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Changeset 0:b8496cb0d3d9 (2019-03-18)

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diff -r 000000000000 -r b8496cb0d3d9 paqmir_postprocess_quantifier/parse_miRDeep2_output.pl
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/paqmir_postprocess_quantifier/parse_miRDeep2_output.pl Mon Mar 18 09:31:00 2019 -0400

[

b'@@ -0,0 +1,520 @@\n+#!/usr/bin/perl \n+#\n+# parse_miRDeep2_output.pl\n+#\n+# Copyright 2019 Sylvain Marthey <sylvain.marthey@inra.fr>\n+# \n+# This program is free software; you can redistribute it and/or modify\n+# it under the terms of the GNU General Public License as published by\n+# the Free Software Foundation; either version 3 of the License, or\n+# (at your option) any later version.\n+# \n+# This program is distributed in the hope that it will be useful,\n+# but WITHOUT ANY WARRANTY; without even the implied warranty of\n+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n+# GNU General Public License for more details.\n+# \n+# You should have received a copy of the GNU General Public License\n+# along with this program; if not, see <http://www.gnu.org/licenses/>.\n+\n+# v1.2 -> v 1.3 : - correct a bug in new precursors annotation (in version 1.2 the know miRNA where not priority over the putatives matures )\n+# - add new informatiosn in log file concerning the new precursors annotations\n+# v1.3 -> v 1.4 15/10/2015 : - correct a bug in precursor shape detection (previously pre likeb ta-chrUn_GJ059918v1_46266 not allowed)\n+\n+use strict;\n+use Getopt::Long;\n+use Pod::Usage;\n+# use Data::Dumper;\n+\n+my ($help,$mature_arf,$expression_file,$debug,$EXP,$structure,$man);\n+\n+# on recupere les options\n+GetOptions("help|?" => \\$help,\n+\t "man" => \\$man,\n+ "mature_arf:s" => \\$mature_arf,\n+ "debug:s" => \\$debug,\n+\t "expression_file:s" => \\$expression_file,\n+\t "structure_file:s" => \\$structure\n+ )\n+or\n+pod2usage(-message=>"Try `$0\' for more information.", -exitval => 2,-verbose=> 0);\n+\n+pod2usage(-exitval =>1, -verbose => 2) if ($help);\n+# on test si les parametres ont bien ete rentres\n+if ($expression_file eq "-" ) {\n+ $EXP = "STDIN";\n+} else {\n+ open($EXP, "< $expression_file") or pod2usage(-message=>"--expression_file parameter missing or is not a valid file path.Try `$0 --help\' for more information.",\n+ -exitval => 2,-verbose=> 0);\n+}\n+ \n+if ($mature_arf eq "" || !-f($mature_arf))\n+ {\n+ pod2usage(-message=>"--mature_arf parameter missing or is not a valid file path.\\nTry `$0 --help\' for more information.",\n+ -exitval => 2,-verbose=> 0);\n+ }\n+if ($structure eq "" || !-f($structure))\n+ {\n+ pod2usage(-message=>"--structure_file parameter missing or is not a valid file path.\\nTry `$0 --help\' for more information.",\n+ -exitval => 2,-verbose=> 0);\n+ }\n+ \n+my $pre_shape = qr/(\\w{3})-([^-]+(-|_)\\d+)_?([a-z]{0,2})(-\\d{1,2})?/; # mirbase v19 mmu-mir-181a-1 || mmu-X_157_mt-1\n+# old v1.3 my $putatif_pre_shape = qr/(\\w{3})-([^_]+_\\d+)(-\\d{1,2})?/; # mirDeep2 species + putatif ID + location\n+my $putatif_pre_shape = qr/(\\w{3})-([^_]+(_\\w+)?_\\d+)(-\\d{1,2})?/; # mirDeep2 species + putatif ID + location (bta-chr3_34604 || bta-chr3_34604 || bta-chrUn_GJ059918v1_46266)\n+\n+my $mature_shape = qr/(\\w{3})-([^-]+(-|_)\\d+)(_[a-z]{0,2})?([a-z]{0,2})(-\\d{1,2})?(-\\d{1}p)?/; # mirbase v19 ex: mmu-miR-181a-1-3p || mmu-X_157_mt-1-3p\n+# old v1.2 $mature_shape = qr/(\\w{3})-([^-]+(-|_)\\d+)_?([a-z]{0,2})(-\\d{1,2})?(-\\d{1}p)?/;\n+\n+my %pre_arf;\n+my %matures_arf;\n+my %seqs;\n+my $id;\n+\n+print STDERR "Read the structure file mapping file $structure file.\\n";\n+# lecture du fichier de structure pour r\xc3\xa9cup\xc3\xa9rer les s\xc3\xa9quences des pr\xc3\xa9curseurs\n+open(STR,$structure) or die "impossible d\'ouvrir le fichier $structure\\n";\n+while(<STR>){\n+ if(/^\\>(\\S+)/){\n+ $id = $1;\n+ }elsif(/^pri_seq\\s+(\\S+)/){\n+ $seqs{$id}{"pri_seq"}=$1;\n+ }\n+}\n+close STR;\n+\n+print STDERR "Read the mature mapping file $mature_arf.\\n";\n+# lecture du fichier de mapping des matures sur les pre\n+open(ARF,$mature_arf) or die "impossible d\'ouvrir le fichier $mature_arf\\n";\n+while(<ARF>){\n+\tmy @line =split(/\\t/,$_);\n+\tif($line[0] =~ /^$mature_shape$/){\n+# \t\tif($debug){print '..b'ition\n+\t\t\t}elsif($$cur_mature{pos}){\n+\t\t\t\t# if the previous don(t have the name, the species and position\n+\t\t\t\tif((lc($$previous_mature{name}) ne lc($$cur_precursor{pre_name}) && (lc($$previous_mature{spec}) ne lc($$cur_precursor{spec})) && (!$$previous_mature{pos}))){\n+\t\t\t\t\t$assign_current++;\n+\t\t\t\t}\n+\t\t\t}\n+\t\t}\t\n+\t} \n+\tif($assign_current){\n+\t\t$$prec{$cur_pre}{"-".$put_pos} = $cur_ct;\n+\t\t$$prec{$cur_pre}{"-".$put_pos."_N"} = $$cur_precursor{pre_name};\n+\t\t$$prec{$cur_pre}{$put_pos} = $cur_mat;\n+\t}\n+# \tif($debug){print " assignation result : $assign_current\\n"};\n+ }\n+ \n+ sub parse_mature_id {\n+\tmy $id = shift;\n+\tmy $mir;\n+\t\n+# \tif($debug){print "parse_mature_id $id\\n"};\n+\t\n+\tif($id =~ /^$mature_shape$/){\n+\t\t$$mir{mir_id} = $1.$2.$4.$5;\n+\t\t$$mir{long_mature_id} = $1.$2.$4.$5.$6;\n+\t\t$$mir{pos}=$7;\n+\t\t$$mir{spec}=$1;\n+\t\t$$mir{name}= $2.$5.$6;\n+\t\tif($4 ne ""){\n+\t\t\t$$mir{is_putatif}=1;\n+\t\t}\n+# \t\tif($debug){print "debug 1:$1 2:$2 3:$3 4:$4 5:$5 6:$6 7:$7 \\n"};\n+\t}else{\n+\t\tprint STDERR "! ".$id." n\'a pas une forme de mature reconnue -> skip line $_ \\n";\n+\t}\n+\treturn $mir;\n+ }\n+ \n+ sub parse_precursor_id {\n+\tmy $id = shift;\n+\tmy $precursor;\n+\t\n+# \tif($debug){print "parse_precursor_id $id\\n"};\n+\t\n+\t# read the pre id \n+\tif($id =~ /^$pre_shape$/){\n+\t\t$$precursor{pre_prefix} = $1.$2.$4;\n+\t\t$$precursor{long_pre_prefix}= $1.$2.$4.$5;\n+\t\t$$precursor{pre_name} = $2.$4.$5;\n+\t\t$$precursor{spec}=$1;\n+# \t\tif($debug){print "id: ".$id." pre_prefix: ".$$precursor{pre_prefix}." long_pre_prefix: ".$$precursor{long_pre_prefix}." pre_name: ".$$precursor{pre_name}." spec: ".$$precursor{spec}."\\n";}\n+\t}else{\n+\t\tprint STDERR "! ".$id." n\'a pas une forme de pre reconnue -> skip line $_ \\n";\n+\t}\n+\treturn $precursor;\n+ }\n+ \n+=pod\n+\n+=head1 NAME\n+\n+parse_miRDeep2_output.pl\n+\n+=head1 SYNOPSIS\n+\n+parse_miRDeep2_output.pl --mature_arf <.arf file> --expression_file <.csv file> --structure_file <.mrd file> \n+\n+=head1 DESCRIPTION\n+\t\n+\tparse_miRDeep2_output.pl assigns mature miRNAs to a set of precursors, and report the quantification of the best two mature (3p & 5p predicted from their position on the precursor) observed for each precursor.\n+\t\n+\tThis script reads the output files provided by the quantifier.pl module from miRdeep2 and assigns the matures to the precursors by using the following order of priority:\n+\t\n+\t\t- Mature known in the species studied (generaly all matures from miRBase known for the species are used)\n+\t\t\n+\t\t- Mature known in another species (all mature from miRBase, or only those corresponding to a subset of closely related species are used). In case where several mature are detected, mature with the highest count is chosen.\n+\t\t\n+\t\t- Mature unknown (generaly matures predicted by miRDeep2.pl module are used)\n+\t\n+\t# attempted know mature id should have following shape : (\\w{3})(-[^-]+-\\d+)([a-z]{0,2})([.-]\\d{1,2})?(-\\d{1}p)? (ex : mmu-mir-181a-1)\n+\t# attempted know precursor id should have following shape : (\\w{3})(-[^-]+-\\d+)([a-z]{0,2})(-\\d{1,2})? (ex : mmu-miR-181a-1-3p)\n+\t# attempted putatif mature id should have following shape : (ex : mmu-26_25392-1-5p )\n+\t# attempted putatif precursor id should have following shape : (\\w{3})(-[^_]+_\\d+)(-\\d{1,2}) (ex : mmu-26_25392-1 )\n+\n+Options:\n+\n+\t--mature_arf\t: path to the file mature_XXX_mapped.arf (provided by the miRDeep2 quantifier.pl module)\n+\n+\t--expression_file\t: path to the file miRNAs_expressed_all_samples_XXX.csv (provided by the miRDeep2 quantifier.pl module)\n+\n+\t--structure_file\t: path to the miRBase.mrd file (provided by the miRDeep2 quantifier.pl module, can be found in the folder expression_analyses_XXX)\n+ \n+=head1 AUTHORS\n+\n+Sylvain Marthey <sylvain.marthey@inra.fr>\n+\n+=head1 VERSION\n+\n+1.4\n+\n+=head1 DATE\n+\n+2019\n+\n+=head1 KEYWORDS\n+\n+miRNA, miRDeep2, annotation, quantification\n+\n+=head1 EXAMPLE\n+\n+parse_miRDeep2_output --mature_arf mature_mapped.arf --expression_file miRNAs_expressed_all_samples_1372870072.csv --structure_file miRBase.mrd\n+\n+=cut\n\\ No newline at end of file\n'

diff -r 000000000000 -r b8496cb0d3d9 paqmir_postprocess_quantifier/postprocess_quantifier.sh
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/paqmir_postprocess_quantifier/postprocess_quantifier.sh Mon Mar 18 09:31:00 2019 -0400

