no no -50.0 + #end if + $mature_file + $precursor_file + ]]> + </command> + <inputs> + <param format="tabular" name="prediction_file" type="data" label="prediction file from miRDeep2" help="Tabular result file from miRDeep2"/> + <param format="txt" name="word" size="30" value="hsa" type="text" label="Species ID" help="3 letter code that identifies the species studied"/> + <param name="mature_file" type="data" format="fasta" label="Known matures" help="File containing all known mature miRNAs"/> + <param name="precursor_file" type="data" format="fasta" label="Reference precursor sequences" help="File containing containing all hairpins of réference species"/> + + <conditional name="specie_choice"> + <param name="specie" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="Same specie for genome and precursor?" help="Select ‘no’ if the matures and hairpins provided for prediction don’t belong to the reference genome used for prediction"/> + <when value="yes"> + <param format="txt" name="score_new" size="30" value="0" type="float" min="0" max="10" label="Score for the filtering of news mirna" hidden="true"/> + </when> + <when value="no"> + <param format="txt" name="score_new" size="30" value="0" type="float" min="0" max="10" label="Score for the filtering of news mirna"/> + </when> + </conditional> + <conditional name="option"> + <param name="choice" type="boolean" truevalue="yes" falsevalue="no" label="More options?"/> + <when value="no"> + </when> + <when value="yes"> + <param name="randfold" type="boolean" truevalue="yes" falsevalue="no" label="Significant randfold" help="Do you want to retrieve only miRNA with significant randfold?"/> + <param name="exemple_mirbase" type="boolean" truevalue="yes" falsevalue="no" label="Example miRNA with same seed region in mirbase" help="Do you want to retrieve only miRNAs without example of same seed region in miRBase?"/> + <param format="txt" name="score_know" size="30" value="-50" type="float" min="-100" label="Score for the filtering of knows miRNA"/> + </when> + </conditional> + </inputs> + <outputs> + <data format="fasta" name="mature_and_new" from_work_dir="mature_and_new.fa" label="${os.path.splitext(str($mature_file.name))[0]}_and_new_predicted_matures.fa"/> + <data format="fasta" name="hairpin_espece_and_new" from_work_dir="hairpin_espece_and_new.fa" label="${os.path.splitext(str($precursor_file.name))[0]}_and_new_predicted_hairpins.fa"/> + </outputs> + <tests> + <test> + <param name="prediction_file" value="Tabular_output_of_PAQmiR_MiRDeep2.tabular"/> + <param name="word" value="bta"/> + <param name="mature_file" value="mature.fasta"/> + <param name="precursor_file" value="hairpin_bta.fa"/> + <param name="specie" value="yes"/> + + + <output name="mature_and_new" file="mature_and_new_predicted_matures.fa"/> + <output name="hairpin_espece_and_new" file="hairpin_bta_and_new_predicted_hairpins.fa"/> + </test> + </tests> + <help> +<![CDATA[ + + | This tool is part of the workflow **PAQmiR** for the *Prediction Annotation and Quantification of miRNA with miRDeep2* + | + | Wrappers are the product of Valentin Marcon, Kevin Normand & Sylvain Marthey (Thanks to INRA Migale, IFB ressources & INRA GABI) + +**What it does** + | This module will use miRDeep2's prediction results to create new reference datasets (hairpin and mature) which can be used for the quantification and annotation of miRNAs. The two reference datasets will be created by combining the prediction results and the reference miRNA/hairpin provided. + | + | *This module allow to implement the three strategies described in this publication : Annotation of the goat genome using next generation sequencing of microRNA expressed by the lactating mammary gland: comparison of three approaches. Mobuchon et al. BMC Genomics. 2015* + +**Input** + | - Tabulate output file from miRDeep2 + | - File containing all known mature miRNAs (usually all matures from mirbase, or a subset of matures from related species). All the provided matures will be used to make the annoation of predicted miRNAs. + | - File containing containing all hairpins of réference species + +**Output** + | - Fasta file containing predicted mature sequences in addition to miRNA sequences provided in input + | - Fasta file containing predicted hairpin sequences in addition to miRNA sequences provided in input + +]]> + </help> + <citations> + <citation type="doi">10.1371/journal.pone.0091938</citation> + <citation type="doi">10.1186/s12864-015-1471-y</citation> + <citation type="doi">10.1093/nar/gkr688</citation> + <citation type="doi">10.1002/0471250953.bi1210s36</citation> + </citations> +</tool> |
| b |
| diff -r 000000000000 -r da3c91b40f61 paqmir_postprocess_mirdeep2/postprocess_mirdeep2_diff_specie.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/paqmir_postprocess_mirdeep2/postprocess_mirdeep2_diff_specie.sh Mon Mar 18 09:27:29 2019 -0400 |
| [ |
| b'@@ -0,0 +1,243 @@\n+#!/bin/bash\n+\n+#################################################################\n+################### creation new_mirna.csv ######################\n+errorcode=0\n+\n+echo "extract new mature sequences from miRDeep2 results files"\n+\n+echo "create filter condition"\n+\n+condition=\'($2>=\'${3}\'\'; #initialize the beginning of the condition to keep only mirna with a score higher than the one chosen\n+\n+if [ ${4} = "yes" ] #check if option "etrieve only miRNA with significant randfold" is activated\n+then\n+\tcondition=${condition}\' && ${9} =="yes"\'\t#if option randfold is true, implements the condition by asking it to verify if "yes" in the column significatively randfold\n+fi\n+if [ ${5} = "yes" ] # check if option "etrieve only miRNAs without example of same seed region in miRBase" is activated\n+then\n+\tcondition=${condition}\' && $11 =="-"\' # icheck the presence of a name or "-" in column\n+fi\n+\n+condition=${condition}\') || $2=="miRDeep2 score"\' #finish the condition with operator "OR" to keep the header\n+\n+echo "condition applied : ${condition}"\t#view the contents of the condition in stdout output\n+\n+cmd="tail -n +27 $1 > new_mirna.raw.csv"\t# extract from results the table containing all predicted miRNAs\n+cmd2="awk -F \'\\t\' \'{if(${condition}) {print \\"${2}-\\" \\$1 \\"\\t\\" \\$0}else if(\\$9 ==\\"\\"){exit}else{next}}\' new_mirna.raw.csv > new_mirna.csv;" \t#apply filter options to keep interesting miRNAs\n+\n+echo "extract from results the table containing all predicted miRNA :"\n+echo $cmd\n+(eval "$cmd")\t#execute the command\n+((errorcode+=$?)) ##check the run of commands\n+if [ $errorcode -gt 0 ] ; then exit 1 ; fi ##check the run of commands\n+\n+echo "apply filter options to keep interesting miRNAs"\n+echo $cmd2\n+(eval "$cmd2")\t#execute the command 2\n+((errorcode+=$?)) ##check the run of commands\n+if [ $errorcode -gt 0 ] ; then exit 1 ; fi ##check the run of commands\n+\n+echo "new_mirna.csv OK"\n+echo ""\n+\n+###################################################################\n+###################### creation new_mirna.fa ######################\n+echo "creation of new fasta file contaning the new miRNAs new_mirna.fa"\n+\n+echo "selected specie : ${2}"\n+\n+cmd3="awk -F \'\\t\' \'{if(\\$1 !=\\"${2}-provisional id\\"){print \\">\\" \\$1 \\"_mt\\n\\" \\$15 }}\' new_mirna.csv > new_mirna.fa"\t#command to extract mirna where "_mt" is present in the identifier of file new_mirna.csv in the file new_mirna.fa\n+cmd4="awk -F \'\\t\' \'{if(\\$1 !