Repository 'paqmir_mirdeep2_mapper'
hg clone https://toolshed.g2.bx.psu.edu/repos/smarthey/paqmir_mirdeep2_mapper

Changeset 0:2e4a523f5bc5 (2019-03-18)
Commit message:
Uploaded
added:
paqmir_mapper/mapper.xml
paqmir_mapper/test-data/cel_cluster.fa
paqmir_mapper/test-data/reads.fa
paqmir_mapper/test-data/reads_sample1.fa
paqmir_mapper/test-data/reads_sample2.fa
paqmir_mapper/tool-data/bowtie2_indices.loc
paqmir_mapper/tool-data/bowtie_indices.loc.sample
paqmir_mapper/tool_data_table_conf.xml.sample
b
diff -r 000000000000 -r 2e4a523f5bc5 paqmir_mapper/mapper.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/paqmir_mapper/mapper.xml Mon Mar 18 09:17:49 2019 -0400
[
b'@@ -0,0 +1,268 @@\n+<tool id="paqmir_mirdeep2_mapper" name="PAQmiR MiRDeep2 Mapper" version="2.1.0 ">\n+    <description>process and map reads to a reference genome</description>\n+    <macros>\n+        <macro name="map_params">\n+            <param name="ownFile" type="data" format="fasta" label="Select the reference genome" />\n+            <param name="map_mismatch" type="boolean" truevalue="-q" falsevalue="" checked="false" label="Map with one mismatch in the seed (mapping takes longer)" help="(-q)"/>\n+            <param name="map_threshold" value="5" type="integer" optional="false" label="A read is allowed to map up to this number of positions in the genome" help="Map threshold. (-r)">\n+                <validator type="in_range" min="1" message="Minimum value is 1"/>\n+            </param>\n+        </macro>\n+    </macros>\n+    <requirements>\n+        <requirement type="package" version="2.0.0.8">mirdeep2</requirement>\n+    </requirements>\n+    <command detect_errors="aggressive">\n+<![CDATA[\n+        #if $operation.collapse_map == "collapse_and_map" or $operation.collapse_map == "only_map"\n+\tbowtie-build \'$ownFile\' custom_bowtie_indices &&\n+        #end if\n+\n+        mapper.pl\n+\n+        #if $input.type == "single":\n+            \'$input.reads\'\n+\n+            #if $input.reads.extension.startswith("fasta")\n+                -c\n+            #else if $input.reads.extension.startswith("fastq")\n+                -e\n+                -h\n+            #end if\n+        #else:\n+            \'$samples\' -d\n+\n+            #if $input.reads_list[0].reads.extension.startswith("fasta")\n+                -c\n+            #else if $input.reads_list[0].reads.extension.startswith("fastq")\n+                -e\n+                -h\n+            #end if\n+        #end if\n+\n+        $remove_non_canon\n+\n+        $convert_rna_dna\n+\n+        #if $clip_adapter.clip == "true"\n+            -k $clip_adapter.adapter_seq\n+        #end if\n+\n+        -l $discard_short_reads\n+\n+        #if $operation.collapse_map == "collapse_and_map" or $operation.collapse_map == "only_collapse"\n+            -m -s \'$output_reads_collapsed\'\n+        #end if\n+\n+        #if $operation.collapse_map == "collapse_and_map" or $operation.collapse_map == "only_map"\n+            -p\n+            custom_bowtie_indices\n+            $operation.map_mismatch\n+            -r $operation.map_threshold\n+\n+            -t \'$output_mapping\'\n+        #end if\n+\n+        -v -n\n+]]>\n+    </command>\n+    <configfiles>\n+        <configfile name="samples"><![CDATA[#if $input.type == "multiple":\n+#for $r in $input.reads_list:\n+$r.reads    $r.sample_name\n+#end for\n+#end if]]></configfile>\n+    </configfiles>\n+    <inputs>\n+        <conditional name="input">\n+            <param name="type" type="select" label="Pool multiple read sets">\n+                <option value="single" selected="true">No</option>\n+                <option value="multiple">Yes</option>\n+            </param>\n+            <when value="single">\n+                <param format="fastq,fasta" name="reads" type="data" label="Deep sequencing reads" help="Reads in fastq or FASTA format"/>\n+            </when>\n+            <when value="multiple">\n+                <repeat name="reads_list" title="Reads">\n+                    <param name="sample_name" value="" type="text" label="Sample name" help="Must be a 3 letters/digits code">\n+                        <validator type="expression" message="The sample name must be a 3 letters/digits code">len(value) == 3 and value.isalnum()</validator>\n+                    </param>\n+                    <param format="fastq,fasta" name="reads" type="data" optional="false" label="Deep sequencing reads" help="Reads in fastq or FASTA format"/>\n+                </repeat>\n+            </when>\n+        </conditional>\n+        <param name="remove_non_canon" type="boolean" truevalue="-j" falsevalue="" checked="false" label="Remove reads with non-standard nucleotides" help="Remove all entries that have a sequence that contains letters oth'..b'm name="sample_name" value="sa2"/>\n+                    <param name="reads" value="reads_sample2.fa"/>\n+                </repeat>\n+            </conditional>\n+            <param name="remove_non_canon" value="True"/>\n+            <param name="clip" value="true"/>\n+            <param name="adapter_seq" value="TCGTATGCCGTCTTCTGCTTGT"/>\n+            <param name="discard_short_reads" value="18"/>\n+            <param name="collapse_map" value="collapse_and_map"/>\n+            <param name="genomeSource" value="history"/>\n+            <param name="ownFile" value="cel_cluster.fa"/>\n+            <output name="output_reads_collapsed">\n+                <assert_contents>\n+                    <has_text text=">sa1_220_x1"/>\n+                    <has_text text="TCACCGGGTGTACATCAGC"/>\n+                    <has_text text=">sa2_0_x250"/>\n+                    <has_text text="AATGACACTGGTTATCTTTTCCATCG"/>\n+                </assert_contents>\n+            </output>\n+            <output name="output_mapping">\n+                <assert_contents>\n+                    <has_line_matching expression="^.