[

@@ -0,0 +1,89 @@
+#!/bin/bash
+
+####filtering results of quantifier####
+errorcode=0
+directory=`dirname $0`
+
+if [ $4 = "no" ] # check if option filter is false
+then
+ cmd0="$directory/parse_miRDeep2_output.pl --mature_arf ${3} --structure_file ${2} --expression_file ${1} > miRNAs_expressed_all_samples.pre_uniq.csv" #command used if there is not filter, assigns mature miRNAs to a set of precursors, and report the quantification of the best two mature (3p & 5p predicted from their position on the precursor) observed for each precursor.
+fi
+
+if [ $4 = "yes" ] # check if option filter is true
+then
+ cmd1="perl -p -e 's/(\d+)\.(\d{2})/\1\,\2/g' ${1} > temp_output" # change number format
+ echo "change decimal separator (if needed):"
+ echo $cmd1 #display the command used in stdout output
+ (eval "$cmd1") #execute the command 1
+ ((errorcode+=$?)) ##check the run of commands
+ if [ $errorcode -gt 0 ] ; then exit 1 ; fi ##check the run of commands
+
+ condition="awk -F '\t' '\$4>=${6}" #create filter
+ i=2
+ #echo "i : ${i}"
+ while [ $i -le ${5} ]
+ do
+ n=$(( $i+4 )) #use to know the column in file ${1}
+ #echo "n : ${n}"
+ condition=${condition}" || \$${n}>=${6}" #add informations for the condition
+ i=$(( $i+1 )) #incrementing of number to arrive at number of condition
+ #echo "nouveau i : ${i}"
+ done
+ echo "condition : ${condition}" #display the condition used in stdout output
+ cmd2=${condition}"' temp_output > temp_output2" #finish the command
+ echo "apply condition to results:"
+ echo $cmd2
+ (eval "$cmd2")
+ ((errorcode+=$?)) ##check the run of commands
+ if [ $errorcode -gt 0 ] ; then exit 1 ; fi ##check the run of commands
+
+ cmd0="$directory/parse_miRDeep2_output.pl --mature_arf ${3} --structure_file ${2} --expression_file temp_output2 > miRNAs_expressed_all_samples.pre_uniq.csv" #command used if there is not filter, assigns mature miRNAs to a set of precursors, and report the quantification of the best two mature (3p & 5p predicted from their position on the precursor) observed for each precursor.
+
+fi
+
+echo "Use perl script to parse results and proceed annotation"
+echo $cmd0
+
+#(eval "$cmd0") 2>>tableau_recapitulatif #execute the command 0 in a summary table ##redirect to log
+(eval "$cmd0") 2>>annotation_statistics.txt #execute the command 0
+((errorcode+=$?)) ##check the run of commands
+if [ $errorcode -gt 0 ] ; then exit 1 ; fi ##check the run of commands
+
+#add header line to results files#
+cmd3="head -n 1 miRNAs_expressed_all_samples.pre_uniq.csv > head_miRNAs_expressed_all_samples.pre_uniq.csv" #recover the first line in the file miRNAs_expressed_all_samples.pre_uniq.csv in the file head_miRNAs_expressed_all_samples.pre_uniq.csv
+cmd4="perl -p -e 's/\#//' head_miRNAs_expressed_all_samples.pre_uniq.csv > miRNAs_expressed_all_samples.pre_uniq.matureSEQ_uniq.csv" #modify the first line and create the file miRNAs_expressed_all_samples.pre_uniq.matureSEQ_uniq.csv
+cmd5="perl -p -e 's/\#//' head_miRNAs_expressed_all_samples.pre_uniq.csv > miRNAs_expressed_all_samples.pre_uniq.matureID_uniq.csv" #modify the first line and create the file miRNAs_expressed_all_samples.pre_uniq.matureID_uniq.csv
+
+echo $cmd3 #display the command used in stdout output
+echo $cmd4 #display the command used in stdout output
+echo $cmd5 #display the command used in stdout output
+
+(eval "$cmd3") #execute the command 3
+((errorcode+=$?))
+(eval "$cmd4") #execute the command 4
+((errorcode+=$?))
+(eval "$cmd5") #execute the command 5
+((errorcode+=$?)) ##check the run of commands
+if [ $errorcode -gt 0 ] ; then exit 1 ; fi ##check the run of commands
+
+
+#mature sequence uniq#
+n=5+${5}*2+1 #use to know the number of the last column
+
+cmd6="grep -v 'read_count' miRNAs_expressed_all_samples.pre_uniq.csv | awk -F '\t' '{if(\$2 > count[\$${n}]){infos[\$${n}] = \$0;count[\$${n}]=\$2}} END {for (var in infos){print infos[var]}}' >> miRNAs_expressed_all_samples.pre_uniq.matureSEQ_uniq.csv" #recuperate mirna and add sequences of matures mirna
+
+echo $cmd6 #display the command used in stdout output
+
+(eval "$cmd6")
+((errorcode+=$?)) ##check the run of commands
+if [ $errorcode -gt 0 ] ; then exit 1 ; fi ##check the run of commands
+
+mature id uniq#
+cmd7="grep -v 'read_count' miRNAs_expressed_all_samples.pre_uniq.csv | perl -p -e 's/(\d+)\,(\d{2})/\1\.\2/g' | awk -F '\t' '{if(\$2 > count[\$1]){infos[\$1] = \$0;count[\$1]=\$2}} END {for (var in infos){print infos[var]}}' >> miRNAs_expressed_all_samples.pre_uniq.matureID_uniq.csv"
+
+echo $cmd7 #display the command used in stdout output
+
+(eval "$cmd7") #execute the command 7
+((errorcode+=$?)) ##check the run of commands
+if [ $errorcode -gt 0 ] ; then exit 1 ; fi ##check the run of commands
+

diff -r 000000000000 -r b8496cb0d3d9 paqmir_postprocess_quantifier/postprocess_quantifier.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/paqmir_postprocess_quantifier/postprocess_quantifier.xml Mon Mar 18 09:31:00 2019 -0400

[

@@ -0,0 +1,88 @@
+<tool id="paqmir_postprocess_quantifier" name="PAQmiR Postprocess Quantifier" version="1.0.0">
+ <description>filters results to quantify, annotate, and eliminate redundancy in miRNAs</description>
+ <stdio>
+            
+            <exit_code range="1:" />
+            <exit_code range=":-1" />
+            
+            <regex match="Error:" />
+            <regex match="Exception:" />
+        </stdio>
+ <command interpreter="bash">
+ <![CDATA[
+ postprocess_quantifier.sh $res_quantifier $miRBase $mature_and_new_mapped $option.filtre $nbCondition
+                #if $option.filtre=="yes"
+ $option.valeur_filtre
+                #else
+ 1
+ #end if
+ ]]>
+ </command>
+        <inputs>
+ <param name="res_quantifier" format="tabular" type="data" label="Quantification file" help="Tabular quantification file from Quantifier"/>
+ <param name="miRBase" format="tabular" type="data" label="MiRBase.mrd file" help="MiRBase.mrd file from Quantifier"/>
+ <param name="mature_and_new_mapped" format="tabular" type="data" label="MiRNA mapping" help="Reference matures against precursors. Mapping file from quantifier in ARF format"/>
+ <param name="nbCondition" format="txt" size="30" value="1" type="integer" min="1" max="99" label="Total number of sample processed" help="Number of read sets used in the initial mapping step (Mapper)"/>
+ <conditional name="option">
+                        <param name="filtre" type="boolean" truevalue="yes" falsevalue="no" label="Apply read count filter?"/>
+ <when value="no">
+ </when>
+ <when value="yes">
+ <param name="valeur_filtre" format="txt" size="30" value="1" type="integer" label="Minimal read count" help="Minimal read count per sample"/>
+ </when>
+ </conditional>
+ </inputs>
+ <outputs>
+ <data name="miRNAs_expressed_all_samples.pre_uniq" format="tabular" from_work_dir="miRNAs_expressed_all_samples.pre_uniq.csv" label="miRNAs_expressed_all_samples.pre_uniq.csv"/>
+ <data name="miRNAs_expressed_all_samples.pre_uniq.matureSEQ_uniq" format="tabular" from_work_dir="miRNAs_expressed_all_samples.pre_uniq.matureSEQ_uniq.csv" label="miRNAs_expressed_all_samples.pre_uniq.matureSEQ_uniq.csv"/>
+ <data name="annotation_statistics" format="txt" from_work_dir="annotation_statistics.txt" label="annotation_statistics.txt"/>
+ </outputs>
+        
+ <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 assigns mature miRNAs to a set of precursors, and report the quantification of the best two mature (3p & 5p predicted from their position on the precursor) observed for each precursor.
+The module uses output files provided by the quantifier.pl module from miRdeep2 and assigns the matures to the precursors by using the following order of priority:
+
+ | - Mature known in the species studied (generaly all matures from miRBase known for the species are used)
+        | - Mature known in another species (all mature from miRBase, or only those corresponding to a subset of closely related species are used). In case where several mature are detected, mature with the highest count is chosen.
+        | - Mature unknown (generaly matures predicted by miRDeep2.pl module are used)
+
+**Input**
+
+ | - Standard results file of Quantifier
+        | - MiRBase.mrd file produced by Quantifier
+ | - Mapping of miRNAs file
+
+**Output**
+
+ | - Quantification pre_uniq file :  tabular file containing the quantification of the two tbest matures (3p & 5p) observed for each precursor.
+ | - Quantification matureSeq_uniq file : tabular subpart of file pre_uniq containing only one quantification per mature sequence.
+ | - Annotation statistics : Txt file containing statistics about annotation process
+]]>
+ </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>

diff -r 000000000000 -r b8496cb0d3d9 paqmir_postprocess_quantifier/test-data/annotation_statistics.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/paqmir_postprocess_quantifier/test-data/annotation_statistics.txt Mon Mar 18 09:31:00 2019 -0400

@@ -0,0 +1,40 @@
+Read the structure file mapping file /projet/galaxydev/galaxy/database/files/042/dataset_42936.dat file.
+Read the mature mapping file /projet/galaxydev/galaxy/database/files/042/dataset_42937.dat.
+! oha-miR-451-?? n'a pas une forme de mature reconnue
+! dre-miR-29b3-3p n'a pas une forme de mature reconnue
+! dre-miR-29b3-3p n'a pas une forme de mature reconnue
+# 11463 matures mapped to the 1067 precursor
+
+Read the expression file /projet/galaxydev/galaxy/database/files/042/dataset_42934.dat.
+
+Print the results.
+######################## General statistics precursors ############
+
+# Total number of presursors in file: 1067
+
+######################## Know precursors ############
+
+# Total number of Know presursors : 1064
+# nb pre with know 5p and 3p mature detected : 87
+# nb pre with only know 5p mature detected : 480
+# nb pre with only know 3p mature detected : 497
+# nb pre with know 5p mature detected and annoted 3p detected (by homologie with mature from other species) : 0
+# nb pre with know 3p mature detected and annoted 5p detected (by homologie with mature from other species) : 0
+
+######################## putatifs precursors ############
+
+# Total number of putatifs presursors : 3
+# nb putative pre with 5p and 3p mature detected : 3
+# ---- nb putative pre with annoted 5p and 3p mature detected : 0
+# ---- nb putative pre with annoted 5p and new putatif 3p mature detected : 0
+# ---- nb putative pre with new putatif 5p and annoted 3p mature detected : 0
+# ---- nb putative pre with new putatif 5p and 3p mature detected : 3
+
+# nb putative pre with only 5p mature detected : 0
+# ---- nb putative pre with only annoted 5p mature detected : 0
+# ---- nb putative pre with only new putatif 5p mature detected : 0
+
+# nb putative pre with only 3p mature detected : 0
+# ---- nb putative pre with only annoted 3p mature detected : 0
+# ---- nb putative pre with only new putatif 3p mature detected : 0
+

diff -r 000000000000 -r b8496cb0d3d9 paqmir_postprocess_quantifier/test-data/matures_and_new_predicted_matures.fa_mapped.arf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/paqmir_postprocess_quantifier/test-data/matures_and_new_predicted_matures.fa_mapped.arf Mon Mar 18 09:31:00 2019 -0400