=\\"${2}-provisional id\\"){print \\">\\" \\$1 \\"_st\\n\\" \\$16 }}\' new_mirna.csv >> new_mirna.fa"\t#command to extract mirna where "_st" is present in the identifier of file new_mirna.csv in the file new_mirna.fa\n+\n+echo "extract _mt candidates"\n+echo $cmd3\t\n+(eval "$cmd3")\t#execute the command 3\n+((errorcode+=$?)) ##check the run of commands\n+if [ $errorcode -gt 0 ] ; then exit 1 ; fi ##check the run of commands\n+\n+echo "extract _st candidates"\n+echo $cmd4\n+(eval "$cmd4")\t#execute the command 4\n+((errorcode+=$?)) ##check the run of commands\n+if [ $errorcode -gt 0 ] ; then exit 1 ; fi ##check the run of commands\n+\n+echo "number of new miRNAs"\n+grep -c \'>\' new_mirna.fa\n+\n+echo "new_mirna.fa created with succes OK"\n+echo ""\n+\n+#######################################################################\n+##################### creation new_hairpin.fa #########################\n+echo "creation of new fasta file contaning the new hairpins new_hairpin.fa"\n+\n+echo "selected specie : ${2}"\n+\n+cmd5="awk -F \'\\t\' \'{if(\\$1 !=\\"${2}-provisional id\\"){print \\">\\" \\$1 \\"\\n\\" \\$17 }}\' new_mirna.csv > new_hairpin.fa"\t#command to recuperate precursors\'mirna of file new_mirna.csv in file new_hairpin.fa\n+\n+echo "extract hairpins: "\n+echo $cmd5\t\t#display the command used in stdout output\n+\n+(eval "$cmd5")\t#execute the command 5\n+((errorcode+=$?)) ##check the run of commands\n+if [ $errorcode -gt 0 ] ; then exit 1 ; fi ##check the run of commands\n+\n+echo "number of new hairpins"\n+grep -c \'>\' new_hairpin.fa\n+\n+echo "new_hairpin.fa OK"\n+echo ""\n+\n+###########################'..b' the creation of npp_with_know_espece_mirna.gff in stdout output\n+echo ""\t#display a blank space in stdout output\n+\n+#########################################################################\n+################ creation identified_espece_mira.pre.id##################\n+echo "create file contating miRNA id of identified miRNA : identified_espece_mirna.pre.id"\t#indicate the beginning of the creation of identified_espece_mirna.pre.id in stdout output\n+\n+cmd14="cat identified_${2}_mirna.id | perl -p -e \'s/-5p|-3p//g\' | perl -p -e \'s/R/r/g\' | sort -u > identified_${2}_mirna.pre.id"\t#command to transform identifiers mirna in identifiers precursors\n+\n+echo "extract miRNA id and convert it to precursor id : "\n+echo $cmd14\t#display the command used in stdout output\n+\n+(eval "$cmd14")\t#execute the command 14\n+((errorcode+=$?)) ##check the run of commands\n+if [ $errorcode -gt 0 ] ; then exit 1 ; fi ##check the run of commands\n+\n+echo "identified_espece_mirna.pre.id OK"\t#display "identified_espece_mirna.pre.id OK" to show the end of the creation of identified_espece_mirna.pre.id in stdout output\n+echo ""\t#display a blank space in stdout output\n+\n+####################################################################################\n+############### creation no_identified_espece_mirna_pre.fasta ######################\n+echo "create fasta file containing no identified precursors : no_identified_espece_mirna_pre.fasta" #indicate the beginning of the creation of no_identified_espece_mirna_pre.fasta in stdout output\n+\n+cmd15="$directory/extract_seqs_by_ids.pl --fasta_in ${8} --ids_file identified_${2}_mirna.pre.id --file_out no_identified_${2}_mirna.pre.fasta --precursor_shape yes --inverse yes"\t\n+#command to recuperate identifiers without word of identified_${2}_mirna.pre.id in no_identified_${2}_mirna.pre.fasta\n+\n+echo "remove identified predicted precursors from precursor reference file : "\n+echo $cmd15\t#display the command used in stdout output\n+\n+(eval "$cmd15")\t#execute the command 15\n+((errorcode+=$?)) ##check the run of commands\n+if [ $errorcode -gt 0 ] ; then exit 1 ; fi ##check the run of commands\n+\n+echo "no_identified_espece_mirna_pre.fasta OK"\n+echo ""\n+\n+#####################################################################\n+################# creation mature_and_new.fa ########################\n+echo "creation of new miRNA dataset : mature_and_new_predicted_matures.fa"\t#indicate the beginning of the creation of mature_and_new.fa in stdout output\n+\n+cmd16="cat new_mirna.fa predicted_know_mirna.fa ${7} | perl -p -e \'s/(>\\S+)\\s.+/\\1/\' > mature_and_new.fa"\t#command to concatenate files new_mirna.fa, predicted_know_mirna.fa and mature_sans_espace.fa in mature_and_new.fa\n+\n+echo $cmd16\t#display the command used in stdout output\n+\n+(eval "$cmd16")\t#execute the command 16\n+((errorcode+=$?)) ##check the run of commands\n+if [ $errorcode -gt 0 ] ; then exit 1 ; fi ##check the run of commands\n+\n+echo "mature_and_new.fa OK"\t#display "mature_and_new.fa OK" to show the end of the creation of mature_and_new.fa in stdout output\n+echo ""\t#display a blank space in stdout output\n+\n+#################################################################\n+################creation hairpin_${2}_and_new.fa#################\n+echo "creation de hairpin_${2}_and_new_predicted_hairpin.fa"\t#indicate the beginning of the creation of hairpin_${2}_and_new.fa in stdout output\n+\n+cmd17="cat new_hairpin.fa predicted_know_hairpin.fa no_identified_${2}_mirna.pre.fasta | perl -p -e \'s/(>\\S+)\\s.+/\\1/\' > hairpin_espece_and_new.fa"\t\n+#command to concatenate new_hairpin.fa, predicted_know_hairpin.fa and no_identified_${2}_mirna.pre.fasta in hairpin_espece_and_new.fa\n+\n+echo $cmd17\t#display the command used in stdout output\n+\n+(eval "$cmd17")\t#execute the command 17\n+((errorcode+=$?)) ##check the run of commands\n+if [ $errorcode -gt 0 ] ; then exit 1 ; fi ##check the run of commands\n+\n+echo "hairpin_${2}_and_new_predicted_hairpin.fa OK"\t\n+echo ""\t#display a blank space in stdout output\n' |
| b |
| diff -r 000000000000 -r da3c91b40f61 paqmir_postprocess_mirdeep2/postprocess_mirdeep2_same_specie.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/paqmir_postprocess_mirdeep2/postprocess_mirdeep2_same_specie.sh Mon Mar 18 09:27:29 2019 -0400 |
| [ |
| @@ -0,0 +1,136 @@ +#!/bin/bash + +################################################################# +################### creation new_mirna.csv ###################### +errorcode=0 + +echo "extract new mature sequences from miRDeep2 results files" + +echo "create filter condition" + +condition='($2>='${3}''; #initialize the beginning of the condition to keep only mirna with a score higher than the one chosen + +if [ ${4} = "yes" ] #check if option "etrieve only miRNA with significant randfold" is activated +then + condition=${condition}' && ${9} =="yes"' #if option randfold is true, implements the condition by asking it to verify if "yes" in the column significatively randfold +fi +if [ ${5} = "yes" ] # check if option "etrieve only miRNAs without example of same seed region in miRBase" is activated +then + condition=${condition}' && $11 =="-"' # icheck the presence of a name or "-" in column +fi + +condition=${condition}') || $2=="miRDeep2 score"' #finish the condition with operator "OR" to keep the header + +echo "condition applied : ${condition}" #view the contents of the condition in stdout output + +cmd="tail -n +27 $1 > new_mirna.raw.csv" # extract from results the table containing all predicted miRNAs +cmd2="awk -F '\t' '{if(${condition}) {print \"${2}-\" \$1 \"\t\" \$0}else if(\$9 ==\"\"){exit}else{next}}' new_mirna.raw.csv > new_mirna.csv;" #apply filter options to keep interesting miRNAs + +echo "extract from results the table containing all predicted miRNA :" +echo $cmd +(eval "$cmd") #execute the command +((errorcode+=$?)) ##check the run of commands +if [ $errorcode -gt 0 ] ; then exit 1 ; fi ##check the run of commands + +echo "apply filter options to keep interesting miRNAs" +echo $cmd2 +(eval "$cmd2") #execute the command 2 +((errorcode+=$?)) ##check the run of commands +if [ $errorcode -gt 0 ] ; then exit 1 ; fi ##check the run of commands + +echo "new_mirna.csv OK" +echo "" + +################################################################### +###################### creation new_mirna.fa ###################### +echo "creation of new fasta file contaning the new miRNAs new_mirna.fa" + +echo "selected specie : ${2}" + +cmd3="awk -F '\t' '{if(\$1 !