Repository 't_coffee'
hg clone https://toolshed.g2.bx.psu.edu/repos/earlhaminst/t_coffee

Changeset 8:ae69d14b6fbf (2021-01-14)
Previous changeset 7:0a189243186d (2019-09-18)
Commit message:
"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 28bbc172f28d9fbe7ed2795043ff61d9e0642d13"
modified:
t_coffee.xml
added:
test-data/output3.clustal
test-data/output3.fasta_aln
test-data/output3.fasta_seq
test-data/output3.msf
test-data/output3.nhx
test-data/output3.phylip
test-data/output3.pir_aln
test-data/output3.pir_seq
test-data/output3.txt
b
diff -r 0a189243186d -r ae69d14b6fbf t_coffee.xml
--- a/t_coffee.xml Wed Sep 18 06:37:40 2019 -0400
+++ b/t_coffee.xml Thu Jan 14 12:14:52 2021 +0000
[
b'@@ -1,7 +1,10 @@\n-<tool id="t_coffee" name="T-Coffee" version="11.0.8_1">\n+<tool id="t_coffee" name="T-Coffee" version="@TOOL_VERSION@">\n     <description>multiple sequence alignment</description>\n+    <macros>\n+        <token name="@TOOL_VERSION@">13.45.0.4846264</token>\n+    </macros>\n     <requirements>\n-        <requirement type="package" version="11.0.8">t_coffee</requirement>\n+        <requirement type="package" version="@TOOL_VERSION@">t-coffee</requirement>\n     </requirements>\n     <stdio>\n         <exit_code range="1:" level="fatal" />\n@@ -60,28 +63,29 @@\n                 <param name="input" type="data" format="fasta" label="FASTA sequences" />\n             </when>\n         </conditional>\n-        <param name="method01" type="select" display="checkboxes" multiple="true" label="Pairwise Structual Method">\n-            <option value="sap_pair">sap_pair</option>\n-            <option value="TMalign_pair">TMalign_pair</option>\n-            <option value="mustang_pair">mustang_pair</option>\n-        </param>\n-        <param name="method02" type="select" display="checkboxes" multiple="true" label="Multiple Sequence Alignment Methods">\n-            <option value="pcma_msa">pcma_msa</option>\n-            <option value="clustalw_msa">clustalw_msa</option>\n-            <option value="dialigntx_msa">dialigntx_msa</option>\n-            <option value="poa_msa">poa_msa</option>\n-            <option value="muscle_msa">muscle_msa</option>\n-            <option value="probcons_msa">probcons_msa</option>\n-            <option value="t_coffee_msa">t_coffee_msa</option>\n-            <option value="amap_msa">amap_msa</option>\n-            <option value="kalign_msa">kalign_msa</option>\n-        </param>\n         <param name="method03" type="select" display="checkboxes" multiple="true" label="Pairwise Sequence Alignment Methods">\n             <option value="fast_pair">fast_pair</option>\n             <option value="clustalw_pair">clustalw_pair</option>\n             <option value="lalign_id_pair">lalign_id_pair</option>\n             <option value="slow_pair">slow_pair</option>\n             <option value="proba_pair">proba_pair</option>\n+            <option value="t_coffee_pair">t_coffee_pair</option>\n+        </param>\n+        <param name="method01" type="select" display="checkboxes" multiple="true" label="Pairwise Structual Alignment Methods">\n+            <option value="sap_pair">sap_pair</option>\n+            <option value="mustang_pair">mustang_pair</option>\n+            <option value="TMalign_pair">TMalign_pair</option>\n+        </param>\n+        <param name="method02" type="select" display="checkboxes" multiple="true" label="Multiple Sequence Alignment Methods">\n+            <option value="3dcoffee_msa">3dcoffee_msa</option>\n+            <option value="mafft_msa">mafft_msa</option>\n+            <option value="clustalw_msa">clustalw_msa</option>\n+            <option value="dialigntx_msa">dialigntx_msa</option>\n+            <option value="poa_msa">poa_msa</option>\n+            <option value="probcons_msa">probcons_msa</option>\n+            <option value="muscle_msa">muscle_msa</option>\n+            <option value="t_coffee_msa">t_coffee_msa</option>\n+            <option value="kalign_msa">kalign_msa</option>\n         </param>\n         <param name="outputs" type="select" multiple="true" optional="false" display="checkboxes" label="Output formats">\n             <option value="clustalw_aln">clustalw_aln</option>\n@@ -97,7 +101,7 @@\n         </param>\n     </inputs>\n     <outputs>\n-        <data name="clustalw_aln" format="clustalw" label="${tool.name} on ${on_string}: clustalw_aln" from_work_dir="t_coffee_out.clustalw_aln">\n+        <data name="clustalw_aln" format="clustal" label="${tool.name} on ${on_string}: clustalw_aln" from_work_dir="t_coffee_out.clustalw_aln">\n             <filter>\'clustalw_aln\' in outputs</filter>\n         </data>\n         <data name="dnd" format="nhx" label="${tool.name} on ${on_string}: newick.dnd" from_work_dir="t_cof'..b'aln" from_work_dir="t_coffee_out.msf_aln">\n             <filter>\'msf_aln\' in outputs</filter>\n         </data>\n-        <data name="phylip" format="phyloxml" label="${tool.name} on ${on_string}: phylip" from_work_dir="t_coffee_out.phylip">\n+        <data name="phylip" format="phylip" label="${tool.name} on ${on_string}: phylip" from_work_dir="t_coffee_out.phylip">\n             <filter>\'phylip\' in outputs</filter>\n         </data>\n         <data name="pir_aln" format="pir" label="${tool.name} on ${on_string}: pir_aln" from_work_dir="t_coffee_out.pir_aln">\n@@ -121,7 +125,7 @@\n         <data name="pir_seq" format="pir" label="${tool.name} on ${on_string}: pir_seq" from_work_dir="t_coffee_out.pir_seq">\n             <filter>\'pir_seq\' in outputs</filter>\n         </data>\n-        <data name="score_ascii" format="ascii" label="${tool.name} on ${on_string}: score_ascii" from_work_dir="t_coffee_out.score_ascii">\n+        <data name="score_ascii" format="txt" label="${tool.name} on ${on_string}: score_ascii" from_work_dir="t_coffee_out.score_ascii">\n             <filter>\'score_ascii\' in outputs</filter>\n         </data>\n         <data name="score_html" format="html" label="${tool.name} on ${on_string}: score_html" from_work_dir="t_coffee_out.score_html">\n@@ -129,20 +133,47 @@\n         </data>\n     </outputs>\n     <tests>\n-        <test>\n+        <test expect_num_outputs="1">\n             <param name="filter_fasta" value="no" />\n             <param name="input" value="input.fasta" ftype="fasta" />\n             <param name="method02" value="clustalw_msa" />\n             <param name="outputs" value="fasta_aln" />\n-            <output name="fasta_aln" file="output1.fasta" ftype="fasta" />\n+            <output name="fasta_aln" file="output1.fasta" />\n         </test>\n-        <test>\n+        <test expect_num_outputs="1">\n             <param name="filter_fasta" value="yes" />\n             <param name="fasta_input" value="input.fasta" ftype="fasta" />\n             <param name="identifiers" value="ids.txt" ftype="txt" />\n             <param name="method02" value="clustalw_msa" />\n             <param name="outputs" value="fasta_aln" />\n-            <output name="fasta_aln" file="output2.fasta" ftype="fasta" />\n+            <output name="fasta_aln" file="output2.fasta" />\n+        </test>\n+        <!