*22\\t1\\t22\\ttcaccgggtggaaactagcagt\\tchrII:11534525-11540624\\t22\\t3060\\t3081.*$"/>\n+                    <has_line_matching expression="^.*21\\t1\\t21\\ttcaccgggtggaaactagcag\\tchrII:11534525-11540624\\t21\\t3060\\t3080.*$"/>\n+                    <has_line_matching expression="^.*22\\t1\\t22\\ttcaccgggtgtacatcagctaa\\tchrII:11534525-11540624\\t22\\t3631\\t3652.*$"/>\n+                </assert_contents>\n+            </output>\n+        </test>\n+    </tests>\n+    <help>\n+<![CDATA[\n+\n+\t| This tool is part of the workflow **PAQmiR** for the *Prediction Annotation and Quantification of miRNA with miRDeep2*\n+\t| \n+        | *This wrapper was forked from the rbc_mirdeep2_mapper wrapper of the RNA-Bioinformatics network*\n+        | ==> https://www.denbi.de/network/rna-bioinformatics-center-rbc\n+        | ==> https://github.com/bgruening\n+        |\n+        | Modifications are the product of Valentin Marcon & Sylvain Marthey (Thanks to INRA Migale, IFB ressources & INRA GABI)\n+\n+**What it does**\n+\n+The MiRDeep2 Mapper module is designed as a tool to process deep sequencing reads and/or map them to the reference genome.\n+The module works in sequence space, and can process or map data that is in sequence FASTA format.\n+A number of the functions of the mapper module are implemented specifically with Solexa/Illumina data in mind.\n+\n+**Input**\n+\n+Default input is a file in FASTA format, seq.txt or qseq.txt format. More input can be given depending on the options used.\n+\n+**Output**\n+\n+The output depends on the options used. Either a FASTA file with processed reads or an arf file with with mapped reads, or both, are output.\n+\n+Arf format:\n+Is a proprietary file format generated and processed by miRDeep2. It contains information of reads mapped to a reference genome. Each line in such a file contains 13 columns:\n+\n+1. read identifier\n+2. length of read sequence\n+3. start position in read sequence that is mapped\n+4. end position in read sequence that is mapped\n+5. read sequence\n+6. identifier of the genome-part to which a read is mapped to. This is either a scaffold id or a chromosome name\n+7. length of the genome sequence a read is mapped to\n+8. start position in the genome where a read is mapped to\n+9. end position in the genome where a read is mapped to\n+10. genome sequence to which a read is mapped\n+11. genome strand information. Plus means the read is aligned to the sense-strand of the genome. Minus means it is aligned to the antisense-strand of the genome.\n+12. Number of mismatches in the read mapping\n+13. Edit string that indicates matches by lowercase \'m\' and mismatches by uppercase \'M\'\n+\n+**Dependency**\n+\n+MiRDeep2_ 2.0.0.8, Conda version\n+\n+.. _mirdeep2: https://anaconda.org/bioconda/mirdeep2\n+]]>\n+    </help>\n+    <citations>\n+        <citation type="doi">10.1093/nar/gkr688</citation>\n+        <citation type="doi">10.1002/0471250953.bi1210s36</citation>\n+    </citations>\n+</tool>\n'
b
diff -r 000000000000 -r 2e4a523f5bc5 paqmir_mapper/test-data/cel_cluster.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/paqmir_mapper/test-data/cel_cluster.fa Mon Mar 18 09:17:49 2019 -0400
b
@@ -0,0 +1,132 @@
+>chrII:11534525-11540624
+tccaaaatattagaggccccacgaaaaggggagcagaacgaaaaggggat
+ctgcaaaaaggggatctgcgaaaaggggagatacgaaaaggggagatacg
+aaaaggggagcaacgaaaaggggatctggcactgtgccaaacgctatttt
+tctcaaagaaaacaatacaacgatgctccgatgttacgcgtcgcgtgttg
+ttaagcgtatcttctagaagaaaatttcaaaaatcaacgtgcgttgcgtg
+agaaaaattgcgttttgtgcgtttggcacagtgccagctccccttttcgt
+tgctccccttttcgtatctccccttttcgtatctccccttttcgcagatc
+ccctttttgcagatccccttttcgttctgctcccctcgtggggcctcaaa
+taatattgtcaatggagcgcagttgcgcacaccgaaatacgcacgaaatt
+tgaaattggcaggcctagaaagtctggatttaaaatatttatgcatatta
+acctgagtttcggcatgtttagataaatttagattaaaatttattaaata
+aaaatatttaaaatttattaaattcaacattatctttaattttacagaaa
+taaaaaccaaaaaaccaacgaagtgtaacttttcgacaataaatatttat
+aaattattcaattaattggaaatctatttatcacatctcatcgtgaacaa
+gcacatggctaaacaatgcctcgactttatccacccatcctggatttttc
+ctgttgaaaatcttcaaatccttcatagtctgctcaattgccttaacagc
+cttttcccttttcacatccttcgtcaattcctcaaccatcgcctctacaa
+gttgtgatcgtgaggccccttcaacgaatttcttgtccaatacatctctg
+agctgaaaaataagtccctttattcatgtgcaccacctgccactcattca
+ttttagatcctaatcctgtatttctctctctctctcactaatcgtcccgt
+catatctgacccactataatgaggggaccaccactttgccccagatttcg
+taatgagccaacatacactaggccctgttctagcacccccattgtgcatg
+ggagacacatcgtctgttggttcgggtcagctgagatgacgtggcagatg
+acgtcatgtttgttctctagcagatccctatcgtaaaataccgttctttg
+ttcgtttatgagcacttcttgggaaacaagaagaatattagagaatattg
+gattttaggaaatttcttgaccctaataatatgtatctcatggggctaat
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+gagttttctggaagaaaaagtatatatagtttgataaaaagttacgtcat
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+tagatctcaaagaatatggttttcctgctgagaaacaaaatttttttttc
+aaatgttcgcgatattatacgatttttttgcgctgaaaaatacggtatcc
+ggactcgacacgacagtttttcaataaattcggaaaggtacatatgcgcc
+tttgaagagtactgtaattttaaacatttgttgatgcagtaaatattctc
+acggatttttagaggtttttttttgaatatttatacagttatattagagt
+taaaaaaataaatctatttttatcgaaatttatgaaaaatctactcccca
+gaaacaaagtttgaatttacttaaaatgtatgtgcgcctttttaaattca
+acaaaaatttatcaaattttgtctttttaatcacttttacttttttttcg