=\"${2}-provisional id\"){print \">\" \$1 \"_mt\n\" \$15 }}' new_mirna.csv > new_mirna.fa" #command to extract mirna where "_mt" is present in the identifier of file new_mirna.csv in the file new_mirna.fa +cmd4="awk -F '\t' '{if(\$1 !=\"${2}-provisional id\"){print \">\" \$1 \"_st\n\" \$16 }}' new_mirna.csv >> new_mirna.fa" #command to extract mirna where "_st" is present in the identifier of file new_mirna.csv in the file new_mirna.fa + +echo "extract _mt candidates" +echo $cmd3 +(eval "$cmd3") #execute the command 3 +((errorcode+=$?)) ##check the run of commands +if [ $errorcode -gt 0 ] ; then exit 1 ; fi ##check the run of commands + +echo "extract _st candidates" +echo $cmd4 +(eval "$cmd4") #execute the command 4 +((errorcode+=$?)) ##check the run of commands +if [ $errorcode -gt 0 ] ; then exit 1 ; fi ##check the run of commands + +echo "number of new miRNAs" +grep -c '>' new_mirna.fa + +echo "new_mirna.fa created with succes OK" +echo "" + +####################################################################### +##################### creation new_hairpin.fa ######################### +echo "creation of new fasta file contaning the new hairpins new_hairpin.fa" + +echo "selected specie : ${2}" + +cmd5="awk -F '\t' '{if(\$1 !=\"${2}-provisional id\"){print \">\" \$1 \"\n\" \$17 }}' new_mirna.csv > new_hairpin.fa" #command to recuperate precursors'mirna of file new_mirna.csv in file new_hairpin.fa + +echo "extract hairpins: " +echo $cmd5 #display the command used in stdout output + +(eval "$cmd5") #execute the command 5 +((errorcode+=$?)) ##check the run of commands +if [ $errorcode -gt 0 ] ; then exit 1 ; fi ##check the run of commands + +echo "number of new hairpins" +grep -c '>' new_hairpin.fa + +echo "new_hairpin.fa OK" +echo "" + +##################################################################### +################### creation new_predicted_precursors.gff ########### +echo "creation of new predicted precursors gff file new_predicted_precursors.gff" #indicate the beginning of the creation of new_predicted_precursors.gff in stdout output + +echo "selected specie : ${2}" + +cmd6="awk -F '\t' '{if(\$1 !=\"${2}-provisional id\"){print \$1 \"\t\" \$18}}' new_mirna.csv | perl -p -e 's/:|\.\./\t/g' | awk -F '\t' '{print \$2 \"\tmiRDeep2\tnew_predicted_precursor\t\" \$3 \"\t\" \$4 \"\t.\t\" \$5 \"\t.\t\" \$1}' > news_predicted_precursors.gff" #command to recuperate positions of precursors on the genome of file new_mirna.csv in file news_predicted_precursors.gff + +echo "creation of gff file " +echo $cmd6 #display the command used in stdout output + +(eval "$cmd6") #execute the command 6 +((errorcode+=$?)) ##check the run of commands +if [ $errorcode -gt 0 ] ; then exit 1 ; fi ##check the run of commands + +echo "new_predicted_precursors.gff OK" +echo "" + +##################################################################### +################# creation mature_and_new.fa ######################## +echo "creation of new miRNA dataset : mature_and_new_predicted_matures.fa" #indicate the beginning of the creation of mature_and_new.fa in stdout output + +cmd12="cat new_mirna.fa ${7} | perl -p -e 's/(>\S+)\s.+/\1/' > mature_and_new.fa" #command to concatenate files new_mirna.fa, predicted_know_mirna.fa and mature_sans_espace.fa in mature_and_new.fa + +(eval "$cmd12") #execute the command 12 +((errorcode+=$?)) ##check the run of commands +if [ $errorcode -gt 0 ] ; then exit 1 ; fi ##check the run of commands + +echo "mature_and_new_predicted_matures.fa OK" +echo "" + +################################################################### +################ creation hairpin_${2}_and_new.fa ################# +echo "creation de hairpin_${2}_and_new_predicted_hairpin.fa" #indicate the beginning of the creation of hairpin_${2}_and_new.fa in stdout output + +cmd13="cat new_hairpin.fa ${8} | perl -p -e 's/(>\S+)\s.+/\1/' > hairpin_espece_and_new.fa" #command to concatenate new_hairpin.fa, predicted_know_hairpin.fa and no_identified_${2}_mirna.pre.fasta in hairpin_espece_and_new.fa + +echo $cmd13 + +(eval "$cmd13") #execute the command 13 +((errorcode+=$?)) ##check the run of commands +if [ $errorcode -gt 0 ] ; then exit 1 ; fi ##check the run of commands + +echo "hairpin_${2}_and_new_predicted_hairpin.fa OK" +echo "" |
| b |
| diff -r 000000000000 -r da3c91b40f61 paqmir_postprocess_mirdeep2/test-data/.directory --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/paqmir_postprocess_mirdeep2/test-data/.directory Mon Mar 18 09:27:29 2019 -0400 |
| [ |
| @@ -0,0 +1,4 @@ +[Dolphin] +Timestamp=2019,2,28,15,52,41 +Version=4 +ViewMode=1 |
| b |
| diff -r 000000000000 -r da3c91b40f61 paqmir_postprocess_mirdeep2/test-data/Tabular_output_of_PAQmiR_MiRDeep2.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/paqmir_postprocess_mirdeep2/test-data/Tabular_output_of_PAQmiR_MiRDeep2.tabular Mon Mar 18 09:27:29 2019 -0400 |
| b |
| b'@@ -0,0 +1,974 @@\n+miRDeep2 score\tnovel miRNAs reported by miRDeep2\tnovel miRNAs, estimated false positives\tnovel miRNAs, estimated true positives\tknown miRNAs in species\tknown miRNAs in data\tknown miRNAs detected by miRDeep2\testimated signal-to-noise\texcision gearing\n+10\t1\t0 +/- 0\t1 +/- 0 (82 +/- 39%)\t1030\t0\t0 (0%)\t4.7\t1\n+9\t1\t0 +/- 0\t1 +/- 0 (82 +/- 39%)\t1030\t0\t0 (0%)\t4.7\t1\n+8\t1\t0 +/- 0\t1 +/- 0 (82 +/- 39%)\t1030\t0\t0 (0%)\t4.7\t1\n+7\t1\t0 +/- 0\t1 +/- 0 (82 +/- 39%)\t1030\t0\t0 (0%)\t4.7\t1\n+6\t1\t0 +/- 0\t1 +/- 0 (82 +/- 39%)\t1030\t0\t0 (0%)\t4.7\t1\n+5\t1\t0 +/- 0\t1 +/- 0 (81 +/- 40%)\t1030\t0\t0 (0%)\t4.5\t1\n+4\t1\t0 +/- 1\t1 +/- 0 (74 +/- 44%)\t1030\t0\t0 (0%)\t3.3\t1\n+3\t1\t1 +/- 1\t0 +/- 0 (38 +/- 49%)\t1030\t0\t0 (0%)\t1.1\t1\n+2\t1\t1 +/- 1\t0 +/- 0 (29 +/- 46%)\t1030\t0\t0 (0%)\t1\t1\n+1\t2\t1 +/- 1\t1 +/- 1 (43 +/- 39%)\t1030\t0\t0 (0%)\t1.6\t1\n+0\t3\t2 +/- 1\t1 +/- 1 (46 +/- 30%)\t1030\t0\t0 (0%)\t1.8\t1\n+-1\t3\t2 +/- 1\t1 +/- 1 (43 +/- 31%)\t1030\t0\t0 (0%)\t1.7\t1\n+-2\t3\t2 +/- 1\t1 +/- 1 (42 +/- 32%)\t1030\t0\t0 (0%)\t1.6\t1\n+-3\t3\t2 +/- 1\t1 +/- 1 (39 +/- 31%)\t1030\t0\t0 (0%)\t1.5\t1\n+-4\t3\t2 +/- 1\t1 +/- 1 (39 +/- 31%)\t1030\t0\t0 (0%)\t1.5\t1\n+-5\t3\t2 +/- 1\t1 +/- 1 (38 +/- 30%)\t1030\t0\t0 (0%)\t1.5\t1\n+-6\t3\t2 +/- 1\t1 +/- 1 (38 +/- 30%)\t1030\t0\t0 (0%)\t1.5\t1\n+-7\t3\t2 +/- 1\t1 +/- 1 (37 +/- 30%)\t1030\t0\t0 (0%)\t1.5\t1\n+-8\t3\t2 +/- 1\t1 +/- 1 (37 +/- 30%)\t1030\t0\t0 (0%)\t1.5\t1\n+-9\t3\t2 +/- 1\t1 +/- 1 (37 +/- 30%)\t1030\t0\t0 (0%)\t1.5\t1\n+-10\t3\t2 +/- 1\t1 +/- 1 (36 +/- 29%)\t1030\t0\t0 (0%)\t1.4\t1\n+\n+\n+\n+novel miRNAs predicted by miRDeep2\n+provisional id\tmiRDeep2 score\testimated probability that the miRNA candidate is a true positive\trfam alert\ttotal read count\tmature read count\tloop read count\tstar read count\tsignificant randfold p-value\tmiRBase miRNA\texample miRBase miRNA with the same seed\tUCSC browser\tNCBI blastn\tconsensus mature sequence\tconsensus star sequence\tconsensus precursor sequence\tprecursor coordinate\n+chr25_10\t138.4\t82 +/- 39%\trRNA\t270\t126\t72\t72\tno\t-\tcre-miR1150.3\t-\t-\tggcagcggagcggg\tccagcaaccc\tggcagcggagcggggagcgcagggcagggcgggggggggggaauccuccccauuguuauguuggcuccucccagcaaccc\tchr25:4011286..4011366:+\n+chr25_36\t1.1\t43 +/- 39%\trRNA/tRNA\t237\t114\t123\t0\tyes\t-\t-\t-\t-\tgaggaggaggag\tucccugcuguc\tgaggaggaggaggaggaggagggagagggaggggacagcaaccagagcgcugaugggacgcugucccuuuaagaggauccagcagguucccugcuguc\tchr25:33768600..33768698:+\n+chr25_114\t0.2\t46 +/- 30%\trRNA/tRNA\t42\t30\t12\t0\tno\t-\tdme-miR-190-3p\t-\t-\taccaggaaggc\tcuuccucuagc\tcuuccucuagccacuugcagaaccacgcggcgcucucaggcgguugaccaucaguguagguggcaaccaggaaggc\tchr25:28645901..28645977:-\n+\n+\n+\n+mature miRBase miRNAs detected by miRDeep2\n+tag id\tmiRDeep2 score\testimated probability that the miRNA is a true positive\trfam alert\ttotal read count\tmature read count\tloop read count\tstar read count\tsignificant randfold p-value\tmature miRBase miRNA\texample