b'@@ -0,0 +1,22665 @@\n+>bta-chr25_10\n+total read count \n+bta-chr25_10_st read count 0\n+bta-chr25_10_mt read count 0\n+remaining read count 0\n+exp MMMMMMMMMMMMMMffffffffffffffffffffffffffffffffffffffffffffffffffffffffMMMMMMMMMM\n+pri_seq ggcagcggagcggggagcgcagggcagggcgggggggggggaauccuccccauuguuauguuggcuccucccagcaaccc\n+pri_struct ((..((((...(((((((.((..(((.(((((.(((((((....))))))).))))).)))))))))))))).))..)).\t#MM\n+\n+\n+\n+>bta-chr25_114\n+total read count \n+bta-chr25_114_st read count 0\n+bta-chr25_114_mt read count 0\n+remaining read count 0\n+exp MMMMMMMMMMMffffffffffffffffffffffffffffffffffffffffffffffffffffffMMMMMMMMMMM\n+pri_seq cuuccucuagccacuugcagaaccacgcggcgcucucaggcgguugaccaucaguguagguggcaaccaggaaggc\n+pri_struct ((((((...((((((((((........(((((((....))).))))........))))))))))....))))))..\t#MM\n+\n+\n+\n+>bta-chr25_36\n+total read count \n+bta-chr25_36_mt read count 0\n+bta-chr25_36_mt read count 0\n+bta-chr25_36_mt read count 0\n+bta-chr25_36_mt read count 0\n+bta-chr25_36_st read count 0\n+remaining read count 0\n+exp MMMMMMMMMMMMMMMMMMMMMffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffMMMMMMMMMMM\n+pri_seq gaggaggaggaggaggaggagggagagggaggggacagcaaccagagcgcugaugggacgcugucccuuuaagaggauccagcagguucccugcuguc\n+pri_struct .((.(((.(((...(..(((........(((((((((((..(((.........)))...))))))))))).......)))..)...)))))).))...\t#MM\n+\n+\n+\n+>bta-let-7a-1\n+total read count 453\n+bta-let-7a-5p read count 345\n+bta-let-7a-3p read count 96\n+remaining read count 12\n+exp fffff5555555555555555555555fffffffffffffffffffffffffffff333333333333333333333fff\n+pri_seq ugggaugagguaguagguuguauaguuuuagggucacacccaccacugggagauaacuauacaaucuacugucuuuccua\n+pri_struct (((((.(((((((((((((((((((((.....(((...((((....)))).)))))))))))))))))))))))))))))\t#MM\n+S01_18725_x2 .....ugagguaguagguuguauag.......................................................\t0\n+S01_29561_x1 .....ugagguaguagUuuguauag.......................................................\t1\n+S03_31777_x1 .....ugagguaguagUuuguauag.......................................................\t1\n+S03_21311_x2 .....ugagguaguagguuguauag.......................................................\t0\n+S02_18343_x2 .....ugagguaguagguuguauag.......................................................\t0\n+S02_46304_x1 .....ugagguaguagUuuguauag.......................................................\t1\n+S02_15078_x4 .....ugagguaguUgguuguauagu......................................................\t1\n+S01_5027_x23 .....ugagguaguagguuguauagu......................................................\t0\n+S02_4958_x23 .....ugagguaguagguuguauagu......................................................\t0\n+S03_4912_x23 .....ugagguaguagguuguauagu......................................................\t0\n+S01_15426_x4 .....ugagguaguUgguuguauagu......................................................\t1\n+S03_15698_x4 .....ugagguaguUgguuguauagu......................................................\t1\n+S03_19035_x2 .....ugagguaguagguuguauaguA..'..b'.......................................caagcucgcuucuaugggucug..........\t0\n+S01_41987_x1 .................................................caagcucgUuucuaugggucug..........\t1\n+S03_24797_x1 .................................................caagcucgUuucuaugggucug..........\t1\n+S02_18355_x2 .................................................caagcucgcuucuaugggucugu.........\t0\n+S01_18329_x2 .................................................caagcucgcuucuaugggucugu.........\t0\n+S03_18827_x2 .................................................caagcucgcuucuaugggucugu.........\t0\n+S02_47421_x1 ..................................................aagcucgcuucuaugggucug..........\t0\n+S01_27611_x1 ..................................................aagcucgcuucuaugggucug..........\t0\n+S02_40425_x1 ..................................................aagcucgUuucuaugggucug..........\t1\n+S03_28682_x1 ..................................................aagcucgcuucuaugggucug..........\t0\n+S01_34383_x1 ..................................................aagcucgUuucuaugggucug..........\t1\n+S03_26685_x1 ..................................................aagcucgUuucuaugggucug..........\t1\n+\n+\n+\n+>bta-mir-99b\n+total read count 66\n+bta-miR-99b read count 42\n+remaining read count 24\n+exp ffffffMMMMMMMMMMMMMMMMMMMMMMffffffffffffffffffffffffffffffffffffffffff\n+pri_seq ggcacccacccguagaaccgaccuugcggggccuucgccgcacacaagcucgugucuguggguccguguc\n+pri_struct (((((..(((((((((..(((.((((.(.(((....))).)...)))).)))..)))))))))..)))))\t#MM\n+S02_8299_x13 ......cacccguagaaccgaccuugcg..........................................\t0\n+S03_8143_x13 ......cacccguagaaccgaccuugcg..........................................\t0\n+S01_8104_x13 ......cacccguagaaccgaccuugcg..........................................\t0\n+S01_34867_x1 ......cacccguagaaccgaccuugcgggg.......................................\t0\n+S03_45675_x1 ......cacccguagaaccgaccuugcgggg.......................................\t0\n+S02_23735_x1 ......cacccguagaaccgaccuugcgggg.......................................\t0\n+S02_41510_x1 ............................................caagcucgugucuguggguc......\t0\n+S01_39672_x1 ............................................caagcucgugucuguggguc......\t0\n+S03_37814_x1 ............................................caagcucgugucuguggguc......\t0\n+S02_13620_x5 ............................................caagcucgugucuguggguccg....\t0\n+S03_14090_x5 ............................................caagcucgugucuguggguccg....\t0\n+S01_14150_x5 ............................................caagcucgugucuguggguccg....\t0\n+S01_43335_x1 ............................................caagcucgugucuguggguccgu...\t0\n+S03_40277_x1 ............................................caagcucgugucuguggguccgu...\t0\n+S02_35348_x1 ............................................caagcucgugucuguggguccgu...\t0\n+S01_33670_x1 .............................................aagcucgugucuguggguccg....\t0\n+S03_34308_x1 .............................................aagcucgugucuguggguccg....\t0\n+S02_32434_x1 .............................................aagcucgugucuguggguccg....\t0\n+\n+\n+\n'

diff -r 000000000000 -r b8496cb0d3d9 paqmir_postprocess_quantifier/test-data/miRBase.mrd
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/paqmir_postprocess_quantifier/test-data/miRBase.mrd Mon Mar 18 09:31:00 2019 -0400