+aaaaaaaaaaaaactttaaaaacaccgaaaattaaaatttttaattaccg
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+tggctccatcttttttatttctggtttttttcccgacacgggaggtcatc
+cgtccacgtcttcaatcttattcgcttctccttctatctatctctcttcc
+aaaaaaatggaacagattgtccgccttctactttccgcatgcgcctattc
+tagacatcgagaagaagcgagagaatccgaaaaactccgccgtccggcgc
+ctagcgttcatcccgtcgcatccaatttccttcacccctgtctccagtct
+ctaatctgtgtttcccagaccttctccttcttcttctcccctctttcttc
+cctttcttttctacgattcctagacctgcccggttgaccatcgggcccac
+catttatcgagcgcgtccgtctgttcgttgctgtgagcgcgcgcgcgcga
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+aatgggcggagacccaatggtgcaccaagtcagcagtataaaaggaatgg
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+tcactttctcccttcttcccctctcctaatttccattcccaactattatt
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+ttagaactatcaccgggtggaaactagcagtggctcgatcttttccactt
+gctccaccgctgtcggggaaccgcgccaattttcgcttcagtgctagacc
+atccaaagtgtctatcaccgggtgaaaattcgcatgggtccccgacgcgg
+aaagataaaatatcttaaaatcgattctagaaacccttggaccagtgtgg
+gtgtccgttgcggtgctacattctctaatctgtatcaccgggtgaacact
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+actacaatggaagcaaaaagagcgacaattaggatcgtcattttagtgga
+gaatgatgaattgacccggctctttgggggttggaggattcattttcccc
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+aataattagaattagaattatatcgttttgtacggattgagaatcccatt
+tgggtcgaaaatgttcttgagcttctttgtcaaaagtcgttcttcaggat
+cttttccgaatgtggagtacggtagcttcagttgaccgattccatgttca
+gctgaaattgacccgccgtgatcgacaacccattcgtagaggaagggata
+gagcctggaatttgaaattattaatagaattaaaattttataaaaaagaa
+aaatctcgaaacttacaatttttcaagttcttcattgtgtttttcagatg
+taatatttaaatgagtgtttccatctcccaaatgtccataagtgacaatt
+cttttagccaaagaaccacatcgttccttcatcacattcgtcaattcata
+ataattttccaatggtaaagaaacatcatgcttatagacatatccatctc
+tggtaaccgccaatggtgcactttctctcaattgccacatcttcgtagct
+tctgcagaagatccagcgagcactccgtcgataatcagattttttgagag
+gcattcatccaaaaatgcgctcattttctccatatcgtgatcttcattgg
+atcctgatgtttcgacaaggatcgagaatggggttggagcattcagtact
+gggtgcaatcctagattcgttttcaaacattccatcgtagcatcgtcgag
+aagttcgaaggaggaaaggatttcagtgaggctggattttgcaagcttca
+gtacttcgcagcattttttgaaggattcgatgcctgaaaaaaattagaaa
+ttgaaaaatttgaacccattatataaatattcaacctaccaagcatcgca
+ctttgtacacttttcggtttaggaaccgcagtcattgtgacgcttgtgat
+aacacccaactgcccttcacttcccaagaataggtgtggagtgtgcaaag
+ttgtgttgtccttccgaatgcttgatcccaaatgtagaacagttccatgt
+tcatcgggaagaaccaccgtgagcccgagaagatgtgcgtgaagacttcc
+gtatcgaatcaaccgaatccctcctgcacacgtggcaatatttcctccaa
+tctgacaggatcctttggctccgagatcaaaaggcatcatatatccgagt
+tttgcaagtttgttgtccaagtcttccagaataaaaccagaatcacactt
+gagaattcccattgtgtcgtcgaaagagaattgcttgttgattttattca
+ttgatataacaacttcatcatgtactggaattgatccaccaacgagtcct
+gtattccctccttgtgggactactgccaatttgttcttggagcaatacgc
+caatattgcagaaacctcttcggtgctcttcgggtagaggacgacactgc
+caggacctggaaattaaaacatttaatatttaaagtacctatttaatatt
+aaataaacctaatcttaaaatacaaatacctttaaattggcctgtccaat
+ctgtagtatgatttgtaatatcgtccttcttcactgcatcttgcccgaga
+aaattctcaaatgccattaaatccgactgcatcacttttgcaaatccttc
+atgtctggcggcaagaactgctgcgtagcttctagttggtcttctgattc
+gtggcaagattttcagaaacatctgaattcagaaacttttcaaaaaataa
+cttgaaacttcaaaagaaatagtaggagacaaagctcggctaggtgaccg
+
+>chrIII:2172325-2172669
+CAGGCAGTCAGTCAGTCTCTCTCCACTCACATTCAGTCAGTCAGTGACCA
+TCACCAGGTTGTGTGTGAGCCCCTTCCATTATTCTTCTGAACCCCCCTCC
+CAACGCGGGAAGACTCGCCGGCAATGACACTGGTTATCTTTTCCATCGTG
+GAATGCCCCCCATTGATTTTTTCCCCTTTTCGGGGGGAAAAAATTGGAAA
+CGAGAAAGGTATCGGGTGTCATAGCCGGCGTGATCATCTTCCTCAAGTAT
+TCCTCTGCTGATTTCGATATTCGGAGGAGCTCGGAGGCTGTTCAGCTGTA
+AAATTGGTTGATTAAGCTCAAAAATCGGCGTTAACGCGGCTTTCC
b
diff -r 000000000000 -r 2e4a523f5bc5 paqmir_mapper/test-data/reads.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/paqmir_mapper/test-data/reads.fa Mon Mar 18 09:17:49 2019 -0400
b
b'@@ -0,0 +1,756666 @@\n+>nematode_1\n+TCACCGGGTGTAAATCAGCTTGTCGTATGCCGTCT\n+>nematode_2\n+TCACCGGGTGAACACTTGCAGTTCGTATGACGTCT\n+>nematode_3\n+TCACCGGGTGAACACTTGCAGTTCGTATGCCGTCT\n+>nematode_4\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_5\n+TCACCGGGTGGAAACTAGCTGTCGTATGCCGTCTT\n+>nematode_6\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_7\n+TCACCGGGGGGAAACTAGCAGTTCGTATGCTGTTT\n+>nematode_8\n+TCACCGGGTGAACACCTGCAGTTCGTATGCCGTCT\n+>nematode_9\n+TCACCGGGCGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_10\n+TCACCGGGTGAACACTTGCAGTTCGTATGCCGTCT\n+>nematode_11\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_12\n+TCACCGGGTGAACACTTGCAGTTCGTATGCCGTCT\n+>nematode_13\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_14\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_15\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_16\n+TCACCGGGTGAACACTTGCAGTTCGTATGCCGTCT\n+>nematode_17\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_18\n+TCACCGGGTGGAAACTAGCAGTCGTATGCCGTCAT\n+>nematode_19\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_20\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_21\n+TCACCGGGTGAAAATTCGCATGTCGTATGCCTTCT\n+>nematode_22\n+TCACCGGGAGGAAACTAGCAGTCGTATGCCGTCTT\n+>nematode_23\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_24\n+TCACCGAGTGAACACTTGCATCGTATGCCGTCTTT\n+>nematode_25\n+TCACCGGGTGGAAACTAGCAGTTTCGTATGCCGTC\n+>nematode_26\n+TCACCGGGTGGAAACTAGCAGTATCGTATGCCGTT\n+>nematode_27\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTTT\n+>nematode_28\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_29\n+TCACCGGGCGAACACTTGCAGTTCGTATGCCGTCT\n+>nematode_30\n+TCACCGGGTGAACACTTGCAGTTCGTATGCCGTCT\n+>nematode_31\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_32\n+TCACCGGGTGGAAACTAGCAGATCGTATGCCGTCT\n+>nematode_33\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_34\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