miRBase miRNA with the same seed\tUCSC browser\tNCBI blastn\tconsensus mature sequence\tconsensus star sequence\tconsensus precursor sequence\tprecursor coordinate\n+\n+#miRBase miRNAs not detected by miRDeep2\n+miRBase precursor id\ttotal read count\tmature read count(s)\tstar read count\tremaining reads\tUCSC browser\tNCBI blastn\tmiRBase mature sequence(s)\tmiRBase star sequence(s)\tmiRBase precursor sequence\n+444\t348\t0\t96\t-\t-\tuuugguccccuucaaccagcug\t-\tcaaugcuuugcuagagcugguaaaauggaaccaaaucgccucuucaauggauuugguccccuucaaccagcuguagcuaugcauuga\t\n+774\t690\t0\t84\t-\t-\tuaaggcacgcggugaaugccaag\tuaaggcacgcggugaaugccaag\t-\tugagggccccucugcguguucacagcggaccuugauuuaaugucuauacaauuaaggcacgcggugaaugccaagagaggcgccucc\t\n+453\t441\t0\t12\t-\t-\tcuauacaaucuacugucuuuc\tugagguaguagguuguauaguu\t-\tgggugagguaguagguuguauaguuuggggcucugcccugcuaugggauaacuauacaaucuacugucuuuccu\t\n+324\t324\t0\t0\t-\t-\tuggaagacuagugauuuuguuguu\t-\tagacuggagcgguuguggucuagugcuguguggaagacuagugauuuuguuguucugauguacuaugacaacaagucacagc\t\n+411\t348\t0\t63\t-\t-\tucuuugguuaucuagcuguaug\tauaaagcuagauaaccg\t-\tggaagcgaguuguuaucuuugguuaucuagcuguaugaguguauuggucuucauaaagcuagauaaccgaaaguaaaaacuccuuca\t\n+366\t294\t0\t72\t-\t-\tuacccuguagauccgaauuugug\t-\tgaucugucugucuucuguauauacccuguagauccgaauuuguguaaggaauuuugugaucacaaauucguaucuaggggaauauguaguugacauaaacacuccgcuc\t\n+342\t288\t0\t54\t-\t-\taacc'..b'ccgaaaagggguucaccgagcaacauucgucguccagaugcaaaguugcucggguaaccucuccccgcguacca\t\n+3\t3\t0\t0\t-\t-\tucugcacagacccuggcuuuuc\t-\tauuuugauauauaaaccaguuuaauguuuucugcacagacccuggcuuuucuuaaauuuuauauauuggaaaccccguguuuguauuggaccuucugguuuguuucauauugaaaauc\t\n+3\t3\t0\t0\t-\t-\tagguuuuuugguuuuguuuu\t-\taagcaaagguuuuuugguuuuguuuucuguaacaaguuugcagagaacgauacuaaagcaggcaccuagcuu\t\n+3\t3\t0\t0\t-\t-\tgccucugguggucgguuugu\t-\tcucgccguuauucggggaagcagggcacuggagagcgcuucagcacugccucugguggucgguuuguggaugggggcggg\t\n+6\t3\t0\t3\t-\t-\tagaacucuugcagucuuagaugu\t-\tcugaauaaagaacucuugcagucuuagauguuauaaaaaauauauauaucugaauuguaagaguuguuagcacagg\t\n+3\t3\t0\t0\t-\t-\tauagccaguuggggaagaaugc\tauuguucuccaaccuggcucuuu\t-\tcuauugagacauagccaguuggggaagaaugcuguuaccuuagagagaagcuggauuguucuccaaccuggcucuuuauguugccgg\t\n+3\t3\t0\t0\t-\t-\tcuggacuuggagucagaagacc\t-\tugggcuuucuggguccaggcagcaguaugcucagggaggcagcuacggugcagagaaagggagcucuggacuuggagucagaagaccucag\t\n+6\t3\t0\t3\t-\t-\tccucagucagccuuguggaugu\t-\tauacccaaugaaugcgaaaaccucagucagccuuguggauguauguucugcagaccugacaucuagaggacugacugaaauuuucacuuucagcuaa\t\n+3\t3\t0\t0\t-\t-\taaaccugaacaaacuuuuuggc\t-\tgccgaaauguucguugaaguuuuuccauggggugucacggaagaaaccugaacaaacuuuuuggc\t\n+3\t3\t0\t0\t-\t-\tgagggcggguggaggagg\t-\tccgcccccgucuccaccccgccccccggagccgcugaguggcggcagcggccccaggaccggguuuccucagacaagagggcggguggaggaggaagcgg\t\n+6\t6\t0\t0\t-\t-\taaaaccugaaugaacucuuugg\taaaaccugaaugaacucuuuggu\t-\taaaaaguucauuccaguuuuucaagacauaucauauagaugggaaaaccugaaugaacucuuuggu\t\n+3\t3\t0\t0\t-\t-\tagguuguuugguuuuguguu\t-\tgugaacaaacacugaauauacucaaucaugagagaaguggggaagguuguuugguuuuguguucau\t\n+3\t3\t0\t0\t-\t-\tgaccgagagggccucggcugu\t-\tgcgggggaccgagagggccucggcugugugaggacaggaggcggccgaggcccgggccgguucccccga\t\n+3\t3\t0\t0\t-\t-\taggcugaggacaggggcugacgu\t-\tcagggaggcugaggacaggggcugacguucauuuucuacaagugugcgucugccccugggcacagcaccccug\t\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+3\t0\t0\t3\t-\t-\tgaauccaccacgaacaacuuc\t-\tuuugguacugaaaaaaguguuguccgugaaugauucgucauaaguaaagcgaauccaccacgaacaacuucucuucaaguaccaca\t\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+3\t0\t0\t3\t-\t-\taauaaguucguuuggguuuuu\t-\taauaaguucguuuggguuuuuccauaagauguaaugggaaaacuugaaugaacuuuuugg\t\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+3\t0\t0\t3\t-\t-\tuauucauuuaucucccagccuac\t-\tcaggcuaggagaaaugauuggauagaaaauuuuauucuauucauuuaucucccagccuac\t\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+3\t0\t0\t3\t-\t-\taaaguucuguagugcacugacu\t-\taaaguucuguagugcacugacuucuaucauauucagagucggagugucucagaacuuugcc\t\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+3\t0\t0\t3\t-\t-\tuuacaauacaaccugauaagu\t-\tuuacaauacaaccugauaagugcuguaacacuuaucagguuguauuauaaug\t\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+6\t0\t0\t6\t-\t-\tuggcaccagcacuggcggugg\t-\tcgcuggcaguguugguggcacuugcgugggggcgguggcaccagcacuggcggugg\t\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+3\t0\t0\t3\t-\t-\tauuugguuccauuuuaccagc\t-\tgccaucaaugcgcagcuacagcugguugaaggggaccaaauccaucgaacaguugauuugguuccauuuuaccagcuuuagcaaagcauucggu\t\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+15\t0\t0\t15\t-\t-\tugguuugccugggacugag\t-\taggauggccaagcauucugguuugccugggacugagugccugagguacgggacuugcagugccaagauuaggauguuguuguugcugc\t\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+3\t0\t0\t3\t-\t-\tgugacaucacauauauggcgac\t-\tguggcagcuugguggucguauguguggcgccaucuacuggaacguuuaggagugacaucacauauauggcgacuaaacugcu\t\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+60\t0\t0\t60\t-\t-\tuagcaucauuugaaaucaguguuu\t-\tcuucuggaagcugguuucacaugguggcuuagauuuuuccaucuuuguaucuagcaucauuugaaaucaguguuuuaggag\t\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+3\t0\t0\t3\t-\t-\tugauugguacuucuuagagugga\t-\tcacuucaggaagugccauccauguggauaaaaauaugauugguacuucuuagagugga\t\n+\n+\n+\n+\n+\n' |
| b |
| diff -r 000000000000 -r da3c91b40f61 paqmir_postprocess_mirdeep2/test-data/hairpin_bta.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/paqmir_postprocess_mirdeep2/test-data/hairpin_bta.fa Mon Mar 18 09:27:29 2019 -0400 |
| b |
| b'@@ -0,0 +1,3020 @@\n+>bta-mir-26a-2\n+GGCUGUGGCUGGAUUCAAGUAAUCCAGGAUAGGCUGUUUCCAUCUGUGAGGCCUAUUCUU\n+GAUUACUUGUUUCUGGAGGCAGCU\n+>bta-mir-18b\n+CUUGUGUUAAGGUGCAUCUAGUGCAGUUAGUGAAGCAGCUCAGAAUCUACUGCCCUAAAU\n+GCUCCUUCUGGCACA\n+>bta-mir-29a\n+AUGACUGAUUUCUUUUGGUGUUCAGAGUCAAUAUAAUUUUCUAGCACCAUCUGAAAUCGG\n+UUAU\n+>bta-let-7f-2\n+UGUGGGAUGAGGUAGUAGAUUGUAUAGUUUUAGGGUCAUACCCCAUCUUGGAGAUAACUA\n+UACAGUCUACUGUCUUUCCCACG\n+>bta-mir-101-2\n+ACUGUCCUUUUUCGGUUAUCAUGGUACCGAUGCUGUAUAUCUGAAAGGUACAGUACUGUG\n+AUAACUGAAGAAUGGUGGU\n+>bta-mir-103-1\n+CUGCCCUCGGCUUCUUUACAGUGCUGCCUUGUUGCAUAUGGAUCAAGCAGCAUUGUACAG\n+GGCUAUGAAGGC\n+>bta-mir-148a\n+GAGGCAAAGUUCUGAGACACUCCGACUCUGAAUAUGAUAGAAGUCAGUGCACUACAGAAC\n+UUUGUCUC\n+>bta-mir-151\n+CCUGCCCUCGAGGAGCUCACAGUCUAGUACGUCUCAUCCCCUACUAGACUGAAGCUCCUU\n+GAGGACAGG\n+>bta-mir-16b\n+CAUACUUGUUCCGCUGUAGCAGCACGUAAAUAUUGGCGUAGUAAAAUAAAUAUUAAACAC\n+CAAUAUUAUUGUGCUGCUUUAGCGUGACAGGGA\n+>bta-mir-18a\n+UGUUCUAAGGUGCAUCUAGUGCAGAUAGUGAAGUAGAUUAGCAUCUACUGCCCUAAGUGC\n+UCCUUCUGGCA\n+>bta-mir-20a\n+GUAGCACUAAAGUGCUUAUAGUGCAGGUAGUGUUUAGUUAUCUACUGCAUUAUGAGCACU\n+UAAAGUACUGC\n+>bta-mir-21\n+UGUCGGGUAGCUUAUCAGACUGAUGUUGACUGUUGAAUCUCAUGGCAACAGCAGUCGAUG\n+GGCUGUCUGACA\n+>bta-mir-221\n+CCAACAUCCAGGUCUAGGGCAUGAACCUGGCAUACAAUGUAGAUUUCUGUGUUUGUUGAG\n+CAACAGCUACAUUGUCUGCUGGGUUUCAGGCUACCUGGAAACACGUUCUU\n+>bta-mir-222\n+GCUGCUGGAAUGUGUAGGUACCCUCAAUGGCUCAGUAGCCAGUGUAGAUCCUGUCUUUUG\n+UAAUCAGUAGCUACAUCUGGCUACUGGGUCUCUGAUGGCAUCUUCUACCU\n+>bta-mir-26b\n+UGCCCGGGACCCAGUUCAAGUAAUUCAGGAUAGGUUGUGUGCUGUCCAGCCUGUUCUCCA\n+UUACUUGGCUCGGGGGCCGGUGCCC\n+>bta-mir-27a\n+UGGCCUGGGGAGCAGGGCUUAGCUGCUUGUGAGCAGGUCCACAUCAAAUCGUGUUCACAG\n+UGGCUAAGUUCCGCCCCC\n+>bta-mir-30d\n+GUUGUUGUAAACAUCCCCGACUGGAAGCUGUACCACACAGCUAAGCUUUCAGUCAGAUGU\n+UUGCUGCUAC\n+>bta-mir-320a-2\n+AAAAACGAAAAAGAGGCCUUCUCUUCCCGGUUCUUCCCGGAGUCGGGAAAAGCUGGGUUG\n+AGAGGGCGAAAAAGGAAGAGGG\n+>bta-mir-484\n+GUCAGGCUCAGUCCCCUCCCGAUAAACCUCUAAAUAGGGACCUUCCCGGGGGGCUACCUC\n+GGC\n+>bta-mir-499\n+GGGCGGGCGGCCGUUAAGACUUGCAGUGAUGUUUAACUCCUCUCCACGUGAACAUCACAG\n+CAAGUCUGUGCUGCUUCCCGUCCCCACGCUGCCUGGGCAGGGU\n+>bta-mir-99a\n+CCCAUUGGCAUAAACCCGUAGAUCCGAUCUUGUGGUGAAGUGGACCGCACAAGCUCGCUU\n+CUAUGGGUCUGUGUCAGUGUG\n+>bta-mir-125a\n+UGCCGGCCUCUGCGUCCCUGAGACCCUUUAACCUGUGAGGACGUCCAGGGUCACAGGUGA\n+GGUUCUUGGGAGCCUGGCGUCCGGCC\n+>bta-mir-125b-1\n+CGCGCGCCUCUCAAUCCCUGAGACCCUAACUUGUGAUGUUUACCGUUUAAAUCCACGGGU\n+UAGGCUCUUGGGAGCUGCGAGUCGCGCC\n+>bta-mir-126\n+UGACGGGACAUUAUUACUUUUGGUACGCGCUGUGACACUUCAAACUCGUACCGUGAGUAA\n+UAAUGCGCUGUCA\n+>bta-mir-128-1\n+UGAGCUGUUGGAUUCGGGGCCGUAGCACUGUCUGAGAGGUUUACAUUUCUCACAGUGAAC\n+CGGUCUCUUUUUCAGCUGCUUC\n+>bta-mir-145\n+CACCUUGUCCUCACGGUCCAGUUUUCCCAGGAAUCCCUUAGAUGCUAAGAUGGGGAUUCC\n+UGGAAAUACUGUUCUUGAGGUCAUGGUU\n+>bta-mir-181a-2\n+UGCCAGGGCCAGGACCCAGUCUUCAGAGGACUCCAAGGAACAUUCAACGCUGUCGGUGAG\n+UUUGGGAUUUGAAAAAACCACCGACCGUUGACUGUACCUUGGGUUCCUUA\n+>bta-mir-199a-1\n+UGGAAGCUUCUGGAGAUCCUGCUCCGUCGCCCCAGUGUUCAGACUACCUGUUCAGGACAA\n+UGCCGUUGUACAGUAGUCUGCACAUUGGUUAGACUGGGCAAGGG\n+>bta-mir-205\n+CUCUUGUCCUUCAUUCCACCGGAGUCUGUCUCGUACCCAACCAGAUUUCAGUGGAGUGAA\n+GUUCAGGAG\n+>bta-mir-27b\n+ACCUCUCUGACGAGGUGCAGAGCUUAGCUGAUUGGUGAACAGUGACUGGUUUCCGCUUUG\n+UUCACAGUGGCUAAGUUCUGCACCUGAAGAGAAGGUG\n+>bta-mir-30b\n+CCAAGUUUUCAGUUCAUGUAAACAUCCUACACUCAGCUGUAACACACGAGUCGGCUGGGA\n+GGUGGAUGUUUACUUCAGCUGACUUGGA\n+>bta-mir-31\n+UCCUGUAACUUGGAACUGGAGAGGAGGCAAGAUGCUGGCAUAGCUGUUGAACUGCGAACC\n+UGCUAUGCCAACAUAUUGCCAUCUCUCUUGUCCG\n+>bta-mir-34b\n+GUGCUCGGUUUGUAGGCAGUGUAAUUAGCUGAUUGUACUCUCAUGCUUACAAUCACUAGU\n+UCCACUGCCAUCAAAACAAGGCAC\n+>bta-mir-106a\n+CCUUGGCCAUGUAAAAGUGCUUACAGUGCAGGUAGCUUUUUGAGAUCUACUGCAAUGCAA\n+GCACUUCUUACAUUACCAUGG\n+>bta-mir-107\n+CUCUCUGCUUUCAGCUUCUUUACAGUGUUGCCUUGUGGCAUGGAGUUCAAGCAGCAUUGU\n+ACAGGGCUAUCAAAGCACAGA\n+>bta-mir-10a\n+GAUCUGUCUGUCUUCUGUAUAUACCCUGUAGAUCCGAAUUUGUGUAAGGAAUUUUGUGAU\n+CACAAAUUCGUAUCUAGGGGAAUAUGUAGUUGACAUAAACACUCCGCUC\n+>bta-mir-127\n+UGAUCACUGUCUCCAGCCUGCUGAAGCUCAGAGGGCUCUGAUUCAGAAAGAUCAUCGGAU\n+CCGUCUGAGCUUGGCUGGUCGGAAGUCUCCUCAUC\n+>bta-mir-139\n+GUGUACUCUACAGUGCACGUGUCUCCAGUGUGGCUCGGAGGCUGGAGACGCGGCCCUGUU\n+GGAGUAAC\n+>bta-mir-140\n+UCUCUCUGUGUCCUGCCAGUGGUUUUACCCUAUGGUAGGUUACGUCAUGCUGUUCUACCA\n+CAGGGUAGAACCACGGA'..b'CAGAAGUGC\n+CU\n+>bta-mir-12030\n+CCCGGGGCCCGGAGCGGCCAGAGCAGCUCGCACGCUGACUCCAGCCCGGCUCCCGCUCCG\n+GGCUCUGCCAGCGGGC\n+>bta-mir-12031\n+UUCUGUAGAUAAGCCCCAGUUACAUAUCCAAUUACAUAUCUGUAAUUGGAGCCAGUCUGC\n+AGAAGC\n+>bta-mir-12032\n+UCUGGCCUGGAGAAGCCCUGGAGUGAAAACAGGCCCAGGGUGCCUCUAGGCUGGUGG\n+>bta-mir-12033\n+UGCCCUGGGAGUGUAAAUAUUGGCACCUAUACCACCUUGGUGCCAAUGUUUACAUUCUCA\n+GGGGGAG\n+>bta-mir-12034\n+UCCCGGGACCCGGGCAGAGGGCGCACGCUGUGCCUAUGCGGUACACAGCUCUCCCCCGGG\n+GAGCCCGGCGGU\n+>bta-mir-12035\n+AGGGGAAGCAGGGCCCUGGAGGAAUGAUAGAUGGUGUCUCACACCAGGACUUGUCUCCCC\n+AGA\n+>bta-mir-2285df\n+AUUGGUUCAUUUGGGUUUUUCCAUAACAUCUUAUGAAAAACCUGAACAGACUUUUGG\n+>bta-mir-194b-2\n+UAACAGCAGCCCCACUGGAACUAGAGGUACUUCCACAUGGAGUUGCUGUUACA\n+>bta-mir-12036\n+CGGCUCCGUGACUCGUCCGUGGACGCCGGUUCGAGCCCCGUCCCGGGCGCCGCGGAGCCU\n+CA\n+>bta-mir-12037\n+UGAAGAGAAAAUAGAAUUCCAUUGUUAUUAUUCAACCAAAAUCUUGCAUUCUGUCUUCUC\n+UUUAGU\n+>bta-mir-12038\n+ACAUUGACAGCUUCUUUGCAGAGGUACCUCGGUCCCUCUGCAGAAGCUGUCAGUGCCU\n+>bta-mir-12039\n+UGGAGAGGCUACCGGGCCCUGAGCUGGCAUUGGACUCCCAGGGCCCUGGCUUCUUCUCU\n+>bta-mir-12040\n+CACAUGGGCAACGAAUAAUUUUGUAGUAUUUCUCGUACAAAAUUAUUGGUUGUUCAUCUG\n+AA\n+>bta-mir-2285dg\n+AAAAAGUUCAUUUUGGGGUUUUUCCAUAAAAUAUUAUGGGAAAAACCGAAAUGAACUUUU\n+GG\n+>bta-mir-12041\n+ACUGAAGGCCUUGCACCUCUGAAUGCUCUCUGAGGUGCAGCCUUUUCUCC\n+>bta-mir-191b\n+GAACGAAAUCCAAGCGCAGCUGGAAUGCUCUGGAGACAACAGCUGCUUUUGGGAUUCCGU\n+UGCC\n+>bta-mir-12042\n+UGUGUCUUUCCUUCUGUGUGUGCUGCAAAUGACUUAGAGCCACACUGGAGGAGGCACUGU\n+>bta-mir-12043\n+ACCUCAUAGGCCUGGGUUAGUGUAGAGUCAUCGCCUCCAGGGCUAGGAGGUGG\n+>bta-mir-3065\n+UCAACAAAAUCACUGAUGCUGGAGUUGCGUGUGUCAUCACUCAGCACCAGGAUAUUGUUG\n+GGG\n+>bta-mir-12044\n+AAUGGAUUACUUCUGAUUGCUGCUUUGAGAGUAGAUUGUAGGGAAAAUCAGAAAUAAUCC\n+AUUUA\n+>bta-mir-12045\n+ACCCGGGAAGUCCCUGACACUCGAUAUUUGACGAAAAGUGGUGUUGAAGGACUUCCCUGG\n+AGG\n+>bta-mir-507b\n+CACUUCAGGAAGUGCCAUCCAUGUGGAUAAAAAUAUGAUUGGUACUUCUUAGAGUGGA\n+>bta-mir-2285dh\n+AAAAAGUUCGCUUGGGCUUUUCCUAUAACAUCAGAUGGAAGGACCCAAAUGAACUUUUUG\n+G\n+>bta-mir-2285di\n+CAAGAUGUUCUUUUGGGUUUUUCUGUAUGAUGUUAUGGAAACCCUGAAGGAACAUUUUGG\n+U\n+>bta-mir-2285dj\n+GAAAGUUUGUUCAGGUUUGUCCCCAAGAUGUCAUGGGAAAACCCAAACAAACUUUUUG\n+>bta-mir-12046\n+CAGGGGCGGGGGGCAUUUCUGACUCCCUUCUGACUUCUGCUCCCUGCCCUGUAG\n+>bta-mir-2285dk\n+AAAAGUUUGUUUGGGUUUUUCCAUACCAUCUUAUGAAAAACCUGAAUGAACAUUUUGGCC\n+AACU\n+>bta-mir-12047\n+CAGGAAACAGGACCUUUGCCUAAGUUCUUUCAGCAGUUAGGCCAAAGGUCAUGUUCCUUU\n+CU\n+>bta-mir-12048\n+CAAGGAGGAGGUGAAGCACCAGAGAAGAGAGGAAUAGCUACUGUGGUGUCUUCCUCCUCC\n+CU\n+>bta-mir-12049\n+UGCCCUGCAGCUUCCUAGGCUGGCUGUAUUUGGAGAGCCCGGGGAGCCACAGGCUUC\n+>bta-mir-12050\n+UGGCUGCUGUCGUCCUUCCUACUGUUACCAAGUGCUACAGUGGAAAGCGCAGACACCAAG\n+>bta-mir-12051\n+GGAGCAGAUGCACGGCGGGGAGAAGAAGAACUCCUGCAGCAUCUGUUCCGA\n+>bta-mir-1949\n+CUGGUUGGCAUUCUGGGCCUGGUUCAUGCCUACUCUGUUAUUAACUAUACCAGGAUGCCA\n+GCAUAGUU\n+>bta-mir-2285dl-1\n+AAAGAGUUCAUUCAGGUUUUCCAUAAGAUGGUACACAAUAACCUGAAUGAACUUUUUGG\n+>bta-mir-2285dl-2\n+AUAAAGUUGACUCAGGUUUGCCCAUAUGAUGUGACAGGAUAACCUGAAUGAACUUUUUGG\n+>bta-mir-2285dm\n+UUGGCCAAAAGUCUGUAUUUUUCAUACCGACUUAUGGUAUGAAAAACUCAAACUCUUUGG\n+CCAACC\n+>bta-mir-12052\n+CCCAAUGAGAUUUCAAACUGAGAAAUGGAAACUCAGUUUGAAAUCUCAUUGGACA\n+>bta-mir-12053\n+UGUAGAACAUGUUUUGGAACUGCUGGCUUUUUGCAUAUCCAGGACUAGGUCUGCAGA\n+>bta-mir-12054\n+GGGGUCUUUACAAAGGGGGCUGGUCCGCACGGAGGAAUAGCUUAUAGGCUGGAGGUGGGG\n+AUGCAC\n+>bta-mir-12055\n+UUCUCCUCGCCCUCGGAGAACUUUGCCGACCUUGACUCAGCUCCCGAGGGUGGAGGAGAG\n+GU\n+>bta-mir-12056\n+UUUCCUAAGCCAUGUUUGGGUGGGUGUCGGGGGGUCCUGAGGGCUGGAGGCUGAGGCUGG\n+CAGCCAGCCUGGGAUGGGGUUGGGAAGGG\n+>bta-mir-12057\n+ACUGGGAGUGGAAGGAGAGCCCAGAGGUUUCCAGGGACUGGUCCUGACCUCUCCCUUCCC\n+UCCCCACAG\n+>bta-mir-12058\n+ACAUGACUACUGGAAAAUCCAUAGCUUUGACUAUAUAUACCUGGUUCUUCCAGUAGUCAU\n+GUGC\n+>bta-mir-12059\n+GAAACAGGAGGGAGAGAUGCUGGAUGGGGCAGGUGGAUGGAGUCCGAGUGGCAACCAGCU\n+CUCCUCCCACCCUGCCUCCU\n+>bta-mir-12060\n+UUGGGAGACCAGGGGAAGACUCCACUAACUAGCCUUCUCCCAUGUGUCUCCUCCGCCCA\n+>bta-mir-12061\n+ACGGGACAAAAGUCUUGCAGCUGGGGCUGUGGGACCUGGGUCUUGUGG\n+>bta-mir-12062\n+UGUCACGUGGUCCAGCCUCAGGGUACAUCCGCAUCCUGGGAUGGUCCUGUGUCACU\n+>bta-mir-12063\n+AACUUCCCUGGUGGUCCAGUAGUUAAGAAUCCGCCUGCCAAGGCAGGGGACACGGGUUCA\n+GUCACUGGUCCAGGAAGAUUCU\n+>bta-mir-12064\n+UGGUAGUAUUCCUAGUGUGGCGAAUAAGUGCCACACUAGGUUAUGCUACAACU\n' |
| b |
| diff -r 000000000000 -r da3c91b40f61 paqmir_postprocess_mirdeep2/test-data/hairpin_bta_and_new_predicted_hairpins.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/paqmir_postprocess_mirdeep2/test-data/hairpin_bta_and_new_predicted_hairpins.fa Mon Mar 18 09:27:29 2019 -0400 |
| b |
| b'@@ -0,0 +1,3026 @@\n+>bta-chr25_10\n+ggcagcggagcggggagcgcagggcagggcgggggggggggaauccuccccauuguuauguuggcuccucccagcaaccc\n+>bta-chr25_36\n+gaggaggaggaggaggaggagggagagggaggggacagcaaccagagcgcugaugggacgcugucccuuuaagaggauccagcagguucccugcuguc\n+>bta-chr25_114\n+cuuccucuagccacuugcagaaccacgcggcgcucucaggcgguugaccaucaguguagguggcaaccaggaaggc\n+>bta-mir-26a-2\n+GGCUGUGGCUGGAUUCAAGUAAUCCAGGAUAGGCUGUUUCCAUCUGUGAGGCCUAUUCUU\n+GAUUACUUGUUUCUGGAGGCAGCU\n+>bta-mir-18b\n+CUUGUGUUAAGGUGCAUCUAGUGCAGUUAGUGAAGCAGCUCAGAAUCUACUGCCCUAAAU\n+GCUCCUUCUGGCACA\n+>bta-mir-29a\n+AUGACUGAUUUCUUUUGGUGUUCAGAGUCAAUAUAAUUUUCUAGCACCAUCUGAAAUCGG\n+UUAU\n+>bta-let-7f-2\n+UGUGGGAUGAGGUAGUAGAUUGUAUAGUUUUAGGGUCAUACCCCAUCUUGGAGAUAACUA\n+UACAGUCUACUGUCUUUCCCACG\n+>bta-mir-101-2\n+ACUGUCCUUUUUCGGUUAUCAUGGUACCGAUGCUGUAUAUCUGAAAGGUACAGUACUGUG\n+AUAACUGAAGAAUGGUGGU\n+>bta-mir-103-1\n+CUGCCCUCGGCUUCUUUACAGUGCUGCCUUGUUGCAUAUGGAUCAAGCAGCAUUGUACAG\n+GGCUAUGAAGGC\n+>bta-mir-148a\n+GAGGCAAAGUUCUGAGACACUCCGACUCUGAAUAUGAUAGAAGUCAGUGCACUACAGAAC\n+UUUGUCUC\n+>bta-mir-151\n+CCUGCCCUCGAGGAGCUCACAGUCUAGUACGUCUCAUCCCCUACUAGACUGAAGCUCCUU\n+GAGGACAGG\n+>bta-mir-16b\n+CAUACUUGUUCCGCUGUAGCAGCACGUAAAUAUUGGCGUAGUAAAAUAAAUAUUAAACAC\n+CAAUAUUAUUGUGCUGCUUUAGCGUGACAGGGA\n+>bta-mir-18a\n+UGUUCUAAGGUGCAUCUAGUGCAGAUAGUGAAGUAGAUUAGCAUCUACUGCCCUAAGUGC\n+UCCUUCUGGCA\n+>bta-mir-20a\n+GUAGCACUAAAGUGCUUAUAGUGCAGGUAGUGUUUAGUUAUCUACUGCAUUAUGAGCACU\n+UAAAGUACUGC\n+>bta-mir-21\n+UGUCGGGUAGCUUAUCAGACUGAUGUUGACUGUUGAAUCUCAUGGCAACAGCAGUCGAUG\n+GGCUGUCUGACA\n+>bta-mir-221\n+CCAACAUCCAGGUCUAGGGCAUGAACCUGGCAUACAAUGUAGAUUUCUGUGUUUGUUGAG\n+CAACAGCUACAUUGUCUGCUGGGUUUCAGGCUACCUGGAAACACGUUCUU\n+>bta-mir-222\n+GCUGCUGGAAUGUGUAGGUACCCUCAAUGGCUCAGUAGCCAGUGUAGAUCCUGUCUUUUG\n+UAAUCAGUAGCUACAUCUGGCUACUGGGUCUCUGAUGGCAUCUUCUACCU\n+>bta-mir-26b\n+UGCCCGGGACCCAGUUCAAGUAAUUCAGGAUAGGUUGUGUGCUGUCCAGCCUGUUCUCCA\n+UUACUUGGCUCGGGGGCCGGUGCCC\n+>bta-mir-27a\n+UGGCCUGGGGAGCAGGGCUUAGCUGCUUGUGAGCAGGUCCACAUCAAAUCGUGUUCACAG\n+UGGCUAAGUUCCGCCCCC\n+>bta-mir-30d\n+GUUGUUGUAAACAUCCCCGACUGGAAGCUGUACCACACAGCUAAGCUUUCAGUCAGAUGU\n+UUGCUGCUAC\n+>bta-mir-320a-2\n+AAAAACGAAAAAGAGGCCUUCUCUUCCCGGUUCUUCCCGGAGUCGGGAAAAGCUGGGUUG\n+AGAGGGCGAAAAAGGAAGAGGG\n+>bta-mir-484\n+GUCAGGCUCAGUCCCCUCCCGAUAAACCUCUAAAUAGGGACCUUCCCGGGGGGCUACCUC\n+GGC\n+>bta-mir-499\n+GGGCGGGCGGCCGUUAAGACUUGCAGUGAUGUUUAACUCCUCUCCACGUGAACAUCACAG\n+CAAGUCUGUGCUGCUUCCCGUCCCCACGCUGCCUGGGCAGGGU\n+>bta-mir-99a\n+CCCAUUGGCAUAAACCCGUAGAUCCGAUCUUGUGGUGAAGUGGACCGCACAAGCUCGCUU\n+CUAUGGGUCUGUGUCAGUGUG\n+>bta-mir-125a\n+UGCCGGCCUCUGCGUCCCUGAGACCCUUUAACCUGUGAGGACGUCCAGGGUCACAGGUGA\n+GGUUCUUGGGAGCCUGGCGUCCGGCC\n+>bta-mir-125b-1\n+CGCGCGCCUCUCAAUCCCUGAGACCCUAACUUGUGAUGUUUACCGUUUAAAUCCACGGGU\n+UAGGCUCUUGGGAGCUGCGAGUCGCGCC\n+>bta-mir-126\n+UGACGGGACAUUAUUACUUUUGGUACGCGCUGUGACACUUCAAACUCGUACCGUGAGUAA\n+UAAUGCGCUGUCA\n+>bta-mir-128-1\n+UGAGCUGUUGGAUUCGGGGCCGUAGCACUGUCUGAGAGGUUUACAUUUCUCACAGUGAAC\n+CGGUCUCUUUUUCAGCUGCUUC\n+>bta-mir-145\n+CACCUUGUCCUCACGGUCCAGUUUUCCCAGGAAUCCCUUAGAUGCUAAGAUGGGGAUUCC\n+UGGAAAUACUGUUCUUGAGGUCAUGGUU\n+>bta-mir-181a-2\n+UGCCAGGGCCAGGACCCAGUCUUCAGAGGACUCCAAGGAACAUUCAACGCUGUCGGUGAG\n+UUUGGGAUUUGAAAAAACCACCGACCGUUGACUGUACCUUGGGUUCCUUA\n+>bta-mir-199a-1\n+UGGAAGCUUCUGGAGAUCCUGCUCCGUCGCCCCAGUGUUCAGACUACCUGUUCAGGACAA\n+UGCCGUUGUACAGUAGUCUGCACAUUGGUUAGACUGGGCAAGGG\n+>bta-mir-205\n+CUCUUGUCCUUCAUUCCACCGGAGUCUGUCUCGUACCCAACCAGAUUUCAGUGGAGUGAA\n+GUUCAGGAG\n+>bta-mir-27b\n+ACCUCUCUGACGAGGUGCAGAGCUUAGCUGAUUGGUGAACAGUGACUGGUUUCCGCUUUG\n+UUCACAGUGGCUAAGUUCUGCACCUGAAGAGAAGGUG\n+>bta-mir-30b\n+CCAAGUUUUCAGUUCAUGUAAACAUCCUACACUCAGCUGUAACACACGAGUCGGCUGGGA\n+GGUGGAUGUUUACUUCAGCUGACUUGGA\n+>bta-mir-31\n+UCCUGUAACUUGGAACUGGAGAGGAGGCAAGAUGCUGGCAUAGCUGUUGAACUGCGAACC\n+UGCUAUGCCAACAUAUUGCCAUCUCUCUUGUCCG\n+>bta-mir-34b\n+GUGCUCGGUUUGUAGGCAGUGUAAUUAGCUGAUUGUACUCUCAUGCUUACAAUCACUAGU\n+UCCACUGCCAUCAAAACAAGGCAC\n+>bta-mir-106a\n+CCUUGGCCAUGUAAAAGUGCUUACAGUGCAGGUAGCUUUUUGAGAUCUACUGCAAUGCAA\n+GCACUUCUUACAUUACCAUGG\n+>bta-mir-107\n+CUCUCUGCUUUCAGCUUCUUUACAGUGUUGCCUUGUGGCAUGGAGUUCAAGCAGCAUUGU\n+ACAGGGCUAUCAAAGCACAGA\n+>bta-mir-10a\n+GAUCUGUCUGUCUUCUGUAUAUACCCUGUAGAUCCGAAUUUGUGUAAGGAAUUUUGUGAU\n+CACAAAUUCGUAUCUAGGGGAAUAUGUAGUUGACAUA'..b'CAGAAGUGC\n+CU\n+>bta-mir-12030\n+CCCGGGGCCCGGAGCGGCCAGAGCAGCUCGCACGCUGACUCCAGCCCGGCUCCCGCUCCG\n+GGCUCUGCCAGCGGGC\n+>bta-mir-12031\n+UUCUGUAGAUAAGCCCCAGUUACAUAUCCAAUUACAUAUCUGUAAUUGGAGCCAGUCUGC\n+AGAAGC\n+>bta-mir-12032\n+UCUGGCCUGGAGAAGCCCUGGAGUGAAAACAGGCCCAGGGUGCCUCUAGGCUGGUGG\n+>bta-mir-12033\n+UGCCCUGGGAGUGUAAAUAUUGGCACCUAUACCACCUUGGUGCCAAUGUUUACAUUCUCA\n+GGGGGAG\n+>bta-mir-12034\n+UCCCGGGACCCGGGCAGAGGGCGCACGCUGUGCCUAUGCGGUACACAGCUCUCCCCCGGG\n+GAGCCCGGCGGU\n+>bta-mir-12035\n+AGGGGAAGCAGGGCCCUGGAGGAAUGAUAGAUGGUGUCUCACACCAGGACUUGUCUCCCC\n+AGA\n+>bta-mir-2285df\n+AUUGGUUCAUUUGGGUUUUUCCAUAACAUCUUAUGAAAAACCUGAACAGACUUUUGG\n+>bta-mir-194b-2\n+UAACAGCAGCCCCACUGGAACUAGAGGUACUUCCACAUGGAGUUGCUGUUACA\n+>bta-mir-12036\n+CGGCUCCGUGACUCGUCCGUGGACGCCGGUUCGAGCCCCGUCCCGGGCGCCGCGGAGCCU\n+CA\n+>bta-mir-12037\n+UGAAGAGAAAAUAGAAUUCCAUUGUUAUUAUUCAACCAAAAUCUUGCAUUCUGUCUUCUC\n+UUUAGU\n+>bta-mir-12038\n+ACAUUGACAGCUUCUUUGCAGAGGUACCUCGGUCCCUCUGCAGAAGCUGUCAGUGCCU\n+>bta-mir-12039\n+UGGAGAGGCUACCGGGCCCUGAGCUGGCAUUGGACUCCCAGGGCCCUGGCUUCUUCUCU\n+>bta-mir-12040\n+CACAUGGGCAACGAAUAAUUUUGUAGUAUUUCUCGUACAAAAUUAUUGGUUGUUCAUCUG\n+AA\n+>bta-mir-2285dg\n+AAAAAGUUCAUUUUGGGGUUUUUCCAUAAAAUAUUAUGGGAAAAACCGAAAUGAACUUUU\n+GG\n+>bta-mir-12041\n+ACUGAAGGCCUUGCACCUCUGAAUGCUCUCUGAGGUGCAGCCUUUUCUCC\n+>bta-mir-191b\n+GAACGAAAUCCAAGCGCAGCUGGAAUGCUCUGGAGACAACAGCUGCUUUUGGGAUUCCGU\n+UGCC\n+>bta-mir-12042\n+UGUGUCUUUCCUUCUGUGUGUGCUGCAAAUGACUUAGAGCCACACUGGAGGAGGCACUGU\n+>bta-mir-12043\n+ACCUCAUAGGCCUGGGUUAGUGUAGAGUCAUCGCCUCCAGGGCUAGGAGGUGG\n+>bta-mir-3065\n+UCAACAAAAUCACUGAUGCUGGAGUUGCGUGUGUCAUCACUCAGCACCAGGAUAUUGUUG\n+GGG\n+>bta-mir-12044\n+AAUGGAUUACUUCUGAUUGCUGCUUUGAGAGUAGAUUGUAGGGAAAAUCAGAAAUAAUCC\n+AUUUA\n+>bta-mir-12045\n+ACCCGGGAAGUCCCUGACACUCGAUAUUUGACGAAAAGUGGUGUUGAAGGACUUCCCUGG\n+AGG\n+>bta-mir-507b\n+CACUUCAGGAAGUGCCAUCCAUGUGGAUAAAAAUAUGAUUGGUACUUCUUAGAGUGGA\n+>bta-mir-2285dh\n+AAAAAGUUCGCUUGGGCUUUUCCUAUAACAUCAGAUGGAAGGACCCAAAUGAACUUUUUG\n+G\n+>bta-mir-2285di\n+CAAGAUGUUCUUUUGGGUUUUUCUGUAUGAUGUUAUGGAAACCCUGAAGGAACAUUUUGG\n+U\n+>bta-mir-2285dj\n+GAAAGUUUGUUCAGGUUUGUCCCCAAGAUGUCAUGGGAAAACCCAAACAAACUUUUUG\n+>bta-mir-12046\n+CAGGGGCGGGGGGCAUUUCUGACUCCCUUCUGACUUCUGCUCCCUGCCCUGUAG\n+>bta-mir-2285dk\n+AAAAGUUUGUUUGGGUUUUUCCAUACCAUCUUAUGAAAAACCUGAAUGAACAUUUUGGCC\n+AACU\n+>bta-mir-12047\n+CAGGAAACAGGACCUUUGCCUAAGUUCUUUCAGCAGUUAGGCCAAAGGUCAUGUUCCUUU\n+CU\n+>bta-mir-12048\n+CAAGGAGGAGGUGAAGCACCAGAGAAGAGAGGAAUAGCUACUGUGGUGUCUUCCUCCUCC\n+CU\n+>bta-mir-12049\n+UGCCCUGCAGCUUCCUAGGCUGGCUGUAUUUGGAGAGCCCGGGGAGCCACAGGCUUC\n+>bta-mir-12050\n+UGGCUGCUGUCGUCCUUCCUACUGUUACCAAGUGCUACAGUGGAAAGCGCAGACACCAAG\n+>bta-mir-12051\n+GGAGCAGAUGCACGGCGGGGAGAAGAAGAACUCCUGCAGCAUCUGUUCCGA\n+>bta-mir-1949\n+CUGGUUGGCAUUCUGGGCCUGGUUCAUGCCUACUCUGUUAUUAACUAUACCAGGAUGCCA\n+GCAUAGUU\n+>bta-mir-2285dl-1\n+AAAGAGUUCAUUCAGGUUUUCCAUAAGAUGGUACACAAUAACCUGAAUGAACUUUUUGG\n+>bta-mir-2285dl-2\n+AUAAAGUUGACUCAGGUUUGCCCAUAUGAUGUGACAGGAUAACCUGAAUGAACUUUUUGG\n+>bta-mir-2285dm\n+UUGGCCAAAAGUCUGUAUUUUUCAUACCGACUUAUGGUAUGAAAAACUCAAACUCUUUGG\n+CCAACC\n+>bta-mir-12052\n+CCCAAUGAGAUUUCAAACUGAGAAAUGGAAACUCAGUUUGAAAUCUCAUUGGACA\n+>bta-mir-12053\n+UGUAGAACAUGUUUUGGAACUGCUGGCUUUUUGCAUAUCCAGGACUAGGUCUGCAGA\n+>bta-mir-12054\n+GGGGUCUUUACAAAGGGGGCUGGUCCGCACGGAGGAAUAGCUUAUAGGCUGGAGGUGGGG\n+AUGCAC\n+>bta-mir-12055\n+UUCUCCUCGCCCUCGGAGAACUUUGCCGACCUUGACUCAGCUCCCGAGGGUGGAGGAGAG\n+GU\n+>bta-mir-12056\n+UUUCCUAAGCCAUGUUUGGGUGGGUGUCGGGGGGUCCUGAGGGCUGGAGGCUGAGGCUGG\n+CAGCCAGCCUGGGAUGGGGUUGGGAAGGG\n+>bta-mir-12057\n+ACUGGGAGUGGAAGGAGAGCCCAGAGGUUUCCAGGGACUGGUCCUGACCUCUCCCUUCCC\n+UCCCCACAG\n+>bta-mir-12058\n+ACAUGACUACUGGAAAAUCCAUAGCUUUGACUAUAUAUACCUGGUUCUUCCAGUAGUCAU\n+GUGC\n+>bta-mir-12059\n+GAAACAGGAGGGAGAGAUGCUGGAUGGGGCAGGUGGAUGGAGUCCGAGUGGCAACCAGCU\n+CUCCUCCCACCCUGCCUCCU\n+>bta-mir-12060\n+UUGGGAGACCAGGGGAAGACUCCACUAACUAGCCUUCUCCCAUGUGUCUCCUCCGCCCA\n+>bta-mir-12061\n+ACGGGACAAAAGUCUUGCAGCUGGGGCUGUGGGACCUGGGUCUUGUGG\n+>bta-mir-12062\n+UGUCACGUGGUCCAGCCUCAGGGUACAUCCGCAUCCUGGGAUGGUCCUGUGUCACU\n+>bta-mir-12063\n+AACUUCCCUGGUGGUCCAGUAGUUAAGAAUCCGCCUGCCAAGGCAGGGGACACGGGUUCA\n+GUCACUGGUCCAGGAAGAUUCU\n+>bta-mir-12064\n+UGGUAGUAUUCCUAGUGUGGCGAAUAAGUGCCACACUAGGUUAUGCUACAACU\n' |
| b |
| diff -r 000000000000 -r da3c91b40f61 paqmir_postprocess_mirdeep2/test-data/mature.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/paqmir_postprocess_mirdeep2/test-data/mature.fasta Mon Mar 18 09:27:29 2019 -0400 |
| b |