-- Test all non-builtin methods and all outputs -->\n+        <test expect_num_outputs="10">\n+            <param name="filter_fasta" value="no" />\n+            <param name="input" value="input.fasta" ftype="fasta" />\n+            <param name="method03" value="clustalw_pair,t_coffee_pair" />\n+            <param name="method01" value="sap_pair,mustang_pair,TMalign_pair" />\n+            <param name="method02" value="mafft_msa,clustalw_msa,dialigntx_msa,poa_msa,probcons_msa,muscle_msa,t_coffee_msa,kalign_msa" />\n+            <param name="outputs" value="clustalw_aln,dnd,fasta_aln,fasta_seq,msf_aln,phylip,pir_aln,pir_seq,score_ascii,score_html" />\n+            <output name="clustalw_aln" file="output3.clustal" />\n+            <output name="dnd" file="output3.nhx" />\n+            <output name="fasta_aln" file="output3.fasta_aln" />\n+            <output name="fasta_seq" file="output3.fasta_seq" />\n+            <output name="msf_aln" file="output3.msf" />\n+            <output name="phylip" file="output3.phylip" />\n+            <output name="pir_aln" file="output3.pir_aln" />\n+            <output name="pir_seq" file="output3.pir_seq" />\n+            <output name="score_ascii" file="output3.txt" />\n+            <output name="score_html">\n+                <assert_contents>\n+                    <has_text text="ENSMUST00000091" />\n+                    <has_text text="ENSCAFT00000026" />\n+                    <has_text text="ENSMUST00000005" />\n+                    <has_text text="ENSRNOT00000019" />\n+                    <has_text text="ENSPTRT00000013" />\n+                </assert_contents>\n+            </output>\n         </test>\n     </tests>\n     <help><![CDATA[\n'
b
diff -r 0a189243186d -r ae69d14b6fbf test-data/output3.clustal
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output3.clustal Thu Jan 14 12:14:52 2021 +0000
b
b'@@ -0,0 +1,599 @@\n+CLUSTAL W (1.83) multiple sequence alignment\n+\n+ENSMUST00000091291_musmusculus       ATGGG-CTTCGGGAGAGGATGTGAGACGACGG-----CTGTGCCATTGCT\n+ENSCAFT00000026349_canisfamiliaris   ATGGCAGT---GCCCAGT--CTGTGCCCATGG-GTCGC-ATGC--CTGCT\n+ENSMUST00000005671_homosapiens       ATGAA-GTCTGGCTCCGGAGGAGGGTCCCCGACCTCGCTGTGG--GGGCT\n+ENSRNOT00000019267_rattusnorvegicus  ATGAA-GTCTGGCTCCGGAGGAGGGTCCCCGACCTCGCTGTGG--GGGCT\n+ENSPTRT00000013802_pantroglodytes    ATGAA-GTCTGGCTCCGGAGGAGGGTCCCCGACCTCGCTGTGG--GGGCT\n+                                     ***    *   *    *     * * *   *      *  **     ***\n+\n+ENSMUST00000091291_musmusculus       GGTGGCCGTGGCCGCGTTGCTGGTGGGCACAGCCGGCCACCTGTACCCTG\n+ENSCAFT00000026349_canisfamiliaris   GGTGATCCTCCTCTCCTTGGGATTTGGCCTGGAC------------ACAC\n+ENSMUST00000005671_homosapiens       CGTGTTTCTCTCCGCCGCGCTC-TCTCTCTGGCCGA---C-----GAGTG\n+ENSRNOT00000019267_rattusnorvegicus  CGTGTTTCTCTCCGCCGCGCTC-TCGCTCTGGCCGA---C-----GAGTG\n+ENSPTRT00000013802_pantroglodytes    CCTGTTTCTCTCCGCCGCGCTC-TCGCTCTGGCCGA---C-----GAGTG\n+                                       **    *   * *   *    *       * *                \n+\n+ENSMUST00000091291_musmusculus       GAGAGG--TGTG-CCCTGGTATGGACATCCGGAACAACC-TGACCAGGCT\n+ENSCAFT00000026349_canisfamiliaris   TAGAGG--TGTG-CCCCAGCCTGGACATCCGCTCAGAGGTGGCGG-AGCT\n+ENSMUST00000005671_homosapiens       