_35\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_36\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_37\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_38\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_39\n+AGCTGATTTCGTCTTGGTAATATCGTATGCCGTCT\n+>nematode_40\n+TCACCGGGTGGCAACTAGCAGTTCGTATTCCGTGT\n+>nematode_41\n+ACCGGGTGGAAACTAGCAGTTCGTATGCCGTCTTC\n+>nematode_42\n+TCACCGGGTGAACACTTGCAGTTCGTATGCCGTCT\n+>nematode_43\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_44\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_45\n+TCACCGGGTGTACATCAGCTAATCGTATGCCGTCT\n+>nematode_46\n+TCACCGGGTGGAAACTATCAGTTCGTATGCCGTCT\n+>nematode_47\n+ACCGGGTGTACATCAGCTAATCGTATGCCGTCTTC\n+>nematode_48\n+TCACCGGGTGAACACTTGCAGTTTCGTATGCAGTC\n+>nematode_49\n+TCACCGGGTGTACATCAGCTAATCGTATGCCGTCT\n+>nematode_50\n+TCACCGGGTGAACACTTGCAGTTCGTATGCCGTCT\n+>nematode_51\n+AGCTAATTTCGTCTTGGTAATATCGTATGCCGTCT\n+>nematode_52\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_53\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_54\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_55\n+TCACCGGGTGAAAATTCGCATGTCGTATGCCGTCT\n+>nematode_56\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_57\n+ACCGGGTGAACACTTGCAGTTCGTATGCCGTCTTT\n+>nematode_58\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_59\n+TCACCGGGTGAACACTTGCAGTTCGTATGCCGTCT\n+>nematode_60\n+TCACCGGGTGGAAACTAGCAGTTTCGTATGCCGTT\n+>nematode_61\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_62\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_63\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_64\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_65\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_66\n+TCACCGGGTGGAAACTAGCATTTCGTATGCCGTCT\n+>nematode_67\n+TCACCGGGTGTACATCAGCTAATCGTATGCCGTCT\n+>nematode_68\n+TCACCGGGTGTACATCAGCTATCGTATGCCGTCTT\n+>nematode_69\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_70\n+TCACCGGGTGTAGATCAGCTAATCGTATGCTGTCT\n+>nematode_71\n+TCACCGGGTGAACACTTGCAGTTCGTATGCCGTCT\n+>nematode_72\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_73\n+ACCGGGTGGAAACTAGCAGTCGTATGCCGTCTTCT\n+>nematode_74\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_75\n+TCACCGCGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_76\n+TCACCGGGTGAACACTTGCAGTTCGTATGCCGTCT\n+>nematode_77\n+TCACCGGGTGAACACTTGCAGTTCGTATGCAGTCT\n+>nematode_78\n+TCACCGGGTGTACATCAGCTAATCGTATGCCGTCT\n+>nematod'..b'GC\n+>nematode_378259\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378260\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378261\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378262\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378263\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378264\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378265\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378266\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378267\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378268\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378269\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378270\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378271\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378272\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378273\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378274\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378275\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378276\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378277\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378278\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378279\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378280\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378281\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378282\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378283\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378284\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378285\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378286\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378287\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378288\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378289\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378290\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378291\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378292\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378293\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378294\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378295\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378296\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378297\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378298\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378299\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378300\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378301\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378302\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378303\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378304\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378305\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378306\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378307\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378308\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378309\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378310\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