b'@@ -0,0 +1,14136 @@\n+bta-chr25_10_mt\t14\t1\t14\tggcagcggagcggg\tbta-chr25_10\t14\t1\t14\tggcagcggagcggg\t+\t0\tmmmmmmmmmmmmmm\n+bta-chr25_36_mt\t12\t1\t12\tgaggaggaggag\tbta-chr25_36\t12\t10\t21\tgaggaggaggag\t+\t0\tmmmmmmmmmmmm\n+bta-chr25_36_mt\t12\t1\t12\tgaggaggaggag\tbta-mir-10176\t12\t7\t18\tgaggaggaggag\t+\t0\tmmmmmmmmmmmm\n+bta-chr25_36_mt\t12\t1\t12\tgaggaggaggag\tbta-chr25_36\t12\t1\t12\tgaggaggaggag\t+\t0\tmmmmmmmmmmmm\n+bta-chr25_36_mt\t12\t1\t12\tgaggaggaggag\tbta-chr25_36\t12\t4\t15\tgaggaggaggag\t+\t0\tmmmmmmmmmmmm\n+bta-chr25_36_mt\t12\t1\t12\tgaggaggaggag\tbta-chr25_36\t12\t7\t18\tgaggaggaggag\t+\t0\tmmmmmmmmmmmm\n+bta-chr25_114_mt\t11\t1\t11\taccaggaaggc\tbta-chr25_114\t11\t66\t76\taccaggaaggc\t+\t0\tmmmmmmmmmmm\n+bta-chr25_10_st\t10\t1\t10\tccagcaaccc\tbta-chr25_10\t10\t71\t80\tccagcaaccc\t+\t0\tmmmmmmmmmm\n+bta-chr25_36_st\t11\t1\t11\ttccctgctgtc\tbta-chr25_36\t11\t88\t98\ttccctgctgtc\t+\t0\tmmmmmmmmmmm\n+bta-chr25_114_st\t11\t1\t11\tcttcctctagc\tbta-chr25_114\t11\t1\t11\tcttcctctagc\t+\t0\tmmmmmmmmmmm\n+cel-let-7-5p\t22\t1\t22\ttgaggtagtaggttgtatagtt\tbta-let-7a-2\t22\t5\t26\ttgaggtagtaggttgtatagtt\t+\t0\tmmmmmmmmmmmmmmmmmmmmmm\n+cel-let-7-5p\t22\t1\t22\ttgaggtagtaggttgtatagtt\tbta-let-7a-3\t22\t4\t25\ttgaggtagtaggttgtatagtt\t+\t0\tmmmmmmmmmmmmmmmmmmmmmm\n+cel-let-7-5p\t22\t1\t22\ttgaggtagtaggttgtatagtt\tbta-let-7a-1\t22\t6\t27\ttgaggtagtaggttgtatagtt\t+\t0\tmmmmmmmmmmmmmmmmmmmmmm\n+cel-miR-1-3p\t21\t1\t21\ttggaatgtaaagaagtatgta\tbta-mir-1-1\t21\t49\t69\ttggaatgtaaagaagtatgta\t+\t0\tmmmmmmmmmmmmmmmmmmmmm\n+cel-miR-1-3p\t21\t1\t21\ttggaatgtaaagaagtatgta\tbta-mir-1-2\t21\t53\t73\ttggaatgtaaagaagtatgta\t+\t0\tmmmmmmmmmmmmmmmmmmmmm\n+hsa-let-7a-5p\t22\t1\t22\ttgaggtagtaggttgtatagtt\tbta-let-7a-1\t22\t6\t27\ttgaggtagtaggttgtatagtt\t+\t0\tmmmmmmmmmmmmmmmmmmmmmm\n+hsa-let-7a-5p\t22\t1\t22\ttgaggtagtaggttgtatagtt\tbta-let-7a-2\t22\t5\t26\ttgaggtagtaggttgtatagtt\t+\t0\tmmmmmmmmmmmmmmmmmmmmmm\n+hsa-let-7a-5p\t22\t1\t22\ttgaggtagtaggttgtatagtt\tbta-let-7a-3\t22\t4\t25\ttgaggtagtaggttgtatagtt\t+\t0\tmmmmmmmmmmmmmmmmmmmmmm\n+hsa-let-7a-3p\t21\t1\t21\tctatacaatctactgtctttc\tbta-let-7a-1\t21\t57\t77\tctatacaatctactgtctttc\t+\t0\tmmmmmmmmmmmmmmmmmmmmm\n+hsa-let-7a-3p\t21\t1\t21\tctatacaatctactgtctttc\tbta-let-7a-3\t21\t52\t72\tctatacaatctactgtctttc\t+\t0\tmmmmmmmmmmmmmmmmmmmmm\n+hsa-let-7a-2-3p\t22\t1\t22\tctgtacagcctcctagctttcc\tbta-let-7a-2\t22\t50\t71\tctgtacagcctcctagctttcc\t+\t0\tmmmmmmmmmmmmmmmmmmmmmm\n+hsa-let-7b-5p\t22\t1\t22\ttgaggtagtaggttgtgtggtt\tbta-let-7b\t22\t6\t27\ttgaggtagtaggttgtgtggtt\t+\t0\tmmmmmmmmmmmmmmmmmmmmmm\n+hsa-let-7c-5p\t22\t1\t22\ttgaggtagtaggttgtatggtt\tbta-let-7c\t22\t11\t32\ttgaggtagtaggttgtatggtt\t+\t0\tmmmmmmmmmmmmmmmmmmmmmm\n+hsa-let-7c-3p\t22\t1\t22\tctgtacaaccttctagctttcc\tbta-let-7c\t22\t56\t77\tctgtacaaccttctagctttcc\t+\t0\tmmmmmmmmmmmmmmmmmmmmmm\n+hsa-let-7d-5p\t22\t1\t22\tagaggtagtaggttgcatagtt\tbta-let-7d\t22\t8\t29\tagaggtagtaggttgcatagtt\t+\t0\tmmmmmmmmmmmmmmmmmmmmmm\n+hsa-let-7d-3p\t22\t1\t22\tctatacgacctgctgcctttct\tbta-let-7d\t22\t62\t83\tctatacgacctgctgcctttct\t+\t0\tmmmmmmmmmmmmmmmmmmmmmm\n+hsa-let-7e-5p\t22\t1\t22\ttgaggtaggaggttgtatagtt\tbta-let-7e\t22\t8\t29\ttgaggtaggaggttgtatagtt\t+\t0\tmmmmmmmmmmmmmmmmmmmmmm\n+hsa-let-7e-3p\t22\t1\t22\tctatacggcctcctagctttcc\tbta-let-7e\t22\t53\t74\tctatacggcctcctagctttcc\t+\t0\tmmmmmmmmmmmmmmmmmmmmmm\n+hsa-let-7f-5p\t22\t1\t22\ttgaggtagtagattgtatagtt\tbta-let-7f-1\t22\t7\t28\ttgaggtagtagattgtatagtt\t+\t0\tmmmmmmmmmmmmmmmmmmmmmm\n+hsa-let-7f-5p\t22\t1\t22\ttgaggtagtagattgtatagtt\tbta-let-7f-2\t22\t8\t29\ttgaggtagtagattgtatagtt\t+\t0\tmmmmmmmmmmmmmmmmmmmmmm\n+hsa-let-7f-1-3p\t22\t1\t22\tctatacaatctattgccttccc\tbta-let-7f-1\t22\t63\t84\tctatacaatctattgccttccc\t+\t0\tmmmmmmmmmmmmmmmmmmmmmm\n+hsa-let-7f-2-3p\t22\t1\t22\tctatacagtctactgtctttcc\tbta-let-7f-2\t22\t58\t79\tctatacagtctactgtctttcc\t+\t0\tmmmmmmmmmmmmmmmmmmmmmm\n+hsa-miR-15a-5p\t22\t1\t22\ttagcagcacataatggtttgtg\tbta-mir-15a\t22\t14\t35\ttagcagcacataatggtttgtg\t+\t0\tmmmmmmmmmmmmmmmmmmmmmm\n+hsa-miR-15a-3p\t22\t1\t22\tcaggccatattgtgctgcctca\tbta-mir-15a\t22\t51\t72\tcaggccatattgtgctgcctca\t+\t0\tmmmmmmmmmmmmmmmmmmmmmm\n+hsa-miR-16-5p\t22\t1\t22\ttagcagcacgtaaatattggcg\tbta-mir-16b\t22\t17\t38\ttagcagcacgtaaatattggcg\t+\t0\tmmmmmmmmmmmmmmmmmmmmmm\n+hsa-miR-16-1-3p\t22\t1\t22\tccagtattaactgtgctgctga\tbta-mir-16a\t22\t56\t77\tccagtattaactgtgctgctga\t+\t0\tmmmmmmmmmmmmmmmmmmmmmm\n+hsa-miR-17-5p\t23\t1\t23\tcaaagtgcttacagtgcaggtag\tbta-mir-17\t2'..b'mmmmmm\n+oga-miR-25\t22\t1\t22\tcattgcacttgtctcggtctga\tbta-mir-25\t22\t52\t73\tcattgcacttgtctcggtctga\t+\t0\tmmmmmmmmmmmmmmmmmmmmmm\n+oga-miR-93\t23\t1\t23\tcaaagtgctgttcgtgcaggtag\tbta-mir-93\t23\t11\t33\tcaaagtgctgttcgtgcaggtag\t+\t0\tmmmmmmmmmmmmmmmmmmmmmmm\n+oga-miR-106b\t22\t1\t22\ttaccgcactgtgggtacttgct\tbta-mir-106b\t22\t48\t69\ttaccgcactgtgggtacttgct\t+\t0\tmmmmmmmmmmmmmmmmmmmmmm\n+oga-miR-192\t21\t1\t21\tctgacctatgaattgacagcc\tbta-mir-192\t21\t20\t40\tctgacctatgaattgacagcc\t+\t0\tmmmmmmmmmmmmmmmmmmmmm\n+oga-let-7i\t22\t1\t22\ttgaggtagtagtttgtgctgtt\tbta-let-7i\t22\t6\t27\ttgaggtagtagtttgtgctgtt\t+\t0\tmmmmmmmmmmmmmmmmmmmmmm\n+oga-miR-149\t22\t1\t22\ttctggctccgtgtcttcactcc\tbta-mir-149\t22\t15\t36\ttctggctccgtgtcttcactcc\t+\t0\tmmmmmmmmmmmmmmmmmmmmmm\n+oga-miR-181e\t22\t1\t22\taacattcattgctgtcggtggg\tbta-mir-181b-1\t22\t36\t57\taacattcattgctgtcggtggg\t+\t0\tmmmmmmmmmmmmmmmmmmmmmm\n+oga-miR-181e\t22\t1\t22\taacattcattgctgtcggtggg\tbta-mir-181b-2\t22\t16\t37\taacattcattgctgtcggtggg\t+\t0\tmmmmmmmmmmmmmmmmmmmmmm\n+oga-miR-455\t23\t1\t23\ttatgtgcctttggactacatcgt\tbta-mir-455\t23\t16\t38\ttatgtgcctttggactacatcgt\t+\t0\tmmmmmmmmmmmmmmmmmmmmmmm\n+oga-miR-181c\t23\t1\t23\taacattcaacctgtcggtgagtt\tbta-mir-181c\t23\t19\t41\taacattcaacctgtcggtgagtt\t+\t0\tmmmmmmmmmmmmmmmmmmmmmmm\n+oga-miR-181d\t23\t1\t23\taacattcattgttgtcggtgggt\tbta-mir-181d\t23\t35\t57\taacattcattgttgtcggtgggt\t+\t0\tmmmmmmmmmmmmmmmmmmmmmmm\n+oga-miR-27a\t20\t1\t20\tttcacagtggctaagttccg\tbta-mir-27a\t20\t54\t73\tttcacagtggctaagttccg\t+\t0\tmmmmmmmmmmmmmmmmmmmm\n+oga-miR-23a\t22\t1\t22\tatcacattgccagggatttcca\tbta-mir-23a\t22\t45\t66\tatcacattgccagggatttcca\t+\t0\tmmmmmmmmmmmmmmmmmmmmmm\n+oga-miR-505\t24\t1\t24\tcgtcaacacttgctggtttcctct\tbta-mir-505\t24\t56\t79\tcgtcaacacttgctggtttcctct\t+\t0\tmmmmmmmmmmmmmmmmmmmmmmmm\n+oga-miR-423\t23\t1\t23\tagctcggtctgaggcccctcagt\tbta-mir-423\t23\t53\t75\tagctcggtctgaggcccctcagt\t+\t0\tmmmmmmmmmmmmmmmmmmmmmmm\n+oga-miR-193a\t22\t1\t22\taactggcctacaaagtcccagt\tbta-mir-193a\t22\t49\t70\taactggcctacaaagtcccagt\t+\t0\tmmmmmmmmmmmmmmmmmmmmmm\n+oga-miR-100\t22\t1\t22\taacccgtagatccgaacttgtg\tbta-mir-100\t22\t13\t34\taacccgtagatccgaacttgtg\t+\t0\tmmmmmmmmmmmmmmmmmmmmmm\n+oga-miR-184\t22\t1\t22\ttggacggagaactgataagggt\tbta-mir-184\t22\t52\t73\ttggacggagaactgataagggt\t+\t0\tmmmmmmmmmmmmmmmmmmmmmm\n+oga-miR-190\t24\t1\t24\ttgatatgtttgatatattaggttg\tbta-mir-190a\t24\t15\t38\ttgatatgtttgatatattaggttg\t+\t0\tmmmmmmmmmmmmmmmmmmmmmmmm\n+gga-miR-191-5p\t23\t1\t23\tcaacggaatcccaaaagcagctg\tbta-mir-191\t23\t15\t37\tcaacggaatcccaaaagcagctg\t+\t0\tmmmmmmmmmmmmmmmmmmmmmmm\n+gga-miR-132a-3p\t22\t1\t22\ttaacagtctacagccatggtcg\tbta-mir-132\t22\t59\t80\ttaacagtctacagccatggtcg\t+\t0\tmmmmmmmmmmmmmmmmmmmmmm\n+gga-miR-212-5p\t23\t1\t23\taccttggctctagactgcttact\tbta-mir-212\t23\t32\t54\taccttggctctagactgcttact\t+\t0\tmmmmmmmmmmmmmmmmmmmmmmm\n+gga-miR-129-5p\t21\t1\t21\tctttttgcggtctgggcttgc\tbta-mir-129-1\t21\t5\t25\tctttttgcggtctgggcttgc\t+\t0\tmmmmmmmmmmmmmmmmmmmmm\n+gga-miR-129-5p\t21\t1\t21\tctttttgcggtctgggcttgc\tbta-mir-129-2\t21\t16\t36\tctttttgcggtctgggcttgc\t+\t0\tmmmmmmmmmmmmmmmmmmmmm\n+gga-miR-129-1-3p\t22\t1\t22\taagcccttaccccaaaaagcat\tbta-mir-129-2\t22\t58\t79\taagcccttaccccaaaaagcat\t+\t0\tmmmmmmmmmmmmmmmmmmmmmm\n+gga-miR-214b-5p\t22\t1\t22\ttgcctgtctgtgcctgctgtac\tbta-mir-3120\t22\t11\t32\ttgcctgtctgtgcctgctgtac\t+\t0\tmmmmmmmmmmmmmmmmmmmmmm\n+gga-miR-214b-3p\t21\t1\t21\tcacagcaagtgtagacaggca\tbta-mir-3120\t21\t51\t71\tcacagcaagtgtagacaggca\t+\t0\tmmmmmmmmmmmmmmmmmmmmm\n+mdo-miR-133b-5p\t22\t1\t22\tgctggtcaaacggaaccaagtc\tbta-mir-133b\t22\t11\t32\tgctggtcaaacggaaccaagtc\t+\t0\tmmmmmmmmmmmmmmmmmmmmmm\n+mdo-miR-133b-3p\t21\t1\t21\ttttggtccccttcaaccagct\tbta-mir-133a-1\t21\t59\t79\ttttggtccccttcaaccagct\t+\t0\tmmmmmmmmmmmmmmmmmmmmm\n+mdo-miR-133b-3p\t21\t1\t21\ttttggtccccttcaaccagct\tbta-mir-133b\t21\t48\t68\ttttggtccccttcaaccagct\t+\t0\tmmmmmmmmmmmmmmmmmmmmm\n+mdo-miR-133b-3p\t21\t1\t21\ttttggtccccttcaaccagct\tbta-mir-133a-2\t21\t52\t72\ttttggtccccttcaaccagct\t+\t0\tmmmmmmmmmmmmmmmmmmmmm\n+mdo-miR-30e-5p\t22\t1\t22\ttgtaaacatccccgactggaag\tbta-mir-30d\t22\t6\t27\ttgtaaacatccccgactggaag\t+\t0\tmmmmmmmmmmmmmmmmmmmmmm\n+mdo-miR-30e-3p\t22\t1\t22\tctttcagtcagatgtttgctgc\tbta-mir-30d\t22\t46\t67\tctttcagtcagatgtttgctgc\t+\t0\tmmmmmmmmmmmmmmmmmmmmmm\n+mdo-miR-1306-5p\t21\t1\t21\tccacctcccctgcaaacgtcc\tbta-mir-1306\t21\t1\t21\tccacctcccctgcaaacgtcc\t+\t0\tmmmmmmmmmmmmmmmmmmmmm\n'

diff -r 000000000000 -r b8496cb0d3d9 paqmir_postprocess_quantifier/test-data/miRNAs_expressed_all_samples.pre_uniq.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/paqmir_postprocess_quantifier/test-data/miRNAs_expressed_all_samples.pre_uniq.csv Mon Mar 18 09:31:00 2019 -0400