| b'@@ -0,0 +1,97770 @@\n+>cel-let-7-5p MIMAT0000001 Caenorhabditis elegans let-7-5p\n+UGAGGUAGUAGGUUGUAUAGUU\n+>cel-let-7-3p MIMAT0015091 Caenorhabditis elegans let-7-3p\n+CUAUGCAAUUUUCUACCUUACC\n+>cel-lin-4-5p MIMAT0000002 Caenorhabditis elegans lin-4-5p\n+UCCCUGAGACCUCAAGUGUGA\n+>cel-lin-4-3p MIMAT0015092 Caenorhabditis elegans lin-4-3p\n+ACACCUGGGCUCUCCGGGUACC\n+>cel-miR-1-5p MIMAT0020301 Caenorhabditis elegans miR-1-5p\n+CAUACUUCCUUACAUGCCCAUA\n+>cel-miR-1-3p MIMAT0000003 Caenorhabditis elegans miR-1-3p\n+UGGAAUGUAAAGAAGUAUGUA\n+>cel-miR-2-5p MIMAT0020302 Caenorhabditis elegans miR-2-5p\n+CAUCAAAGCGGUGGUUGAUGUG\n+>cel-miR-2-3p MIMAT0000004 Caenorhabditis elegans miR-2-3p\n+UAUCACAGCCAGCUUUGAUGUGC\n+>cel-miR-34-5p MIMAT0000005 Caenorhabditis elegans miR-34-5p\n+AGGCAGUGUGGUUAGCUGGUUG\n+>cel-miR-34-3p MIMAT0015093 Caenorhabditis elegans miR-34-3p\n+ACGGCUACCUUCACUGCCACCC\n+>cel-miR-35-5p MIMAT0020303 Caenorhabditis elegans miR-35-5p\n+UGCUGGUUUCUUCCACAGUGGUA\n+>cel-miR-35-3p MIMAT0000006 Caenorhabditis elegans miR-35-3p\n+UCACCGGGUGGAAACUAGCAGU\n+>cel-miR-36-5p MIMAT0020304 Caenorhabditis elegans miR-36-5p\n+CGCCAAUUUUCGCUUCAGUGCUA\n+>cel-miR-36-3p MIMAT0000007 Caenorhabditis elegans miR-36-3p\n+UCACCGGGUGAAAAUUCGCAUG\n+>cel-miR-37-5p MIMAT0015094 Caenorhabditis elegans miR-37-5p\n+UGUGGGUGUCCGUUGCGGUGCUA\n+>cel-miR-37-3p MIMAT0000008 Caenorhabditis elegans miR-37-3p\n+UCACCGGGUGAACACUUGCAGU\n+>cel-miR-38-5p MIMAT0020305 Caenorhabditis elegans miR-38-5p\n+UCCGGUUUUUUCCGUGGUGAUA\n+>cel-miR-38-3p MIMAT0000009 Caenorhabditis elegans miR-38-3p\n+UCACCGGGAGAAAAACUGGAGU\n+>cel-miR-39-5p MIMAT0020306 Caenorhabditis elegans miR-39-5p\n+AGCUGAUUUCGUCUUGGUAAUA\n+>cel-miR-39-3p MIMAT0000010 Caenorhabditis elegans miR-39-3p\n+UCACCGGGUGUAAAUCAGCUUG\n+>cel-miR-40-5p MIMAT0020307 Caenorhabditis elegans miR-40-5p\n+AGUGGAUGUAUGCCAUGAUGAUA\n+>cel-miR-40-3p MIMAT0000011 Caenorhabditis elegans miR-40-3p\n+UCACCGGGUGUACAUCAGCUAA\n+>cel-miR-41-5p MIMAT0020770 Caenorhabditis elegans miR-41-5p\n+GGUGGUUUUUCUCUGCAGUGAUA\n+>cel-miR-41-3p MIMAT0000012 Caenorhabditis elegans miR-41-3p\n+UCACCGGGUGAAAAAUCACCUA\n+>cel-miR-42-5p MIMAT0015095 Caenorhabditis elegans miR-42-5p\n+GUGGGUGUUUGCUUUUUCGGUGAAG\n+>cel-miR-42-3p MIMAT0000013 Caenorhabditis elegans miR-42-3p\n+UCACCGGGUUAACAUCUACAGA\n+>cel-miR-43-5p MIMAT0020308 Caenorhabditis elegans miR-43-5p\n+GACAUCAAGAAACUAGUGAUUAUG\n+>cel-miR-43-3p MIMAT0000014 Caenorhabditis elegans miR-43-3p\n+UAUCACAGUUUACUUGCUGUCGC\n+>cel-miR-44-5p MIMAT0020771 Caenorhabditis elegans miR-44-5p\n+CUGGAUGUGCUCGUUGGUCAUA\n+>cel-miR-44-3p MIMAT0000015 Caenorhabditis elegans miR-44-3p\n+UGACUAGAGACACAUUCAGCU\n+>cel-miR-45-5p MIMAT0020772 Caenorhabditis elegans miR-45-5p\n+CUGGAUGUGCUCGUUAGUCAUA\n+>cel-miR-45-3p MIMAT0000016 Caenorhabditis elegans miR-45-3p\n+UGACUAGAGACACAUUCAGCU\n+>cel-miR-46-5p MIMAT0015096 Caenorhabditis elegans miR-46-5p\n+AAGAGAGCCGUCUAUUGACAGU\n+>cel-miR-46-3p MIMAT0000017 Caenorhabditis elegans miR-46-3p\n+UGUCAUGGAGUCGCUCUCUUCA\n+>cel-miR-47-5p MIMAT0015097 Caenorhabditis elegans miR-47-5p\n+AAGAGAGCAGUCUAUUGACAGU\n+>cel-miR-47-3p MIMAT0000018 Caenorhabditis elegans miR-47-3p\n+UGUCAUGGAGGCGCUCUCUUCA\n+>cel-miR-48-5p MIMAT0000019 Caenorhabditis elegans miR-48-5p\n+UGAGGUAGGCUCAGUAGAUGCGA\n+>cel-miR-48-3p MIMAT0015098 Caenorhabditis elegans miR-48-3p\n+ACAUCCACCAGCCUAGCUCGCA\n+>cel-miR-49-5p MIMAT0020309 Caenorhabditis elegans miR-49-5p\n+CGCAGUUUGUUGUGAUGUGCUCC\n+>cel-miR-49-3p MIMAT0000020 Caenorhabditis elegans miR-49-3p\n+AAGCACCACGAGAAGCUGCAGA\n+>cel-miR-50-5p MIMAT0000021 Caenorhabditis elegans miR-50-5p\n+UGAUAUGUCUGGUAUUCUUGGGUU\n+>cel-miR-50-3p MIMAT0020310 Caenorhabditis elegans miR-50-3p\n+CCCGCAUAUUAGACGUAUCGAC\n+>cel-miR-51-5p MIMAT0000022 Caenorhabditis elegans miR-51-5p\n+UACCCGUAGCUCCUAUCCAUGUU\n+>cel-miR-51-3p MIMAT0015099 Caenorhabditis elegans miR-51-3p\n+CAUGGAAGCAGGUACAGGUGCA\n+>cel-miR-52-5p MIMAT0000023 Caenorhabditis elegans miR-52-5p\n+CACCCGUACAUAUGUUUCCGUGCU\n+>cel-miR-52-3p MIMAT0020311 Caenorhabditis elegans miR-52-3p\n+CACGUUACAAUGAAAGGGUAGC\n+>cel-miR-53-5p MIMAT000'..b'GACUUGCCAAGGU\n+>mdo-miR-12404-3p MIMAT0050450 Monodelphis domestica miR-12404-3p\n+CUUAAGCAAGUCCCUUCCCCUCU\n+>mdo-miR-12405-5p MIMAT0050451 Monodelphis domestica miR-12405-5p\n+UAGUCCCAACUCCGCCACUAAG\n+>mdo-miR-12405-3p MIMAT0050452 Monodelphis domestica miR-12405-3p\n+UAGUGGAAGAACUGGGAUUAGA\n+>mdo-miR-12406-5p MIMAT0050453 Monodelphis domestica miR-12406-5p\n+UGAGCUUCCAAUUUGGUUGGA\n+>mdo-miR-12406-3p MIMAT0050454 Monodelphis domestica miR-12406-3p\n+UUCAACAGAUAGGGCGCUCAU\n+>mdo-miR-12407-5p MIMAT0050455 Monodelphis domestica miR-12407-5p\n+UGUGCUGCCUCGCUGCCUCAC\n+>mdo-miR-12407-3p MIMAT0050456 Monodelphis domestica miR-12407-3p\n+AGAGGACACAUGGUGAGCACAU\n+>mdo-miR-12408-5p MIMAT0050457 Monodelphis domestica miR-12408-5p\n+UUGCAGCCCCCAAGGAGCAG\n+>mdo-miR-12408-3p MIMAT0050458 Monodelphis domestica miR-12408-3p\n+UUCUCCUUAAGAGACUGCAAGC\n+>mdo-miR-12409-5p MIMAT0050459 Monodelphis domestica miR-12409-5p\n+UCUGGCCACCAGUUGCUUUCC\n+>mdo-miR-12409-3p MIMAT0050460 Monodelphis domestica miR-12409-3p\n+AGGAAGGGAGCUGUUGGCCCC\n+>mdo-miR-12366b-5p MIMAT0050461 Monodelphis domestica miR-12366b-5p\n+CCUGCAGCUCUGAGAUUCUAUG\n+>mdo-miR-12366b-3p MIMAT0050462 Monodelphis domestica miR-12366b-3p\n+UCAUAGAGUGUUAGUGCUGGGA\n+>mdo-miR-12410-5p MIMAT0050463 Monodelphis domestica miR-12410-5p\n+AAGGAAACUGAGAUCCAGGAGG\n+>mdo-miR-12411-3p MIMAT0050464 Monodelphis domestica miR-12411-3p\n+UCCUCUCUUGUCUCCUGGCAG\n+>mdo-miR-12412-5p MIMAT0050465 Monodelphis domestica miR-12412-5p\n+UGGAGGGCUCGAAGAUCUUGGA\n+>mdo-miR-12412-3p MIMAT0050466 Monodelphis domestica miR-12412-3p\n+GUCCAAGAACUCGGCCUCCCCC\n+>aga-miR-12413-3p MIMAT0050467 Anopheles gambiae miR-12413-3p\n+UAUGACUUGUCUGCCAGAGCAAGGGG\n+>aga-miR-12414-3p MIMAT0050468 Anopheles gambiae miR-12414-3p\n+AAGACGCUGGUUCUCUUCACACA\n+>aga-miR-12415-3p MIMAT0050469 Anopheles gambiae miR-12415-3p\n+CGAUUGUGGAACCGCGUAGGCUGCCU\n+>aga-miR-12416-3p MIMAT0050470 Anopheles gambiae miR-12416-3p\n+UGACGGGUUUGGUCUCUCCA\n+>aga-miR-12417-5p MIMAT0050471 Anopheles gambiae miR-12417-5p\n+UAGUCGUUUUCUGCUUUGCGGUU\n+>aga-miR-12418-3p MIMAT0050472 Anopheles gambiae miR-12418-3p\n+UGUUCGAUCGUUACUGUCAUAU\n+>aga-miR-12419-5p MIMAT0050473 Anopheles gambiae miR-12419-5p\n+AGCUGUUCUGACUUGAUGUACU\n+>smc-miR-12455-5p MIMAT0050474 Symbiodinium microadriaticum miR-12455-5p\n+CUGUGACCGUCCCAUCCUUGCG\n+>smc-miR-12455-3p MIMAT0050475 Symbiodinium microadriaticum miR-12455-3p\n+CAAGGAUGGGAUGCUCAGAGAA\n+>smc-miR-12456-5p MIMAT0050476 Symbiodinium microadriaticum miR-12456-5p\n+CCUCGUCGUCUGCUCUUUGAGC\n+>smc-miR-12456-3p MIMAT0050477 Symbiodinium microadriaticum miR-12456-3p\n+UCAGAGACCAGACGCAGAGGCU\n+>smc-miR-12457-5p MIMAT0050478 Symbiodinium microadriaticum miR-12457-5p\n+CUUUGUAUCCCGGAUCCUGAUA\n+>smc-miR-12457-3p MIMAT0050479 Symbiodinium microadriaticum miR-12457-3p\n+UCAAGACCCGGGAUAUAUAUGU\n+>smc-miR-12455-2-3p MIMAT0050480 Symbiodinium microadriaticum miR-12455-2-3p\n+CAAGGAUGGGAUGGUCAGAGAA\n+>smc-miR-12458-5p MIMAT0050481 Symbiodinium microadriaticum miR-12458-5p\n+CAGUCGGCCAAAGUGCUGGACC\n+>smc-miR-12458-3p MIMAT0050482 Symbiodinium microadriaticum miR-12458-3p\n+UCCAGCACUUUGGCUGUCUGCC\n+>smc-miR-12459-5p MIMAT0050483 Symbiodinium microadriaticum miR-12459-5p\n+UACCGUCCCUGAGAGUUCAAUG\n+>smc-miR-12459-3p MIMAT0050484 Symbiodinium microadriaticum miR-12459-3p\n+UCGAACUUUCAGGAAUAGUAUC\n+>smc-miR-12460-5p MIMAT0050485 Symbiodinium microadriaticum miR-12460-5p\n+UCAGUGGCAGAAGCUGGGAACU\n+>smc-miR-12460-3p MIMAT0050486 Symbiodinium microadriaticum miR-12460-3p\n+UUCCCAGCUUGUGCCACUGAAA\n+>smc-miR-12461-5p MIMAT0050487 Symbiodinium microadriaticum miR-12461-5p\n+GAGGAUGCUGAUCAUUCACUGG\n+>smc-miR-12461-3p MIMAT0050488 Symbiodinium microadriaticum miR-12461-3p\n+AGUAAAUGAUCAGCAUCCUCCA\n+>gga-miR-1784b-5p MIMAT0050489 Gallus gallus miR-1784b-5p\n+UUCUGCUCCUAUUUAAGUCAAU\n+>gga-miR-1784b-3p MIMAT0050490 Gallus gallus miR-1784b-3p\n+UGAUUUCAAUAAGAGCAGAAUU\n+>mdo-miR-7385g-3p MIMAT0050491 Monodelphis domestica miR-7385g-3p\n+AGCAUAGAAUGUCAGAUCUAG\n+>mdo-miR-7385g-2-3p MIMAT0050492 Monodelphis domestica miR-7385g-2-3p\n+AGCAUAGAAUGUCAGGUCUAG\n' |
| b |
| diff -r 000000000000 -r da3c91b40f61 paqmir_postprocess_mirdeep2/test-data/mature_and_new_predicted_matures.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/paqmir_postprocess_mirdeep2/test-data/mature_and_new_predicted_matures.fa Mon Mar 18 09:27:29 2019 -0400 |
| b |