378311\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378312\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378313\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378314\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378315\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378316\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378317\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378318\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378319\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378320\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378321\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378322\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378323\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378324\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378325\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378326\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378327\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378328\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378329\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378330\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378331\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378332\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n'
b
diff -r 000000000000 -r 2e4a523f5bc5 paqmir_mapper/test-data/reads_sample1.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/paqmir_mapper/test-data/reads_sample1.fa Mon Mar 18 09:17:49 2019 -0400
b
b'@@ -0,0 +1,500 @@\n+>nematode_1\n+TCACCGGGTGTAAATCAGCTTGTCGTATGCCGTCT\n+>nematode_2\n+TCACCGGGTGAACACTTGCAGTTCGTATGACGTCT\n+>nematode_3\n+TCACCGGGTGAACACTTGCAGTTCGTATGCCGTCT\n+>nematode_4\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_5\n+TCACCGGGTGGAAACTAGCTGTCGTATGCCGTCTT\n+>nematode_6\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_7\n+TCACCGGGGGGAAACTAGCAGTTCGTATGCTGTTT\n+>nematode_8\n+TCACCGGGTGAACACCTGCAGTTCGTATGCCGTCT\n+>nematode_9\n+TCACCGGGCGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_10\n+TCACCGGGTGAACACTTGCAGTTCGTATGCCGTCT\n+>nematode_11\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_12\n+TCACCGGGTGAACACTTGCAGTTCGTATGCCGTCT\n+>nematode_13\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_14\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_15\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_16\n+TCACCGGGTGAACACTTGCAGTTCGTATGCCGTCT\n+>nematode_17\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_18\n+TCACCGGGTGGAAACTAGCAGTCGTATGCCGTCAT\n+>nematode_19\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_20\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_21\n+TCACCGGGTGAAAATTCGCATGTCGTATGCCTTCT\n+>nematode_22\n+TCACCGGGAGGAAACTAGCAGTCGTATGCCGTCTT\n+>nematode_23\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_24\n+TCACCGAGTGAACACTTGCATCGTATGCCGTCTTT\n+>nematode_25\n+TCACCGGGTGGAAACTAGCAGTTTCGTATGCCGTC\n+>nematode_26\n+TCACCGGGTGGAAACTAGCAGTATCGTATGCCGTT\n+>nematode_27\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTTT\n+>nematode_28\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_29\n+TCACCGGGCGAACACTTGCAGTTCGTATGCCGTCT\n+>nematode_30\n+TCACCGGGTGAACACTTGCAGTTCGTATGCCGTCT\n+>nematode_31\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_32\n+TCACCGGGTGGAAACTAGCAGATCGTATGCCGTCT\n+>nematode_33\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_34\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_35\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_36\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_37\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_38\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_39\n+AGCTGATTTCGTCTTGGTAATATCGTATGCCGTCT\n+>nematode_40\n+TCACCGGGTGGCAACTAGCAGTTCGTATTCCGTGT\n+>nematode_41\n+ACCGGGTGGAAACTAGCAGTTCGTATGCCGTCTTC\n+>nematode_42\n+TCACCGGGTGAACACTTGCAGTTCGTATGCCGTCT\n+>nematode_43\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_44\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_45\n+TCACCGGGTGTACATCAGCTAATCGTATGCCGTCT\n+>nematode_46\n+TCACCGGGTGGAAACTATCAGTTCGTATGCCGTCT\n+>nematode_47\n+ACCGGGTGTACATCAGCTAATCGTATGCCGTCTTC\n+>nematode_48\n+TCACCGGGTGAACACTTGCAGTTTCGTATGCAGTC\n+>nematode_49\n+TCACCGGGTGTACATCAGCTAATCGTATGCCGTCT\n+>nematode_50\n+TCACCGGGTGAACACTTGCAGTTCGTATGCCGTCT\n+>nematode_51\n+AGCTAATTTCGTCTTGGTAATATCGTATGCCGTCT\n+>nematode_52\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_53\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_54\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_55\n+TCACCGGGTGAAAATTCGCATGTCGTATGCCGTCT\n+>nematode_56\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_57\n+ACCGGGTGAACACTTGCAGTTCGTATGCCGTCTTT\n+>nematode_58\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_59\n+TCACCGGGTGAACACTTGCAGTTCGTATGCCGTCT\n+>nematode_60\n+TCACCGGGTGGAAACTAGCAGTTTCGTATGCCGTT\n+>nematode_61\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_62\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_63\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_64\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_65\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_66\n+TCACCGGGTGGAAACTAGCATTTCGTATGCCGTCT\n+>nematode_67\n+TCACCGGGTGTACATCAGCTAATCGTATGCCGTCT\n+>nematode_68\n+TCACCGGGTGTACATCAGCTATCGTATGCCGTCTT\n+>nematode_69\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_70\n+TCACCGGGTGTAGATCAGCTAATCGTATGCTGTCT\n+>nematode_71\n+TCACCGGGTGAACACTTGCAGTTCGTATGCCGTCT\n+>nematode_72\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