b'@@ -0,0 +1,1158 @@\n+#miRNA\tread_count\tprecursor\tpredicted_position\ttotal\tS01\tS02\tS03\tS01(norm)\tS02(norm)\tS03(norm)\tmature_seq\n+bta-miR-2331-5p\t0.00\tbta-mir-2331\t5p\t0.00\t0\t0\t0\t0\t0\t0\tggcttccgtgcctgcagatgtct\n+bta-miR-2331-3p\t3.00\tbta-mir-2331\t3p\t3.00\t1.00\t1.00\t1.00\t79.20\t79.20\t79.20\taccctgcagccaaagaagcta\n+bta-miR-12001\t0.00\tbta-mir-12001\t5p\t0.00\t0\t0\t0\t0\t0\t0\tcctgtgagggcttcaccctgga\n+bta-miR-2284d\t0.00\tbta-mir-2284d\t5p\t0.00\t0\t0\t0\t0\t0\t0\taaaaagttcgttagggtttttc\n+bta-miR-2299-5p\t0.00\tbta-mir-2299\t5p\t0.00\t0\t0\t0\t0\t0\t0\tactggattcatttctctgaaa\n+bta-miR-2299-3p\t0.00\tbta-mir-2299\t3p\t0.00\t0\t0\t0\t0\t0\t0\ttccggggaatggatccagcgt\n+bta-miR-9-5p\t297.00\tbta-mir-9-1\t5p\t297.00\t99.00\t99.00\t99.00\t7840.96\t7840.96\t7840.96\ttctttggttatctagctgtatg\n+bta-miR-9-3p\t51.00\tbta-mir-9-1\t3p\t51.00\t17.00\t17.00\t17.00\t1346.43\t1346.43\t1346.43\tataaagctagataaccg\n+bta-miR-2478\t3.00\tbta-mir-2478\t3p\t3.00\t1.00\t1.00\t1.00\t79.20\t79.20\t79.20\tgtatcccacttctgacacca\n+bta-miR-7858\t0.00\tbta-mir-7858\t3p\t0.00\t0\t0\t0\t0\t0\t0\tacgcaattcttcaaaatcttagc\n+bta-miR-2390\t0.00\tbta-mir-2390\t5p\t0.00\t0\t0\t0\t0\t0\t0\tgttgtgtgtttttgttttcc\n+bta-miR-584\t0.00\tbta-mir-584-6\t5p\t0.00\t0\t0\t0\t0\t0\t0\ttggtttgcctgggactgag\n+bta-miR-2362\t0.00\tbta-mir-2362\t3p\t0.00\t0\t0\t0\t0\t0\t0\tcactgtgatggagcgttctgacc\n+bta-miR-2473\t0.00\tbta-mir-2473\t3p\t0.00\t0\t0\t0\t0\t0\t0\taaattggcagagcttcctctt\n+bta-miR-2285d\t0.00\tbta-mir-2285d\t3p\t0.00\t0\t0\t0\t0\t0\t0\taaacctgaacgaaatttttggc\n+bta-miR-2285ap\t0.00\tbta-mir-2285ap\t3p\t0.00\t0\t0\t0\t0\t0\t0\taaacccggatgaactttttggc\n+bta-miR-11986b\t0.00\tbta-mir-11986b\t5p\t0.00\t0\t0\t0\t0\t0\t0\tttttccaatgagttagtccttt\n+bta-miR-1291\t12.00\tbta-mir-1291\t5p\t12.00\t4.00\t4.00\t4.00\t316.81\t316.81\t316.81\ttggccctgactgaagacctgcagt\n+bta-miR-12038\t0.00\tbta-mir-12038\t3p\t0.00\t0\t0\t0\t0\t0\t0\ttctgcagaagctgtcagtgcct\n+bta-miR-2469\t0.00\tbta-mir-2469\t5p\t0.00\t0\t0\t0\t0\t0\t0\tttactgtagggcctgcggctt\n+bta-miR-2285aw\t0.00\tbta-mir-2285aw\t3p\t0.00\t0\t0\t0\t0\t0\t0\taaaacctgaacaaactttttg\n+bta-miR-19b\t195.00\tbta-mir-19b\t3p\t195.00\t65.00\t65.00\t65.00\t5148.11\t5148.11\t5148.11\ttgtgcaaatccatgcaaaactga\n+bta-miR-1260b\t27.00\tbta-mir-1260b\t5p\t27.00\t9.00\t9.00\t9.00\t712.81\t712.81\t712.81\tatcccaccactgccacca\n+bta-miR-6536\t0.00\tbta-mir-6536-1\t5p\t0.00\t0\t0\t0\t0\t0\t0\ttttaagtatacgatgaactgc\n+bta-miR-10163-3p\t0.00\tbta-mir-10163\t3p\t0.00\t0\t0\t0\t0\t0\t0\ttgacaagcatggttctctctct\n+bta-miR-12063\t0.00\tbta-mir-12063\t3p\t0.00\t0\t0\t0\t0\t0\t0\tactggtccaggaagattct\n+bta-miR-210\t114.00\tbta-mir-210\t3p\t114.00\t38.00\t38.00\t38.00\t3009.66\t3009.66\t3009.66\tactgtgcgtgtgacagcggctga\n+bta-miR-584\t0.00\tbta-mir-584-1\t5p\t0.00\t0\t0\t0\t0\t0\t0\ttggtttgcctgggactgag\n+bta-miR-101\t216.00\tbta-mir-101-1\t3p\t216.00\t72.00\t72.00\t72.00\t5702.52\t5702.52\t5702.52\ttacagtactgtgataactgaa\n+bta-miR-2388-5p\t0.00\tbta-mir-2388\t5p\t0.00\t0\t0\t0\t0\t0\t0\tagctcccgtctcctctgtgctga\n+bta-miR-2388-3p\t0.00\tbta-mir-2388\t3p\t0.00\t0\t0\t0\t0\t0\t0\tgctcgaggaagctggagatga\n+bta-miR-10184-3p\t0.00\tbta-mir-10184\t3p\t0.00\t0\t0\t0\t0\t0\t0\ttttaatgtagaaaacccaatgg\n+bta-miR-2285g\t0.00\tbta-mir-2285g-3\t3p\t0.00\t0\t0\t0\t0\t0\t0\taaacctgaacaagctttttgg\n+bta-miR-144\t105.00\tbta-mir-144\t3p\t105.00\t35.00\t35.00\t35.00\t2772.06\t2772.06\t2772.06\ttacagtatagatgatgtactag\n+bta-miR-2286\t0.00\tbta-mir-2286\t3p\t0.00\t0\t0\t0\t0\t0\t0\tgaagcagggcggaacgatgtgt\n+bta-miR-2285as\t0.00\tbta-mir-2285as-3\t3p\t0.00\t0\t0\t0\t0\t0\t0\taagccctgaatgaactttttgg\n+bta-miR-34a\t141.00\tbta-mir-34a\t5p\t141.00\t47.00\t47.00\t47.00\t3722.48\t3722.48\t3722.48\ttggcagtgtcttagctggttgt\n+bta-miR-2285at\t0.00\tbta-mir-2285at-2\t3p\t0.00\t0\t0\t0\t0\t0\t0\taaaacccgaaggaactttttg\n+bta-miR-6522\t0.00\tbta-mir-6522\t5p\t0.00\t0\t0\t0\t0\t0\t0\ttcggaattgtttgtgtacctgt\n+bta-miR-2429\t0.00\tbta-mir-2429\t3p\t0.00\t0\t0\t0\t0\t0\t0\taaaaacttttcccttttttt\n+bta-miR-1248\t15.00\tbta-mir-1248-2\t5p\t15.00\t5.00\t5.00\t5.00\t396.01\t396.01\t396.01\taccttcttgtataagcactgtgctaaa\n+bta-miR-2899\t0.00\tbta-mir-2899\t3p\t0.00\t0\t0\t0\t0\t0\t0\taggcgggccggggttgga\n+bta-miR-6121-5p\t0.00\tbta-mir-6121\t5p\t0.00\t0\t0\t0\t0\t0\t0\ttcggagcgccctcgccagac\n+bta-miR-2285ae\t0.00\tbta-mir-2285ae\t5p\t0.00\t0\t0\t0\t0\t0\t0\tagaaagttcatttaggtttttc\n+bta-miR-2285k\t0.00\tbta-mir-2285k-3\t3p\t0.00\t0\t0\t0\t0\t0\t0\taaaaccggaatgaactttttg\n+bta-miR-485\t42.00\tbta-mir-485\t5p\t42.00\t14.00\t14.00\t14.00\t1108.82\t1108.82\t1108.82\tagaggctggccgtgat'..b'agttggcgcttt\n+bta-miR-592\t36.00\tbta-mir-592\t5p\t36.00\t12.00\t12.00\t12.00\t950.42\t950.42\t950.42\tattgtgtcaatatgcgatgatgt\n+bta-miR-199a-5p\t162.00\tbta-mir-199a-2\t5p\t162.00\t54.00\t54.00\t54.00\t4276.89\t4276.89\t4276.89\tcccagtgttcagactacctgtt\n+bta-miR-199a-3p\t192.00\tbta-mir-199a-2\t3p\t192.00\t64.00\t64.00\t64.00\t5068.91\t5068.91\t5068.91\tacagtagtctgcacattggtta\n+bta-miR-11987\t0.00\tbta-mir-11987\t5p\t0.00\t0\t0\t0\t0\t0\t0\tcgaggaatctctggtggaggt\n+bta-miR-30b-5p\t144.00\tbta-mir-30b\t5p\t144.00\t48.00\t48.00\t48.00\t3801.68\t3801.68\t3801.68\ttgtaaacatcctacactcagct\n+bta-miR-30b-3p\t36.00\tbta-mir-30b\t3p\t36.00\t12.00\t12.00\t12.00\t950.42\t950.42\t950.42\tctgggaggtggatgtttactt\n+bta-miR-135a\t225.00\tbta-mir-135a-1\t5p\t225.00\t75.00\t75.00\t75.00\t5940.12\t5940.12\t5940.12\ttatggctttttattcctatgtga\n+bta-miR-12021\t0.00\tbta-mir-12021\t3p\t0.00\t0\t0\t0\t0\t0\t0\tttgagaaaaatctgccagct\n+bta-miR-382\t48.00\tbta-mir-382\t5p\t48.00\t16.00\t16.00\t16.00\t1267.23\t1267.23\t1267.23\tgaagttgttcgtggtggattcg\n+bta-miR-505\t54.00\tbta-mir-505\t3p\t54.00\t18.00\t18.00\t18.00\t1425.63\t1425.63\t1425.63\tcgtcaacacttgctggtttcct\n+bta-miR-411a\t63.00\tbta-mir-411a\t5p\t63.00\t21.00\t21.00\t21.00\t1663.23\t1663.23\t1663.23\tatagtagaccgtatagcgtacg\n+bta-miR-542-5p\t42.00\tbta-mir-542\t5p\t42.00\t14.00\t14.00\t14.00\t1108.82\t1108.82\t1108.82\ttcggggatcatcatgtcacgag\n+bta-miR-6525\t0.00\tbta-mir-6525\t5p\t0.00\t0\t0\t0\t0\t0\t0\tctggggaaagcaggagtgag\n+bta-miR-195\t66.00\tbta-mir-195\t5p\t66.00\t22.00\t22.00\t22.00\t1742.44\t1742.44\t1742.44\ttagcagcacagaaatattggca\n+bta-miR-12044\t0.00\tbta-mir-12044\t5p\t0.00\t0\t0\t0\t0\t0\t0\taatggattacttctgattgct\n+bta-miR-2285bo\t0.00\tbta-mir-2285bo\t5p\t0.00\t0\t0\t0\t0\t0\t0\ttgaaaagttcgttcgagtttt\n+bta-miR-187\t105.00\tbta-mir-187\t3p\t105.00\t35.00\t35.00\t35.00\t2772.06\t2772.06\t2772.06\ttcgtgtcttgtgttgcagccgg\n+bta-miR-2285cr\t0.00\tbta-mir-2285cr-2\t5p\t0.00\t0\t0\t0\t0\t0\t0\taaaagttcgttcaggtttct\n+bta-miR-2284j\t0.00\tbta-mir-2284j\t5p\t0.00\t0\t0\t0\t0\t0\t0\tgaaaagttcgttcaggtttt\n+bta-miR-181d\t57.00\tbta-mir-181d\t5p\t57.00\t19.00\t19.00\t19.00\t1504.83\t1504.83\t1504.83\taacattcattgttgtcggtgggt\n+bta-miR-96\t135.00\tbta-mir-96\t5p\t135.00\t45.00\t45.00\t45.00\t3564.07\t3564.07\t3564.07\ttttggcactagcacatttttgct\n+bta-miR-6518\t0.00\tbta-mir-6518\t3p\t0.00\t0\t0\t0\t0\t0\t0\ttcacggagaggagaaactgcac\n+bta-miR-761\t27.00\tbta-mir-761\t5p\t27.00\t9.00\t9.00\t9.00\t712.81\t712.81\t712.81\tgcagcagggtgaaactgacaca\n+bta-miR-16a\t108.00\tbta-mir-16a\t5p\t108.00\t36.00\t36.00\t36.00\t2851.26\t2851.26\t2851.26\ttagcagcacgtaaatattggtg\n+bta-miR-2285ch\t0.00\tbta-mir-2285ch\t3p\t0.00\t0\t0\t0\t0\t0\t0\tatcaatgaactttttggccagc\n+bta-miR-12026\t0.00\tbta-mir-12026-2\t3p\t0.00\t0\t0\t0\t0\t0\t0\tcccggggactgctggccagg\n+bta-miR-2389\t0.00\tbta-mir-2389\t5p\t0.00\t0\t0\t0\t0\t0\t0\tgaggggactcgggagtcggag\n+bta-miR-500\t42.00\tbta-mir-500\t5p\t42.00\t14.00\t14.00\t14.00\t1108.82\t1108.82\t1108.82\ttaatccttgctacctgggtgaga\n+bta-miR-2303\t0.00\tbta-mir-2303\t5p\t0.00\t0\t0\t0\t0\t0\t0\ttctgaatgatgtcgactgatg\n+bta-miR-410\t63.00\tbta-mir-410\t3p\t63.00\t21.00\t21.00\t21.00\t1663.23\t1663.23\t1663.23\taatataacacagatggcctgt\n+bta-miR-2337\t0.00\tbta-mir-2337\t5p\t0.00\t0\t0\t0\t0\t0\t0\tgtggtttcttattccttttt\n+bta-miR-190b\t117.00\tbta-mir-190b\t5p\t117.00\t39.00\t39.00\t39.00\t3088.86\t3088.86\t3088.86\ttgatatgtttgatattgggtt\n+bta-miR-138\t138.00\tbta-mir-138-2\t5p\t138.00\t46.00\t46.00\t46.00\t3643.28\t3643.28\t3643.28\tagctggtgttgtgaatcaggccg\n+bta-miR-2368-5p\t0.00\tbta-mir-2368\t5p\t0.00\t0\t0\t0\t0\t0\t0\tagagggtggcctggtatctg\n+bta-miR-2368-3p\t0.00\tbta-mir-2368\t3p\t0.00\t0\t0\t0\t0\t0\t0\tactgtcagaccacctctgcc\n+bta-miR-450a\t78.00\tbta-mir-450a-2\t5p\t78.00\t26.00\t26.00\t26.00\t2059.24\t2059.24\t2059.24\tttttgcgatgtgttcctaatat\n+bta-miR-4444\t3.00\tbta-mir-4444\t3p\t3.00\t1.00\t1.00\t1.00\t79.20\t79.20\t79.20\tctcgagttggaagaggcg\n+bta-miR-2284aa\t0.00\tbta-mir-2284aa-1\t5p\t0.00\t0\t0\t0\t0\t0\t0\taaaaaagtttgtttgggtttt\n+bta-miR-12002b\t0.00\tbta-mir-12002b\t3p\t0.00\t0\t0\t0\t0\t0\t0\tcctcatgtggaatctttagct\n+bta-miR-2285ad\t0.00\tbta-mir-2285ad\t3p\t0.00\t0\t0\t0\t0\t0\t0\taaaacccaaatgaactttttgg\n+bta-miR-502b\t3.00\tbta-mir-502b\t3p\t3.00\t1.00\t1.00\t1.00\t79.20\t79.20\t79.20\taatccacctgggcaaggattc\n+bta-miR-3432a\t3.00\tbta-mir-3432a-2\t5p\t3.00\t1.00\t1.00\t1.00\t79.20\t79.20\t79.20\ttgcgggatctttagttgtggtg\n+bta-miR-2284e\t0.00\tbta-mir-2284e\t5p\t0.00\t0\t0\t0\t0\t0\t0\taagttcgttcggatttttcc\n'