| b'@@ -0,0 +1,97782 @@\n+>bta-chr25_10_mt\n+ggcagcggagcggg\n+>bta-chr25_36_mt\n+gaggaggaggag\n+>bta-chr25_114_mt\n+accaggaaggc\n+>bta-chr25_10_st\n+ccagcaaccc\n+>bta-chr25_36_st\n+ucccugcuguc\n+>bta-chr25_114_st\n+cuuccucuagc\n+>cel-let-7-5p\n+UGAGGUAGUAGGUUGUAUAGUU\n+>cel-let-7-3p\n+CUAUGCAAUUUUCUACCUUACC\n+>cel-lin-4-5p\n+UCCCUGAGACCUCAAGUGUGA\n+>cel-lin-4-3p\n+ACACCUGGGCUCUCCGGGUACC\n+>cel-miR-1-5p\n+CAUACUUCCUUACAUGCCCAUA\n+>cel-miR-1-3p\n+UGGAAUGUAAAGAAGUAUGUA\n+>cel-miR-2-5p\n+CAUCAAAGCGGUGGUUGAUGUG\n+>cel-miR-2-3p\n+UAUCACAGCCAGCUUUGAUGUGC\n+>cel-miR-34-5p\n+AGGCAGUGUGGUUAGCUGGUUG\n+>cel-miR-34-3p\n+ACGGCUACCUUCACUGCCACCC\n+>cel-miR-35-5p\n+UGCUGGUUUCUUCCACAGUGGUA\n+>cel-miR-35-3p\n+UCACCGGGUGGAAACUAGCAGU\n+>cel-miR-36-5p\n+CGCCAAUUUUCGCUUCAGUGCUA\n+>cel-miR-36-3p\n+UCACCGGGUGAAAAUUCGCAUG\n+>cel-miR-37-5p\n+UGUGGGUGUCCGUUGCGGUGCUA\n+>cel-miR-37-3p\n+UCACCGGGUGAACACUUGCAGU\n+>cel-miR-38-5p\n+UCCGGUUUUUUCCGUGGUGAUA\n+>cel-miR-38-3p\n+UCACCGGGAGAAAAACUGGAGU\n+>cel-miR-39-5p\n+AGCUGAUUUCGUCUUGGUAAUA\n+>cel-miR-39-3p\n+UCACCGGGUGUAAAUCAGCUUG\n+>cel-miR-40-5p\n+AGUGGAUGUAUGCCAUGAUGAUA\n+>cel-miR-40-3p\n+UCACCGGGUGUACAUCAGCUAA\n+>cel-miR-41-5p\n+GGUGGUUUUUCUCUGCAGUGAUA\n+>cel-miR-41-3p\n+UCACCGGGUGAAAAAUCACCUA\n+>cel-miR-42-5p\n+GUGGGUGUUUGCUUUUUCGGUGAAG\n+>cel-miR-42-3p\n+UCACCGGGUUAACAUCUACAGA\n+>cel-miR-43-5p\n+GACAUCAAGAAACUAGUGAUUAUG\n+>cel-miR-43-3p\n+UAUCACAGUUUACUUGCUGUCGC\n+>cel-miR-44-5p\n+CUGGAUGUGCUCGUUGGUCAUA\n+>cel-miR-44-3p\n+UGACUAGAGACACAUUCAGCU\n+>cel-miR-45-5p\n+CUGGAUGUGCUCGUUAGUCAUA\n+>cel-miR-45-3p\n+UGACUAGAGACACAUUCAGCU\n+>cel-miR-46-5p\n+AAGAGAGCCGUCUAUUGACAGU\n+>cel-miR-46-3p\n+UGUCAUGGAGUCGCUCUCUUCA\n+>cel-miR-47-5p\n+AAGAGAGCAGUCUAUUGACAGU\n+>cel-miR-47-3p\n+UGUCAUGGAGGCGCUCUCUUCA\n+>cel-miR-48-5p\n+UGAGGUAGGCUCAGUAGAUGCGA\n+>cel-miR-48-3p\n+ACAUCCACCAGCCUAGCUCGCA\n+>cel-miR-49-5p\n+CGCAGUUUGUUGUGAUGUGCUCC\n+>cel-miR-49-3p\n+AAGCACCACGAGAAGCUGCAGA\n+>cel-miR-50-5p\n+UGAUAUGUCUGGUAUUCUUGGGUU\n+>cel-miR-50-3p\n+CCCGCAUAUUAGACGUAUCGAC\n+>cel-miR-51-5p\n+UACCCGUAGCUCCUAUCCAUGUU\n+>cel-miR-51-3p\n+CAUGGAAGCAGGUACAGGUGCA\n+>cel-miR-52-5p\n+CACCCGUACAUAUGUUUCCGUGCU\n+>cel-miR-52-3p\n+CACGUUACAAUGAAAGGGUAGC\n+>cel-miR-53-5p\n+CACCCGUACAUUUGUUUCCGUGCU\n+>cel-miR-53-3p\n+CACGGCACAAUAUAUGGGUCGC\n+>cel-miR-54-5p\n+AGGAUAUGAGACGACGAGAACA\n+>cel-miR-54-3p\n+UACCCGUAAUCUUCAUAAUCCGAG\n+>cel-miR-55-5p\n+CGGCAGAAACCUAUCGGUUAUA\n+>cel-miR-55-3p\n+UACCCGUAUAAGUUUCUGCUGAG\n+>cel-miR-56-5p\n+UGGCGGAUCCAUUUUGGGUUGUACC\n+>cel-miR-56-3p\n+UACCCGUAAUGUUUCCGCUGAG\n+>cel-miR-57-5p\n+UACCCUGUAGAUCGAGCUGUGUGU\n+>cel-miR-57-3p\n+ACGAGCUAGACUACAAGGUGCA\n+>cel-miR-58a-5p\n+UGCCCUACUCUUCGCAUCUCAUC\n+>cel-miR-58a-3p\n+UGAGAUCGUUCAGUACGGCAAU\n+>cel-miR-59-5p\n+UCGUCCUGAAAACGAAACGGAA\n+>cel-miR-59-3p\n+UCGAAUCGUUUAUCAGGAUGAUG\n+>cel-miR-60-5p\n+AACUGGAAGAGUGCCAUAAAAUC\n+>cel-miR-60-3p\n+UAUUAUGCACAUUUUCUAGUUCA\n+>cel-miR-61-5p\n+UGGGUUACGGGGCUUAGUCCUU\n+>cel-miR-61-3p\n+UGACUAGAACCGUUACUCAUC\n+>cel-miR-62\n+UGAUAUGUAAUCUAGCUUACAG\n+>cel-miR-63-5p\n+UCUAACUCGUCGGUAGUCAUCGU\n+>cel-miR-63-3p\n+UAUGACACUGAAGCGAGUUGGAAA\n+>cel-miR-64-5p\n+UAUGACACUGAAGCGUUACCGAA\n+>cel-miR-64-3p\n+GUGCAACGAUCAGUGGCAUGC\n+>cel-miR-65-5p\n+UAUGACACUGAAGCGUAACCGAA\n+>cel-miR-65-3p\n+CUGCUACGCGCAGUGCCAUGC\n+>cel-miR-66-5p\n+CAUGACACUGAUUAGGGAUGUGA\n+>cel-miR-66-3p\n+AAAUUCCUAACGGUGUCAAAC\n+>cel-miR-67-5p\n+CGCUCAUUCUGCCGGUUGUUAUG\n+>cel-miR-67-3p\n+UCACAACCUCCUAGAAAGAGUAGA\n+>cel-miR-70-5p\n+CGAAAUACUAUCGACGAAUAACA\n+>cel-miR-70-3p\n+UAAUACGUCGUUGGUGUUUCCAU\n+>cel-miR-71-5p\n+UGAAAGACAUGGGUAGUGAGACG\n+>cel-miR-71-3p\n+UAUCACUAUUCUGUUUUUCGC\n+>cel-miR-72-5p\n+AGGCAAGAUGUUGGCAUAGCUGA\n+>cel-miR-72-3p\n+AGCUUCGCCACAUUCUGCCACG\n+>cel-miR-73-5p\n+UGGACUUCCAUAUCGAGCCACAGC\n+>cel-miR-73-3p\n+UGGCAAGAUGUAGGCAGUUCAGU\n+>cel-miR-74-5p\n+CGGGCUUCCAUCUCUUUCCCAGC\n+>cel-miR-74-3p\n+UGGCAAGAAAUGGCAGUCUACA\n+>cel-miR-75-5p\n+CAGUCGGUUGCAAGCUUAAAUA\n+>cel-miR-75-3p\n+UUAAAGCUACCAACCGGCUUCA\n+>cel-miR-76-5p\n+UGGGCUUCACAAUAGUCGAAUA\n+>cel-miR-76-3p\n+UUCGUUGUUGAUGAAGCCUUGA\n+>cel-miR-77-5p\n+GAUGGUUGUGCUCUGAGGAAAU\n+>cel-miR-77-3p\n+UUCAUCAGGCCAUAGCUGUCCA\n+>cel-miR-78\n+UGGAGGCCUGGUUGUUUGUGC\n+>cel-miR-79-5p\n+CUUUGGUGAUUCAGCUUCAAUGA\n+>cel-miR-79-3p\n+AUAAAGCUAGGUUACCAAAGCU'..b'3p\n+AAACUGUGCAAAGGCUUUUGGG\n+>mdo-miR-12402-5p\n+AUGGCUGAUGUUUGGAGGGUGA\n+>mdo-miR-12402-3p\n+ACCCCUCCUGAUACAGCCAGGACU\n+>mdo-miR-16b-5p\n+UAGCAGCACGUCAAAACUGGAG\n+>mdo-miR-16b-3p\n+CCAGUAUUGCCUUGCUGCUUGA\n+>mdo-miR-7386p-5p\n+AUGUGGAAAAGGUCCUCCAUU\n+>mdo-miR-7386p-3p\n+AAAAGAGGCCCUUGUCCAUAGA\n+>mdo-miR-7371o-5p\n+AGUUGUACCAGAUGUUACCUUU\n+>mdo-miR-7371o-3p\n+AAGGUACUUCCUGUGCAAUAGA\n+>mdo-miR-7371n-5p\n+AGUUGUACCAGGUGUUACAUUU\n+>mdo-miR-7371n-3p\n+AUGAUACAUCUAGUGCAACGGU\n+>mdo-miR-7371q-5p\n+AUUUGGACAAGGUGCUCUGUUU\n+>mdo-miR-7371q-3p\n+AAAAGAGCAUCUUGUCCAUAGA\n+>mdo-miR-7371m-5p\n+AGCUGUACCAGAUGCUACAUUU\n+>mdo-miR-7371m-3p\n+AAAUGUUGCAUCUAGUGCACU\n+>mdo-miR-7371k-5p\n+AGUUGUACCAGAUGCUCGAUUUU\n+>mdo-miR-7371k-3p\n+AACGUUGCGUCUUGUACAAUUG\n+>mdo-miR-7386q-5p\n+AUCUGGACUAUGUUCUUCAAU\n+>mdo-miR-7386q-3p\n+AUAGAAGAAUAAGGUCCAUAGA\n+>mdo-miR-7371l-5p\n+CGUUGUACUAGGUGCUCCAUU\n+>mdo-miR-7371l-3p\n+AACGUUGCAUCUUGUACAAUAGU\n+>mdo-miR-7371p-5p\n+UUUGCACAAGGUGCUCUAUUCUGU\n+>mdo-miR-7371p-3p\n+UGAAGAGCUCCUUGUUCGUAGU\n+>mdo-miR-7373e-5p\n+AAGCCCUUUUUUUUAGCAGUGAGU\n+>mdo-miR-7373e-3p\n+UCAGCUACGAUUGAAGGGCUUGC\n+>mdo-miR-12403-5p\n+UAGCCCUUGCCCUUUUCUGUCUUAG\n+>mdo-miR-12403-3p\n+AAGACAGAAAGUAAGGGUUUGC\n+>mdo-miR-7375c-4-5p\n+UAGCCCUUACCCCCCCAACUAG\n+>mdo-miR-7375c-3p\n+UGUUAGGGAGGGGAAAGGCAUUGC\n+>mdo-miR-7375c-5p\n+UAGCCCUUACCCCCCCGACUAG\n+>mdo-miR-7375e-5p\n+UAGCCCUUACCCCACCAAUUAAU\n+>mdo-miR-7375e-3p\n+UAGAGUGGGGGAAGGUACUGC\n+>mdo-miR-7375d-5p\n+UAGCCCUUACCCCCCCAACUAG\n+>mdo-miR-7375d-3p\n+UAGGGCGGGGAAAGGCAUUG\n+>mdo-miR-7374d-5p\n+AAGCCCUUACCCAUCUAGCUGA\n+>mdo-miR-7374d-3p\n+AGGUAGAGAGGAAGGGGUUGC\n+>mdo-miR-7373f-5p\n+AAGCCCUUUUAUUAAUGAUUGAG\n+>mdo-miR-7373f-3p\n+CAGGCACUAAUAAAGGGUUUAU\n+>mdo-miR-7262i-5p\n+AAAGUCUUUGUGUAGUUUUAAGC\n+>mdo-miR-7262i-3p\n+UUAAACUGUACUAAGACUUUUG\n+>mdo-miR-7394c-5p\n+ACACAUAUGCCCAGGUGACAUG\n+>mdo-miR-7394c-3p\n+UGUGACCUCACCAUAUGUGUU\n+>mdo-miR-7398v-5p\n+UGUGUAGAGGUGGGAAAAUAUGCC\n+>mdo-miR-7398v-3p\n+UAAAUCCUUACCUCUCGCAGU\n+>mdo-miR-7398w-5p\n+UGUGUAGAGCCAAGAAAUACGUCG\n+>mdo-miR-7398w-3p\n+GUAAAUUUCUUGCCUCUCUCAUU\n+>mdo-miR-7398x-3p\n+UAUCUCACCCUCUCUGGCUGU\n+>mdo-miR-7398y-5p\n+UGUGUAGAGGGGGAUGAGGAUGCC\n+>mdo-miR-7398y-3p\n+UAACCUUCCCUUCUCUCACAGU\n+>mdo-miR-12404-5p\n+AGGUGAAGUGACUUGCCAAGGU\n+>mdo-miR-12404-3p\n+CUUAAGCAAGUCCCUUCCCCUCU\n+>mdo-miR-12405-5p\n+UAGUCCCAACUCCGCCACUAAG\n+>mdo-miR-12405-3p\n+UAGUGGAAGAACUGGGAUUAGA\n+>mdo-miR-12406-5p\n+UGAGCUUCCAAUUUGGUUGGA\n+>mdo-miR-12406-3p\n+UUCAACAGAUAGGGCGCUCAU\n+>mdo-miR-12407-5p\n+UGUGCUGCCUCGCUGCCUCAC\n+>mdo-miR-12407-3p\n+AGAGGACACAUGGUGAGCACAU\n+>mdo-miR-12408-5p\n+UUGCAGCCCCCAAGGAGCAG\n+>mdo-miR-12408-3p\n+UUCUCCUUAAGAGACUGCAAGC\n+>mdo-miR-12409-5p\n+UCUGGCCACCAGUUGCUUUCC\n+>mdo-miR-12409-3p\n+AGGAAGGGAGCUGUUGGCCCC\n+>mdo-miR-12366b-5p\n+CCUGCAGCUCUGAGAUUCUAUG\n+>mdo-miR-12366b-3p\n+UCAUAGAGUGUUAGUGCUGGGA\n+>mdo-miR-12410-5p\n+AAGGAAACUGAGAUCCAGGAGG\n+>mdo-miR-12411-3p\n+UCCUCUCUUGUCUCCUGGCAG\n+>mdo-miR-12412-5p\n+UGGAGGGCUCGAAGAUCUUGGA\n+>mdo-miR-12412-3p\n+GUCCAAGAACUCGGCCUCCCCC\n+>aga-miR-12413-3p\n+UAUGACUUGUCUGCCAGAGCAAGGGG\n+>aga-miR-12414-3p\n+AAGACGCUGGUUCUCUUCACACA\n+>aga-miR-12415-3p\n+CGAUUGUGGAACCGCGUAGGCUGCCU\n+>aga-miR-12416-3p\n+UGACGGGUUUGGUCUCUCCA\n+>aga-miR-12417-5p\n+UAGUCGUUUUCUGCUUUGCGGUU\n+>aga-miR-12418-3p\n+UGUUCGAUCGUUACUGUCAUAU\n+>aga-miR-12419-5p\n+AGCUGUUCUGACUUGAUGUACU\n+>smc-miR-12455-5p\n+CUGUGACCGUCCCAUCCUUGCG\n+>smc-miR-12455-3p\n+CAAGGAUGGGAUGCUCAGAGAA\n+>smc-miR-12456-5p\n+CCUCGUCGUCUGCUCUUUGAGC\n+>smc-miR-12456-3p\n+UCAGAGACCAGACGCAGAGGCU\n+>smc-miR-12457-5p\n+CUUUGUAUCCCGGAUCCUGAUA\n+>smc-miR-12457-3p\n+UCAAGACCCGGGAUAUAUAUGU\n+>smc-miR-12455-2-3p\n+CAAGGAUGGGAUGGUCAGAGAA\n+>smc-miR-12458-5p\n+CAGUCGGCCAAAGUGCUGGACC\n+>smc-miR-12458-3p\n+UCCAGCACUUUGGCUGUCUGCC\n+>smc-miR-12459-5p\n+UACCGUCCCUGAGAGUUCAAUG\n+>smc-miR-12459-3p\n+UCGAACUUUCAGGAAUAGUAUC\n+>smc-miR-12460-5p\n+UCAGUGGCAGAAGCUGGGAACU\n+>smc-miR-12460-3p\n+UUCCCAGCUUGUGCCACUGAAA\n+>smc-miR-12461-5p\n+GAGGAUGCUGAUCAUUCACUGG\n+>smc-miR-12461-3p\n+AGUAAAUGAUCAGCAUCCUCCA\n+>gga-miR-1784b-5p\n+UUCUGCUCCUAUUUAAGUCAAU\n+>gga-miR-1784b-3p\n+UGAUUUCAAUAAGAGCAGAAUU\n+>mdo-miR-7385g-3p\n+AGCAUAGAAUGUCAGAUCUAG\n+>mdo-miR-7385g-2-3p\n+AGCAUAGAAUGUCAGGUCUAG\n' |