_73\n+ACCGGGTGGAAACTAGCAGTCGTATGCCGTCTTCT\n+>nematode_74\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_75\n+TCACCGCGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_76\n+TCACCGGGTGAACACTTGCAGTTCGTATGCCGTCT\n+>nematode_77\n+TCACCGGGTGAACACTTGCAGTTCGTATGCAGTCT\n+>nematode_78\n+TCACCGGGTGTACATCAGCTAATCGTATGCCGTCT\n+>nematode_7'..b'atode_174\n+TCACCGGGGGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_175\n+TCACCGGGTGCACATCAGCTAATCGTATGCCGTCT\n+>nematode_176\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_177\n+TCACCGGGTGAACACTTGCAGTTCGTATGCCGTCT\n+>nematode_178\n+TCACCGGGTGAACACTTGCAGTTCGTATGCCGTCT\n+>nematode_179\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_180\n+TCACCGGGTGAAAATTCGCATGTCGTATGCCGTCT\n+>nematode_181\n+TCACCGGGTGAACACTGGCAGTTCGTATGCCGTTT\n+>nematode_182\n+TCACCGGGTGAACACTTGCAGTTCGTATGCCGTCT\n+>nematode_183\n+TCACCGGGTGAACACTTGCAGTTCGTATGCCGTCT\n+>nematode_184\n+TCACCGGGTGAAAATTCGCATGTCGTATGCCGTCT\n+>nematode_185\n+TCACCGGGTGAACACTTGCAGTTCGTATGCCGTCT\n+>nematode_186\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_187\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_188\n+TCACCGGGTGAACACTTGCAGTTCGTATGCCGTCT\n+>nematode_189\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_190\n+TCACCGGGGGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_191\n+TCACCGGGTGAACACTTGCAGTTCGTATGCCTTCT\n+>nematode_192\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_193\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_194\n+TCACCGGGTGGTAACTAGCAGTTCGTATGCCGTCT\n+>nematode_195\n+TCACCGGGTGGAAACTAGCAGTTCGTATGACGCCT\n+>nematode_196\n+TCACCGGGAGAACACTTGCAGTTCGTATGCTGTCT\n+>nematode_197\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_198\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_199\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_200\n+TCACCGGGTGAAAATTCGCATGTCGTATGCCGTCT\n+>nematode_201\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_202\n+TCACCGGGTGAACACTTGCAGTTCGTATGCCGTCT\n+>nematode_203\n+TCACCGGGCGAACACTTGCAGTTCGTATGACGTCT\n+>nematode_204\n+TCACAGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_205\n+TCACCGGGTGAAAATTCGCATGTCGTATGCCGTCT\n+>nematode_206\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_207\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_208\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_209\n+TCACCGGGCGAACACTTGCAGTTCGTATGCCGTCT\n+>nematode_210\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_211\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_212\n+TCACCGGGTGAACACTTGCAGTTCGTATGCCGTCT\n+>nematode_213\n+TCACCGGGCGGAAACTAGCAGTTCGTATCCCTTCT\n+>nematode_214\n+TCACCGGGTGTACTTCAGCTAATCGTATGCCGTCT\n+>nematode_215\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_216\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_217\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_218\n+TCACCGGGTGAACACTTGCAGTTCGTATGCCGTCT\n+>nematode_219\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_220\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_221\n+TCACCGGGTGGAAACTAGCAGTCGTATGCCGTCTT\n+>nematode_222\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_223\n+TCACCGGGTGAAAATTCGCATGTCGTATGCCGTCT\n+>nematode_224\n+TCACCGGGAGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_225\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_226\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCTGTCT\n+>nematode_227\n+TCACCGGGTGAACACTTGCAGTTCGTATGCCGTCT\n+>nematode_228\n+TCACCGGGGGAACACTTGCAGTTCGTATGCCGTCT\n+>nematode_229\n+TCACCGGGTGGAAACTAGCAGTTTCGTATGCCGTC\n+>nematode_230\n+TCACAGGGTGTACATCAGCTAATCGTATGCCGTCT\n+>nematode_231\n+TCACCGGGTGAACACTTGCAGTTCGTATGCCGTCT\n+>nematode_232\n+TCACCGGGTGAACACTTGCAGTTCGTATGCCGTCT\n+>nematode_233\n+TCACCGGGTGAAAATTCGCATGTCGTATGCCGTCT\n+>nematode_234\n+TCACCGGGTGAACACTTGCAGTTCGTATGCAGTCT\n+>nematode_235\n+TCACCGGGTGGAAACTAGCAGTCGTATGCCGTCTT\n+>nematode_236\n+TCACCGGGTGTACATCAGCTCGTATGCCGTCTTCT\n+>nematode_237\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_238\n+TCACCGGGTGAACACTTGCAGTTCGTATGCCGTCT\n+>nematode_239\n+TCACCGGGTGGAAACTAGCAGTTTCGTATGCCGTC\n+>nematode_240\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_241\n+TCACCGGGTGGAAACTAGCAGTCGTATGCCGTCTT\n+>nematode_242\n+TCACCGGGTGTACATCAGCTAATTCGTATGCCGTC\n+>nematode_243\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_244\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_245\n+TCACCGGGTGAACACTTGCAGTTCGTATGCCGTCT\n+>nematode_246\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_247\n+TCACCGGGTGAACACTTGCAGTTCGTATGCCGTCT\n+>nematode_248\n+TCACCGGGTGAAAATTCGCATGTCGTATGCCGTCT\n+>nematode_249\n+TCACCGGGTGAACACTTGCAGTTCGTATGCCGTCT\n+>nematode_250\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n'
b
diff -r 000000000000 -r 2e4a523f5bc5 paqmir_mapper/test-data/reads_sample2.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/paqmir_mapper/test-data/reads_sample2.fa Mon Mar 18 09:17:49 2019 -0400
b