diff -r 000000000000 -r b8496cb0d3d9 paqmir_postprocess_quantifier/test-data/miRNAs_expressed_all_samples.pre_uniq.matureSEQ_uniq.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/paqmir_postprocess_quantifier/test-data/miRNAs_expressed_all_samples.pre_uniq.matureSEQ_uniq.csv Mon Mar 18 09:31:00 2019 -0400

b'@@ -0,0 +1,85 @@\n+miRNA\tread_count\tprecursor\tpredicted_position\ttotal\tS01\tS02\tS03\tS01(norm)\tS02(norm)\tS03(norm)\tmature_seq\n+bta-miR-125b\t285.00\tbta-mir-125b-2\t5p\t285.00\t95.00\t95.00\t95.00\t7524.16\t7524.16\t7524.16\ttccctgagaccctaacttgtga\n+bta-miR-7\t321.00\tbta-mir-7-2\t5p\t321.00\t107.00\t107.00\t107.00\t8474.58\t8474.58\t8474.58\ttggaagactagtgattttgttgtt\n+bta-miR-191\t108.00\tbta-mir-191\t5p\t108.00\t36.00\t36.00\t36.00\t2851.26\t2851.26\t2851.26\tcaacggaatcccaaaagcagctg\n+bta-miR-7\t324.00\tbta-mir-7-3\t5p\t324.00\t108.00\t108.00\t108.00\t8553.78\t8553.78\t8553.78\ttggaagactagtgattttgttgtt\n+bta-miR-193a-3p\t111.00\tbta-mir-193a\t3p\t111.00\t37.00\t37.00\t37.00\t2930.46\t2930.46\t2930.46\taactggcctacaaagtcccagt\n+bta-miR-210\t114.00\tbta-mir-210\t3p\t114.00\t38.00\t38.00\t38.00\t3009.66\t3009.66\t3009.66\tactgtgcgtgtgacagcggctga\n+bta-miR-338\t129.00\tbta-mir-338\t3p\t129.00\t43.00\t43.00\t43.00\t3405.67\t3405.67\t3405.67\ttccagcatcagtgattttgttga\n+bta-let-7a-5p\t345.00\tbta-let-7a-2\t5p\t345.00\t115.00\t115.00\t115.00\t9108.19\t9108.19\t9108.19\ttgaggtagtaggttgtatagtt\n+bta-miR-15a\t132.00\tbta-mir-15a\t5p\t132.00\t44.00\t44.00\t44.00\t3484.87\t3484.87\t3484.87\ttagcagcacataatggtttgt\n+bta-miR-194\t147.00\tbta-mir-194-2\t5p\t147.00\t49.00\t49.00\t49.00\t3880.88\t3880.88\t3880.88\ttgtaacagcaactccatgtgga\n+bta-miR-30e-5p\t135.00\tbta-mir-30e\t5p\t135.00\t45.00\t45.00\t45.00\t3564.07\t3564.07\t3564.07\ttgtaaacatccttgactggaagct\n+bta-miR-183\t150.00\tbta-mir-183\t5p\t150.00\t50.00\t50.00\t50.00\t3960.08\t3960.08\t3960.08\ttatggcactggtagaattcactg\n+bta-miR-222\t153.00\tbta-mir-222\t3p\t153.00\t51.00\t51.00\t51.00\t4039.28\t4039.28\t4039.28\tagctacatctggctactgggt\n+bta-let-7g\t171.00\tbta-let-7g\t5p\t171.00\t57.00\t57.00\t57.00\t4514.49\t4514.49\t4514.49\ttgaggtagtagtttgtacagtt\n+bta-miR-503-3p\t9.00\tbta-mir-503\t3p\t9.00\t3.00\t3.00\t3.00\t237.60\t237.60\t237.60\tggagtattgtttctgctgcccgg\n+bta-miR-107\t174.00\tbta-mir-107\t3p\t174.00\t58.00\t58.00\t58.00\t4593.70\t4593.70\t4593.70\tagcagcattgtacagggctatc\n+bta-miR-20a\t189.00\tbta-mir-20a\t5p\t189.00\t63.00\t63.00\t63.00\t4989.70\t4989.70\t4989.70\ttaaagtgcttatagtgcaggtag\n+bta-miR-1291\t12.00\tbta-mir-1291\t5p\t12.00\t4.00\t4.00\t4.00\t316.81\t316.81\t316.81\ttggccctgactgaagacctgcagt\n+bta-miR-130a\t210.00\tbta-mir-130a\t3p\t210.00\t70.00\t70.00\t70.00\t5544.12\t5544.12\t5544.12\tcagtgcaatgttaaaagggcat\n+bta-miR-1260b\t27.00\tbta-mir-1260b\t5p\t27.00\t9.00\t9.00\t9.00\t712.81\t712.81\t712.81\tatcccaccactgccacca\n+bta-miR-199a-3p\t192.00\tbta-mir-199a-1\t3p\t192.00\t64.00\t64.00\t64.00\t5068.91\t5068.91\t5068.91\tacagtagtctgcacattggtta\n+bta-miR-1248\t15.00\tbta-mir-1248-2\t5p\t15.00\t5.00\t5.00\t5.00\t396.01\t396.01\t396.01\taccttcttgtataagcactgtgctaaa\n+bta-miR-29b\t213.00\tbta-mir-29b-2\t3p\t213.00\t71.00\t71.00\t71.00\t5623.32\t5623.32\t5623.32\ttagcaccatttgaaatcagtgtt\n+bta-miR-744\t30.00\tbta-mir-744\t5p\t30.00\t10.00\t10.00\t10.00\t792.02\t792.02\t792.02\ttgcggggctagggctaacagca\n+bta-miR-19b\t195.00\tbta-mir-19b\t3p\t195.00\t65.00\t65.00\t65.00\t5148.11\t5148.11\t5148.11\ttgtgcaaatccatgcaaaactga\n+bta-miR-101\t216.00\tbta-mir-101-1\t3p\t216.00\t72.00\t72.00\t72.00\t5702.52\t5702.52\t5702.52\ttacagtactgtgataactgaa\n+bta-miR-1197\t33.00\tbta-mir-1197\t3p\t33.00\t11.00\t11.00\t11.00\t871.22\t871.22\t871.22\ttaggacacatggtctacttct\n+bta-miR-1\t231.00\tbta-mir-1-2\t3p\t231.00\t77.00\t77.00\t77.00\t6098.53\t6098.53\t6098.53\ttggaatgtaaagaagtatgtat\n+bta-miR-342\t48.00\tbta-mir-342\t3p\t48.00\t16.00\t16.00\t16.00\t1267.23\t1267.23\t1267.23\ttctcacacagaaatcgcacccatct\n+bta-miR-33b\t36.00\tbta-mir-33b\t5p\t36.00\t12.00\t12.00\t12.00\t950.42\t950.42\t950.42\tgtgcattgctgttgcattgc\n+bta-miR-9-3p\t51.00\tbta-mir-9-1\t3p\t51.00\t17.00\t17.00\t17.00\t1346.43\t1346.43\t1346.43\tataaagctagataaccg\n+bta-miR-423-5p\t54.00\tbta-mir-423\t5p\t54.00\t18.00\t18.00\t18.00\t1425.63\t1425.63\t1425.63\ttgaggggcagagagcgagacttt\n+bta-miR-216b\t69.00\tbta-mir-216b\t5p\t69.00\t23.00\t23.00\t23.00\t1821.64\t1821.64\t1821.64\taaatctctgcaggcaaatgtga\n+bta-miR-2331-3p\t3.00\tbta-mir-2331\t3p\t3.00\t1.00\t1.00\t1.00\t79.20\t79.20\t79.20\taccctgcagccaaagaagcta\n+bta-miR-497\t72.00\tbta-mir-497\t5p\t72.00\t24.00\t24.00\t24.00\t1900.84\t1900.84\t1900.84\tcagcagcacactgtggtttgta\n+bta-miR-32\t87.00\tbta-mir-32\t5p\t87.00\t29.00\t29.00\t29.00\t2296.85\t2296.85\t2296.85\ttattgcacatgactaagttgcat\n+bta-miR-191b\t6.00\tbta-mir-191b\t5'..b'gtgatgttt\n+bta-miR-133a\t348.00\tbta-mir-133a-1\t3p\t348.00\t116.00\t116.00\t116.00\t9187.39\t9187.39\t9187.39\ttttggtccccttcaaccagctg\n+bta-miR-217\t123.00\tbta-mir-217\t5p\t123.00\t41.00\t41.00\t41.00\t3247.27\t3247.27\t3247.27\ttactgcatcaggaactgattggat\n+bta-miR-137\t138.00\tbta-mir-137\t3p\t138.00\t46.00\t46.00\t46.00\t3643.28\t3643.28\t3643.28\tttattgcttaagaatacgcgtag\n+bta-miR-155\t126.00\tbta-mir-155\t5p\t126.00\t42.00\t42.00\t42.00\t3326.47\t3326.47\t3326.47\tttaatgctaatcgtgataggggt\n+bta-miR-34a\t141.00\tbta-mir-34a\t5p\t141.00\t47.00\t47.00\t47.00\t3722.48\t3722.48\t3722.48\ttggcagtgtcttagctggttgt\n+bta-miR-19a\t144.00\tbta-mir-19a\t3p\t144.00\t48.00\t48.00\t48.00\t3801.68\t3801.68\t3801.68\ttgtgcaaatctatgcaaaactga\n+bta-miR-29c\t159.00\tbta-mir-29c\t3p\t159.00\t53.00\t53.00\t53.00\t4197.69\t4197.69\t4197.69\ttagcaccatttgaaatcggtta\n+bta-miR-199a-5p\t162.00\tbta-mir-199a-1\t5p\t162.00\t54.00\t54.00\t54.00\t4276.89\t4276.89\t4276.89\tcccagtgttcagactacctgtt\n+bta-miR-204\t177.00\tbta-mir-204\t5p\t177.00\t59.00\t59.00\t59.00\t4672.90\t4672.90\t4672.90\tttccctttgtcatcctatgcct\n+bta-miR-19b\t198.00\tbta-mir-19b-2\t3p\t198.00\t66.00\t66.00\t66.00\t5227.31\t5227.31\t5227.31\ttgtgcaaatccatgcaaaactga\n+bta-miR-18a\t165.00\tbta-mir-18a\t5p\t165.00\t55.00\t55.00\t55.00\t4356.09\t4356.09\t4356.09\ttaaggtgcatctagtgcagata\n+bta-miR-181b\t180.00\tbta-mir-181b-1\t5p\t180.00\t60.00\t60.00\t60.00\t4752.10\t4752.10\t4752.10\taacattcattgctgtcggtgggtt\n+bta-miR-301a\t201.00\tbta-mir-301a\t3p\t201.00\t67.00\t67.00\t67.00\t5306.51\t5306.51\t5306.51\tcagtgcaatagtattgtcaaagcat\n+bta-miR-453\t18.00\tbta-mir-453\t3p\t18.00\t6.00\t6.00\t6.00\t475.21\t475.21\t475.21\taggttgtccgtggtgagttcgca\n+bta-miR-218\t183.00\tbta-mir-218-2\t5p\t183.00\t61.00\t61.00\t61.00\t4831.30\t4831.30\t4831.30\tttgtgcttgatctaaccatgtg\n+bta-miR-196a\t204.00\tbta-mir-196a-1\t5p\t204.00\t68.00\t68.00\t68.00\t5385.71\t5385.71\t5385.71\ttaggtagtttcatgttgttggg\n+bta-miR-149-3p\t21.00\tbta-mir-149\t3p\t21.00\t7.00\t7.00\t7.00\t554.41\t554.41\t554.41\tgagggagggacgggggctgtgc\n+bta-miR-22-3p\t219.00\tbta-mir-22\t3p\t219.00\t73.00\t73.00\t73.00\t5781.72\t5781.72\t5781.72\taagctgccagttgaagaactg\n+bta-miR-24-3p\t186.00\tbta-mir-24-1\t3p\t186.00\t62.00\t62.00\t62.00\t4910.50\t4910.50\t4910.50\ttggctcagttcagcaggaacag\n+bta-miR-1247-5p\t24.00\tbta-mir-1247\t5p\t24.00\t8.00\t8.00\t8.00\t633.61\t633.61\t633.61\tacccgtcccgtgcgtccccgga\n+bta-miR-6529a\t39.00\tbta-mir-6529a\t5p\t39.00\t13.00\t13.00\t13.00\t1029.62\t1029.62\t1029.62\tgagagatcagaggcgcagagt\n+bta-miR-135a\t225.00\tbta-mir-135a-2\t5p\t225.00\t75.00\t75.00\t75.00\t5940.12\t5940.12\t5940.12\ttatggctttttattcctatgtga\n+bta-miR-485\t42.00\tbta-mir-485\t5p\t42.00\t14.00\t14.00\t14.00\t1108.82\t1108.82\t1108.82\tagaggctggccgtgatgaattcg\n+bta-miR-103\t240.00\tbta-mir-103-1\t3p\t240.00\t80.00\t80.00\t80.00\t6336.13\t6336.13\t6336.13\tagcagcattgtacagggctatga\n+bta-miR-208a\t57.00\tbta-mir-208a\t3p\t57.00\t19.00\t19.00\t19.00\t1504.83\t1504.83\t1504.83\tataagacgagcaaaaagcttgt\n+bta-miR-433\t45.00\tbta-mir-433\t3p\t45.00\t15.00\t15.00\t15.00\t1188.02\t1188.02\t1188.02\tatcatgatgggctcctcggtgt\n+bta-miR-92a\t243.00\tbta-mir-92a-1\t3p\t243.00\t81.00\t81.00\t81.00\t6415.33\t6415.33\t6415.33\ttattgcacttgtcccggcctgt\n+bta-miR-328\t60.00\tbta-mir-328\t3p\t60.00\t20.00\t20.00\t20.00\t1584.03\t1584.03\t1584.03\tctggccctctctgcccttccgt\n+bta-let-7f\t246.00\tbta-let-7f-1\t5p\t246.00\t82.00\t82.00\t82.00\t6494.54\t6494.54\t6494.54\ttgaggtagtagattgtatagtt\n+bta-miR-361\t63.00\tbta-mir-361\t5p\t63.00\t21.00\t21.00\t21.00\t1663.23\t1663.23\t1663.23\tttatcagaatctccaggggtac\n+bta-miR-184\t261.00\tbta-mir-184\t3p\t261.00\t87.00\t87.00\t87.00\t6890.54\t6890.54\t6890.54\ttggacggagaactgataagggt\n+bta-miR-381\t78.00\tbta-mir-381\t3p\t78.00\t26.00\t26.00\t26.00\t2059.24\t2059.24\t2059.24\ttatacaagggcaagctctctgt\n+bta-miR-486\t66.00\tbta-mir-486\t5p\t66.00\t22.00\t22.00\t22.00\t1742.44\t1742.44\t1742.44\ttcctgtactgagctgccccgag\n+bta-miR-9-5p\t297.00\tbta-mir-9-1\t5p\t297.00\t99.00\t99.00\t99.00\t7840.96\t7840.96\t7840.96\ttctttggttatctagctgtatg\n+bta-miR-551b\t81.00\tbta-mir-551b\t3p\t81.00\t27.00\t27.00\t27.00\t2138.44\t2138.44\t2138.44\tggcgacccatacttggtttcag\n+bta-miR-383\t84.00\tbta-mir-383\t5p\t84.00\t28.00\t28.00\t28.00\t2217.65\t2217.65\t2217.65\tagatcagaaggtgattgtggct\n+bta-miR-125b\t282.00\tbta-mir-125b-1\t5p\t282.00\t94.00\t94.00\t94.00\t7444.95\t7444.95\t7444.95\ttccctgagaccctaacttgtga\n'

diff -r 000000000000 -r b8496cb0d3d9 paqmir_postprocess_quantifier/test-data/quantifier_output.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/paqmir_postprocess_quantifier/test-data/quantifier_output.tsv Mon Mar 18 09:31:00 2019 -0400

b'@@ -0,0 +1,1165 @@\n+#miRNA\tread_count\tprecursor\ttotal\tS01\tS02\tS03\tS01(norm)\tS02(norm)\tS03(norm)\n+bta-chr25_10_mt\t0.00\tbta-chr25_10\t0.00\t0\t0\t0\t0\t0\t0\n+bta-chr25_10_st\t0.00\tbta-chr25_10\t0.00\t0\t0\t0\t0\t0\t0\n+bta-chr25_114_mt\t0.00\tbta-chr25_114\t0.00\t0\t0\t0\t0\t0\t0\n+bta-chr25_114_st\t0.00\tbta-chr25_114\t0.00\t0\t0\t0\t0\t0\t0\n+bta-chr25_36_mt\t0.00\tbta-chr25_36\t0.00\t0\t0\t0\t0\t0\t0\n+bta-chr25_36_mt\t0.00\tbta-chr25_36\t0.00\t0\t0\t0\t0\t0\t0\n+bta-chr25_36_mt\t0.00\tbta-chr25_36\t0.00\t0\t0\t0\t0\t0\t0\n+bta-chr25_36_mt\t0.00\tbta-chr25_36\t0.00\t0\t0\t0\t0\t0\t0\n+bta-chr25_36_st\t0.00\tbta-chr25_36\t0.00\t0\t0\t0\t0\t0\t0\n+bta-let-7a-5p\t345.00\tbta-let-7a-1\t345.00\t115.00\t115.00\t115.00\t9108.19\t9108.19\t9108.19\n+bta-let-7a-3p\t96.00\tbta-let-7a-1\t96.00\t32.00\t32.00\t32.00\t2534.45\t2534.45\t2534.45\n+bta-let-7a-5p\t345.00\tbta-let-7a-2\t345.00\t115.00\t115.00\t115.00\t9108.19\t9108.19\t9108.19\n+bta-let-7a-5p\t345.00\tbta-let-7a-3\t345.00\t115.00\t115.00\t115.00\t9108.19\t9108.19\t9108.19\n+bta-let-7a-3p\t96.00\tbta-let-7a-3\t96.00\t32.00\t32.00\t32.00\t2534.45\t2534.45\t2534.45\n+bta-let-7b\t132.00\tbta-let-7b\t132.00\t44.00\t44.00\t44.00\t3484.87\t3484.87\t3484.87\n+bta-let-7c\t183.00\tbta-let-7c\t183.00\t61.00\t61.00\t61.00\t4831.30\t4831.30\t4831.30\n+bta-let-7d\t78.00\tbta-let-7d\t78.00\t26.00\t26.00\t26.00\t2059.24\t2059.24\t2059.24\n+bta-let-7e\t63.00\tbta-let-7e\t63.00\t21.00\t21.00\t21.00\t1663.23\t1663.23\t1663.23\n+bta-let-7f\t246.00\tbta-let-7f-1\t246.00\t82.00\t82.00\t82.00\t6494.54\t6494.54\t6494.54\n+bta-let-7f\t243.00\tbta-let-7f-2\t243.00\t81.00\t81.00\t81.00\t6415.33\t6415.33\t6415.33\n+bta-let-7g\t171.00\tbta-let-7g\t171.00\t57.00\t57.00\t57.00\t4514.49\t4514.49\t4514.49\n+bta-let-7i\t132.00\tbta-let-7i\t132.00\t44.00\t44.00\t44.00\t3484.87\t3484.87\t3484.87\n+bta-miR-1\t231.00\tbta-mir-1-1\t231.00\t77.00\t77.00\t77.00\t6098.53\t6098.53\t6098.53\n+bta-miR-1\t231.00\tbta-mir-1-2\t231.00\t77.00\t77.00\t77.00\t6098.53\t6098.53\t6098.53\n+bta-miR-100\t288.00\tbta-mir-100\t288.00\t96.00\t96.00\t96.00\t7603.36\t7603.36\t7603.36\n+bta-miR-10020\t0.00\tbta-mir-10020\t0.00\t0\t0\t0\t0\t0\t0\n+bta-miR-101\t216.00\tbta-mir-101-1\t216.00\t72.00\t72.00\t72.00\t5702.52\t5702.52\t5702.52\n+bta-miR-101\t213.00\tbta-mir-101-2\t213.00\t71.00\t71.00\t71.00\t5623.32\t5623.32\t5623.32\n+bta-miR-10161-5p\t0.00\tbta-mir-10161\t0.00\t0\t0\t0\t0\t0\t0\n+bta-miR-10162-5p\t0.00\tbta-mir-10162\t0.00\t0\t0\t0\t0\t0\t0\n+bta-miR-10163-3p\t0.00\tbta-mir-10163\t0.00\t0\t0\t0\t0\t0\t0\n+bta-miR-10164-3p\t0.00\tbta-mir-10164\t0.00\t0\t0\t0\t0\t0\t0\n+bta-miR-10165-5p\t0.00\tbta-mir-10165\t0.00\t0\t0\t0\t0\t0\t0\n+bta-miR-10166-5p\t0.00\tbta-mir-10166\t0.00\t0\t0\t0\t0\t0\t0\n+bta-miR-10167-3p\t0.00\tbta-mir-10167\t0.00\t0\t0\t0\t0\t0\t0\n+bta-miR-10168-5p\t0.00\tbta-mir-10168\t0.00\t0\t0\t0\t0\t0\t0\n+bta-miR-10169-3p\t0.00\tbta-mir-10169\t0.00\t0\t0\t0\t0\t0\t0\n+bta-miR-10170-5p\t0.00\tbta-mir-10170\t0.00\t0\t0\t0\t0\t0\t0\n+bta-miR-10171-3p\t0.00\tbta-mir-10171\t0.00\t0\t0\t0\t0\t0\t0\n+bta-miR-10172-5p\t0.00\tbta-mir-10172\t0.00\t0\t0\t0\t0\t0\t0\n+bta-miR-10172-3p\t0.00\tbta-mir-10172\t0.00\t0\t0\t0\t0\t0\t0\n+bta-miR-10173-5p\t0.00\tbta-mir-10173\t0.00\t0\t0\t0\t0\t0\t0\n+bta-miR-10174-5p\t66.00\tbta-mir-10174\t66.00\t22.00\t22.00\t22.00\t1742.44\t1742.44\t1742.44\n+bta-miR-10174-3p\t165.00\tbta-mir-10174\t165.00\t55.00\t55.00\t55.00\t4356.09\t4356.09\t4356.09\n+bta-miR-10175-5p\t0.00\tbta-mir-10175\t0.00\t0\t0\t0\t0\t0\t0\n+bta-miR-10175-3p\t0.00\tbta-mir-10175\t0.00\t0\t0\t0\t0\t0\t0\n+bta-miR-10176-5p\t0.00\tbta-mir-10176\t0.00\t0\t0\t0\t0\t0\t0\n+bta-miR-10177-5p\t0.00\tbta-mir-10177\t0.00\t0\t0\t0\t0\t0\t0\n+bta-miR-10178-5p\t0.00\tbta-mir-10178\t0.00\t0\t0\t0\t0\t0\t0\n+bta-miR-10179-5p\t0.00\tbta-mir-10179\t0.00\t0\t0\t0\t0\t0\t0\n+bta-miR-10180-3p\t0.00\tbta-mir-10180\t0.00\t0\t0\t0\t0\t0\t0\n+bta-miR-10181-5p\t0.00\tbta-mir-10181\t0.00\t0\t0\t0\t0\t0\t0\n+bta-miR-10182-5p\t0.00\tbta-mir-10182\t0.00\t0\t0\t0\t0\t0\t0\n+bta-miR-10182-3p\t0.00\tbta-mir-10182\t0.00\t0\t0\t0\t0\t0\t0\n+bta-miR-10183-5p\t0.00\tbta-mir-10183\t0.00\t0\t0\t0\t0\t0\t0\n+bta-miR-10184-3p\t0.00\tbta-mir-10184\t0.00\t0\t0\t0\t0\t0\t0\n+bta-miR-10185-5p\t0.00\tbta-mir-10185\t0.00\t0\t0\t0\t0\t0\t0\n+bta-miR-10225a\t0.00\tbta-mir-10225a\t0.00\t0\t0\t0\t0\t0\t0\n+bta-miR-10225b\t0.00\tbta-mir-10225b\t0.00\t0\t0\t0\t0\t0\t0\n+bta-miR-103\t240.00\tbta-mir-103-1\t240.00\t80.00\t80.00\t80.00\t6336.13\t6336.13\t6336.13\n+bta-miR-103\t240.00\tbta-mir-103-2\t240.00\t80.00\t80.00\t80.00\t6336.13\t6336.13\t6336.13\n+bta-miR-105a\t'..b'40\n+bta-miR-669\t0.00\tbta-mir-669\t0.00\t0\t0\t0\t0\t0\t0\n+bta-miR-670\t21.00\tbta-mir-670\t21.00\t7.00\t7.00\t7.00\t554.41\t554.41\t554.41\n+bta-miR-671\t39.00\tbta-mir-671\t39.00\t13.00\t13.00\t13.00\t1029.62\t1029.62\t1029.62\n+bta-miR-6715\t0.00\tbta-mir-6715\t0.00\t0\t0\t0\t0\t0\t0\n+bta-miR-677\t0.00\tbta-mir-677\t0.00\t0\t0\t0\t0\t0\t0\n+bta-miR-6775\t0.00\tbta-mir-6775\t0.00\t0\t0\t0\t0\t0\t0\n+bta-miR-7\t321.00\tbta-mir-7-1\t321.00\t107.00\t107.00\t107.00\t8474.58\t8474.58\t8474.58\n+bta-miR-7\t321.00\tbta-mir-7-2\t321.00\t107.00\t107.00\t107.00\t8474.58\t8474.58\t8474.58\n+bta-miR-7\t324.00\tbta-mir-7-3\t324.00\t108.00\t108.00\t108.00\t8553.78\t8553.78\t8553.78\n+bta-miR-708\t57.00\tbta-mir-708\t57.00\t19.00\t19.00\t19.00\t1504.83\t1504.83\t1504.83\n+bta-miR-7180\t12.00\tbta-mir-7180\t12.00\t4.00\t4.00\t4.00\t316.81\t316.81\t316.81\n+bta-miR-744\t30.00\tbta-mir-744\t30.00\t10.00\t10.00\t10.00\t792.02\t792.02\t792.02\n+bta-miR-758\t48.00\tbta-mir-758\t48.00\t16.00\t16.00\t16.00\t1267.23\t1267.23\t1267.23\n+bta-miR-759\t18.00\tbta-mir-759\t18.00\t6.00\t6.00\t6.00\t475.21\t475.21\t475.21\n+bta-miR-760-5p\t15.00\tbta-mir-760\t15.00\t5.00\t5.00\t5.00\t396.01\t396.01\t396.01\n+bta-miR-760-3p\t39.00\tbta-mir-760\t39.00\t13.00\t13.00\t13.00\t1029.62\t1029.62\t1029.62\n+bta-miR-761\t27.00\tbta-mir-761\t27.00\t9.00\t9.00\t9.00\t712.81\t712.81\t712.81\n+bta-miR-763\t9.00\tbta-mir-763\t9.00\t3.00\t3.00\t3.00\t237.60\t237.60\t237.60\n+bta-miR-764\t0.00\tbta-mir-764\t0.00\t0\t0\t0\t0\t0\t0\n+bta-miR-767\t27.00\tbta-mir-767\t27.00\t9.00\t9.00\t9.00\t712.81\t712.81\t712.81\n+bta-miR-769\t27.00\tbta-mir-769\t27.00\t9.00\t9.00\t9.00\t712.81\t712.81\t712.81\n+bta-miR-7691\t0.00\tbta-mir-7691\t0.00\t0\t0\t0\t0\t0\t0\n+bta-miR-7857-5p\t0.00\tbta-mir-7857-1\t0.00\t0\t0\t0\t0\t0\t0\n+bta-miR-7857-5p\t0.00\tbta-mir-7857-2\t0.00\t0\t0\t0\t0\t0\t0\n+bta-miR-7857-3p\t3.00\tbta-mir-7857-2\t3.00\t1.00\t1.00\t1.00\t79.20\t79.20\t79.20\n+bta-miR-7858\t0.00\tbta-mir-7858\t0.00\t0\t0\t0\t0\t0\t0\n+bta-miR-7859\t0.00\tbta-mir-7859\t0.00\t0\t0\t0\t0\t0\t0\n+bta-miR-7860\t0.00\tbta-mir-7860\t0.00\t0\t0\t0\t0\t0\t0\n+bta-miR-7861\t0.00\tbta-mir-7861\t0.00\t0\t0\t0\t0\t0\t0\n+bta-miR-7862\t0.00\tbta-mir-7862\t0.00\t0\t0\t0\t0\t0\t0\n+bta-miR-7863\t0.00\tbta-mir-7863\t0.00\t0\t0\t0\t0\t0\t0\n+bta-miR-7864\t0.00\tbta-mir-7864\t0.00\t0\t0\t0\t0\t0\t0\n+bta-miR-7865\t0.00\tbta-mir-7865\t0.00\t0\t0\t0\t0\t0\t0\n+bta-miR-8548\t0.00\tbta-mir-8548\t0.00\t0\t0\t0\t0\t0\t0\n+bta-miR-8549\t0.00\tbta-mir-8549\t0.00\t0\t0\t0\t0\t0\t0\n+bta-miR-8550\t0.00\tbta-mir-8550\t0.00\t0\t0\t0\t0\t0\t0\n+bta-miR-873\t48.00\tbta-mir-873\t48.00\t16.00\t16.00\t16.00\t1267.23\t1267.23\t1267.23\n+bta-miR-874\t51.00\tbta-mir-874\t51.00\t17.00\t17.00\t17.00\t1346.43\t1346.43\t1346.43\n+bta-miR-875\t30.00\tbta-mir-875\t30.00\t10.00\t10.00\t10.00\t792.02\t792.02\t792.02\n+bta-miR-876\t27.00\tbta-mir-876\t27.00\t9.00\t9.00\t9.00\t712.81\t712.81\t712.81\n+bta-miR-877\t33.00\tbta-mir-877\t33.00\t11.00\t11.00\t11.00\t871.22\t871.22\t871.22\n+bta-miR-885\t30.00\tbta-mir-885\t30.00\t10.00\t10.00\t10.00\t792.02\t792.02\t792.02\n+bta-miR-9-5p\t297.00\tbta-mir-9-1\t297.00\t99.00\t99.00\t99.00\t7840.96\t7840.96\t7840.96\n+bta-miR-9-3p\t51.00\tbta-mir-9-1\t51.00\t17.00\t17.00\t17.00\t1346.43\t1346.43\t1346.43\n+bta-miR-9-5p\t297.00\tbta-mir-9-2\t297.00\t99.00\t99.00\t99.00\t7840.96\t7840.96\t7840.96\n+bta-miR-9-3p\t51.00\tbta-mir-9-2\t51.00\t17.00\t17.00\t17.00\t1346.43\t1346.43\t1346.43\n+bta-miR-92a\t243.00\tbta-mir-92a-1\t243.00\t81.00\t81.00\t81.00\t6415.33\t6415.33\t6415.33\n+bta-miR-92a\t243.00\tbta-mir-92a-2\t243.00\t81.00\t81.00\t81.00\t6415.33\t6415.33\t6415.33\n+bta-miR-92b\t117.00\tbta-mir-92b\t117.00\t39.00\t39.00\t39.00\t3088.86\t3088.86\t3088.86\n+bta-miR-93\t102.00\tbta-mir-93\t102.00\t34.00\t34.00\t34.00\t2692.86\t2692.86\t2692.86\n+bta-miR-935\t15.00\tbta-mir-935\t15.00\t5.00\t5.00\t5.00\t396.01\t396.01\t396.01\n+bta-miR-940\t0.00\tbta-mir-940\t0.00\t0\t0\t0\t0\t0\t0\n+bta-miR-95\t39.00\tbta-mir-95\t39.00\t13.00\t13.00\t13.00\t1029.62\t1029.62\t1029.62\n+bta-miR-96\t135.00\tbta-mir-96\t135.00\t45.00\t45.00\t45.00\t3564.07\t3564.07\t3564.07\n+bta-miR-98\t132.00\tbta-mir-98\t132.00\t44.00\t44.00\t44.00\t3484.87\t3484.87\t3484.87\n+bta-miR-9851\t0.00\tbta-mir-9851\t0.00\t0\t0\t0\t0\t0\t0\n+bta-miR-99a-5p\t150.00\tbta-mir-99a\t150.00\t50.00\t50.00\t50.00\t3960.08\t3960.08\t3960.08\n+bta-miR-99a-3p\t54.00\tbta-mir-99a\t54.00\t18.00\t18.00\t18.00\t1425.63\t1425.63\t1425.63\n+bta-miR-99b\t42.00\tbta-mir-99b\t42.00\t14.00\t14.00\t14.00\t1108.82\t1108.82\t1108.82\n'