b'@@ -0,0 +1,500 @@\n+>nematode_378083\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378084\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378085\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378086\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378087\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378088\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378089\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378090\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378091\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378092\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378093\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378094\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378095\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378096\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378097\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378098\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378099\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378100\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378101\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378102\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378103\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378104\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378105\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378106\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378107\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378108\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378109\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378110\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378111\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378112\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378113\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378114\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378115\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378116\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378117\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378118\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378119\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378120\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378121\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378122\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378123\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378124\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378125\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378126\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378127\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378128\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378129\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378130\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378131\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378132\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378133\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378134\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378135\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378136\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378137\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378138\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378139\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378140\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378141\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378142\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378143\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378144\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378145\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378146\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378147\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378148\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378149\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378150\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378151\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378152\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378153\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378154\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378155\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378156\n+AATGACACTGGTTATCTTTT'..b'GC\n+>nematode_378259\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378260\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378261\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378262\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378263\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378264\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378265\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378266\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378267\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378268\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378269\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378270\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378271\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378272\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378273\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378274\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378275\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378276\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378277\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378278\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378279\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378280\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378281\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378282\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378283\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378284\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378285\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378286\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378287\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378288\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378289\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378290\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378291\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378292\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378293\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378294\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378295\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378296\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378297\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378298\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378299\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378300\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378301\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378302\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378303\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378304\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378305\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378306\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378307\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378308\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378309\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378310\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378311\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378312\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378313\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378314\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378315\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378316\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378317\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378318\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378319\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378320\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378321\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378322\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378323\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378324\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378325\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378326\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378327\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378328\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378329\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378330\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378331\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378332\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n'
b
diff -r 000000000000 -r 2e4a523f5bc5 paqmir_mapper/tool-data/bowtie2_indices.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/paqmir_mapper/tool-data/bowtie2_indices.loc Mon Mar 18 09:17:49 2019 -0400
b
@@ -0,0 +1,2 @@
+hg18canon hg18 hg18 Canonical /projet/gabi/work/smarthey/miRNA_pipeline_template/mapper/reads_vs_genome_bta8.arf
+hg18full hg18 hg18 Full /projet/gabi/work/smarthey/miRNA_pipeline_template/mapper/reads_vs_genome_bta8.arf
b
diff -r 000000000000 -r 2e4a523f5bc5 paqmir_mapper/tool-data/bowtie_indices.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/paqmir_mapper/tool-data/bowtie_indices.loc.sample Mon Mar 18 09:17:49 2019 -0400
b
@@ -0,0 +1,37 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of Bowtie indexed sequences data files. You will
+#need to create these data files and then create a bowtie_indices.loc
+#file similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The bowtie_indices.loc
+#file has this format (longer white space characters are TAB characters):
+#
+#<unique_build_id>   <dbkey>   <display_name>   <file_base_path>
+#
+#So, for example, if you had hg18 indexed stored in
+#/depot/data2/galaxy/bowtie/hg18/,
+#then the bowtie_indices.loc entry would look like this:
+#
+#hg18 hg18 hg18 /depot/data2/galaxy/bowtie/hg18/hg18
+#
+#and your /depot/data2/galaxy/bowtie/hg18/ directory
+#would contain hg18.*.ebwt files:
+#
+#-rw-r--r--  1 james    universe 830134 2005-09-13 10:12 hg18.1.ebwt
+#-rw-r--r--  1 james    universe 527388 2005-09-13 10:12 hg18.2.ebwt
+#-rw-r--r--  1 james    universe 269808 2005-09-13 10:12 hg18.3.ebwt
+#...etc...
+#
+#Your bowtie_indices.loc file should include an entry per line for each
+#index set you have stored. The "file" in the path does not actually
+#exist, but it is the prefix for the actual index files. For example:
+#
+#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/bowtie/hg18/hg18canon
+#hg18full hg18 hg18 Full /depot/data2/galaxy/bowtie/hg18/hg18full
+#/orig/path/hg19 hg19 hg19 /depot/data2/galaxy/bowtie/hg19/hg19
+#...etc...
+#
+#Note that for backwards compatibility with workflows, the unique ID of
+#an entry must be the path that was in the original loc file, because that
+#is the value stored in the workflow for that parameter. That is why the
+#hg19 entry above looks odd. New genomes can be better-looking.
+#
b
diff -r 000000000000 -r 2e4a523f5bc5 paqmir_mapper/tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/paqmir_mapper/tool_data_table_conf.xml.sample Mon Mar 18 09:17:49 2019 -0400
b
@@ -0,0 +1,8 @@
+<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc-->
+<tables>
+    <!-- Locations of indexes in the Bowtie mapper format -->
+    <table name="bowtie_indexes" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/bowtie_indices.loc" />
+    </table>
+</tables>