GAGAAATCTGTGGGCCCGGCATTGACATCCGCAACGACTATCAGC-AGCT\n+ENSRNOT00000019267_rattusnorvegicus  GAGAAATTTGTGGGCCCGGCATTGACATCCGCAACGACTATCAGC-AGCT\n+ENSPTRT00000013802_pantroglodytes    GAGAAATCTGCGGGCCAGGCATCGACATCCGCAACGACTATCAGC-AGCT\n+                                      ***    ** *  **  *  * ********     *          ***\n+\n+ENSMUST00000091291_musmusculus       ACATGAGCTGGAGAACTGCTCAGTCATTGAGGGCCATCTGCAGATCCTCC\n+ENSCAFT00000026349_canisfamiliaris   GCGCCGGCTGGAGAACTGCAGCGTGGTGGAGGGCCATCTGCAGATCCTGC\n+ENSMUST00000005671_homosapiens       GAAGCGCCTGGAAAACTGCACGGTGATCGAGGGCTTCCTCCACATCCTGC\n+ENSRNOT00000019267_rattusnorvegicus  GAAGCGCCTGGAAAACTGCACGGTGATCGAGGGCTTCCTCCACATCCTGC\n+ENSPTRT00000013802_pantroglodytes    GAAGCGCCTGGAGAACTGCACGGTGATCGAGGGCTACCTCCACATCCTGC\n+                                            ***** ******   **  * ******   ** ** ***** *\n+\n+ENSMUST00000091291_musmusculus       TGATGTTCAAGACCAGACCCGAAGATTTCCGAGACCTCAGTTTCCCCAAA\n+ENSCAFT00000026349_canisfamiliaris   TCATGTTCACGGCCACGGGCGAGGACTTCCGCGGCCTCAGCTTCCCGCGC\n+ENSMUST00000005671_homosapiens       TCATCTCCAAGG------CCGAGGACTACCGAAGCTACCGCTTCCCCAAG\n+ENSRNOT00000019267_rattusnorvegicus  TCATCTCCAAGG------CCGAGGACTACCGAAGCTACCGCTTCCCCAAG\n+ENSPTRT00000013802_pantroglodytes    TCATCTCCAAGG------CCGAGGACTACCGCAGCTACCGCTTCCCCAAG\n+                                     * ** * ** *        *** ** * ***   *  * * *****    \n+\n+ENSMUST00000091291_musmusculus       CTCATCATGATCACAGATTACCTGCTTCTCTTCCGTGTCTATGGTCTGGA\n+ENSCAFT00000026349_canisfamiliaris   CTCACTCAGGTCACTGACTACCTGCTGCTCTTCCGCGTGTATGGCCTGGA\n+ENSMUST00000005671_homosapiens       CTCACCGTCATCACTGAGTACTTGCTGCTCTTCCGAGTCGCTGGCCTCGA\n+ENSRNOT00000019267_rattusnorvegicus  CTCACGGTCATCACCGAGTACTTGCTGCTGTTTCGAGTGGCCGGCCTCGA\n+ENSPTRT00000013802_pantroglodytes    CTCACGGTCATTACCGAGTACTTGCTGCTGTTCCGAGTGGCTGGCCTCGA\n+                                     ****      * ** ** *** **** ** ** ** **    ** ** **\n+\n+ENSMUST00000091291_musmusculus       AAGTCTGAAAGACCTCTTCCCAAATCTCACAGTCATCCGAGGCTCCCGTC\n+ENSCAFT00000026349_canisfamiliaris   GAGCCTGCGGGACCTCTTCCCCAACCTCGCGGTCGTGCGTGGCGCCCGCC\n+ENSMUST00000005671_homosapiens       GAGCCTGGGAGACCTCTTCCCCAACCTCACAGTCATCCGTGGCTGGAAAC\n+ENSRNOT00000019267_rattusnorvegicus  GAGCCTGGGAGACCTCTTCCCGAACCTCACAGTCATCCGTGGCTGGAAAC\n+ENSPTRT00000013802_pantroglodytes    GAGCCTCGGAGACCTCTTCCCCAACCTCACGGTCATCCGCGGCTGGAAAC\n+                                      ** **    *********** ** *** * *** * ** ***      *\n+\n+ENSMUST00000091291_musmusculus       TCTTCTTCAACTATGCCCTGGTTATCTTCGAGATGGTCCACCTGAAGGAG\n+ENSCAFT00000026349_canisfamiliaris   TCTTCCTGGGTTATGCGCTGGTGGTCTACGAGATGCCGCACCTGCGGGAC\n+EN'..b'AGTATAACCCCAAGATGCGGCCCTCCTTCCTGG\n+ENSRNOT00000019267_rattusnorvegicus  TATGCGCATGTGCTGGCAGTACAACCCCAAGATGCGGCCCTCCTTCCTGG\n+ENSPTRT00000013802_pantroglodytes    GATGCGCATGTGCTGGCAGTATAACCCCAAGATGAGGCCTTCCTTCCTGG\n+                                      *** **   *********   *****     ** ****  *****    \n+\n+ENSMUST00000091291_musmusculus       AAATCGTCAACCTGCTCAAGGATGACCTCCACCCCAGCTTTCCAGAAGTT\n+ENSCAFT00000026349_canisfamiliaris   ACATCCTGGACAGCATTCGGGGGGAACTGCGGCCCTCTTTCCGCCTCTTT\n+ENSMUST00000005671_homosapiens       AGATCATCGGCAGCATCAAGGATGAGATGGAGCCCAGCTTCCAGGAGGTC\n+ENSRNOT00000019267_rattusnorvegicus  AGATCATCGGAAGCATCAAGGATGAGATGGAGCCCAGTTTCCAGGAGGTC\n+ENSPTRT00000013802_pantroglodytes    AGATCATCAGCAGCATCAAAGAGGAGATGGAGCCTGGCTTCCGGGAGGTC\n+                                     * *** *        *    *  **  *    **    ** *      * \n+\n+ENSMUST00000091291_musmusculus       TCCTTCTTCTACAGCGAGGAGAACAAGGCTCCTGAGAGTGAGGAGCTGGA\n+ENSCAFT00000026349_canisfamiliaris   TCCTTCTATTACAGCCCAGAGTG-------------CCAGGGGAGCCAGG\n+ENSMUST00000005671_homosapiens       TCCTTCTACTACAGCGAGGAGAACAAGCCTCCCGAGCCAGAGGAGCTGGA\n+ENSRNOT00000019267_rattusnorvegicus  TCCTTCTACTACAGCGAGGAGAACAAGCCTCCAGAGCCGGAGGAGCTGGA\n+ENSPTRT00000013802_pantroglodytes    TCCTTCTACTACAGCGAGGAGAACAAGCTGCCCGAGCCGGAGGAGCTGGA\n+                                     *******  ******   ***                  * *****  * \n+\n+ENSMUST00000091291_musmusculus       ----GAT------------GGAGTTTGAAGACATGGAGAATGTCCCGTTG\n+ENSCAFT00000026349_canisfamiliaris   GGGCCCT------------GCTGCCTAATGCC-----------------A\n+ENSMUST00000005671_homosapiens       ----GAT------------GGAGCCTGAGAACATGGAGAGCGTCCCACTG\n+ENSRNOT00000019267_rattusnorvegicus  ----GATGGAGCTGGAGCTGGAGCCCGAGAACATGGAGAGCGTCCCGCTG\n+ENSPTRT00000013802_pantroglodytes    ----CCT------------GGAGCCAGAGAACATGGAGAGCGTCCCCCTG\n+                                           *            *  *    *   *                  \n+\n+ENSMUST00000091291_musmusculus       GATCGTTC----------------CTCTCACTGTCAGAGAGAA---GAG-\n+ENSCAFT00000026349_canisfamiliaris   AACCCAA-------------CTCCCTACCA-----------A--------\n+ENSMUST00000005671_homosapiens       GACCCTTCGGCCTCCTCAGCCTCCCTGCCTCTGCCTGAAAGACACTCAGG\n+ENSRNOT00000019267_rattusnorvegicus  GACCCTTCGGCCTCCTCAGCCTCCCTGCCTCTGCCTGAAAGACACTCAGG\n+ENSPTRT00000013802_pantroglodytes    GACCCCTCGGC---------CTCCCTGCCACTGCCCGACAGACACTCAGG\n+                                      * *                    **  *            *        \n+\n+ENSMUST00000091291_musmusculus       GCTGGGGGCCGGGAGGGA---GGGTCCTCA----CTGAGCATCAAACGGA\n+ENSCAFT00000026349_canisfamiliaris   -------CCCCAGAAGGG-----GCTC------------CCTC-------\n+ENSMUST00000005671_homosapiens       ACACAAGGCTGAGAATGGCCCGGGCCCTGGCGTGCTCGTTCTCCGCGCCA\n+ENSRNOT00000019267_rattusnorvegicus  ACACAAGGCTGAGAACGG------CCCTGGCGTGCTGGTTCTCCGTGCCA\n+ENSPTRT00000013802_pantroglodytes    ACACAAGGCCGAGAACGGCCCCGGCCCTGGGGTGCTGGTCCTCCGCGCCA\n+                                             *   **  *         *              **       \n+\n+ENSMUST00000091291_musmusculus       CCTATGATGA-ACACATCCCCTATACCCACATGAATGGGGGCAAGAAGAA\n+ENSCAFT00000026349_canisfamiliaris   -----------AGACTG-C---ATGCCC-CA-AAATGGGGGTC-------\n+ENSMUST00000005671_homosapiens       GTTTTGATGAGAGACAG-CCTTACGCTCACATGAACGGGGGACGCGCCAA\n+ENSRNOT00000019267_rattusnorvegicus  GTTTTGATGAGAGACAG-CCTTACGCTCACATGAATGGGGGACGCGCCAA\n+ENSPTRT00000013802_pantroglodytes    GCTTCGACGAGAGACAG-CCGTACGCACACATGAACGGGGGCCGCAAGAA\n+                                                * **   *   *  * * **  ** *****         \n+\n+ENSMUST00000091291_musmusculus       CGGACGTGTCCTTACCCTGCCAAGGTCAAACCCTTCCTAA\n+ENSCAFT00000026349_canisfamiliaris   ----------C-----------AGGGC--------ACTGA\n+ENSMUST00000005671_homosapiens       CGAGAGGGCCTTGCCTCTGCCCCAGTCCTCGACCTGCTGA\n+ENSRNOT00000019267_rattusnorvegicus  CGAGAGGGCCTTGCCTCTGCCCCAGTCCTCAA---CCTGC\n+ENSPTRT00000013802_pantroglodytes    CGAGCGGGCCTTGCCGCTGCCCCAGTCTTCGACCTGCTGA\n+                                                             * *         **  \n+\n+\n+\n'
b
diff -r 0a189243186d -r ae69d14b6fbf test-data/output3.fasta_aln
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output3.fasta_aln Thu Jan 14 12:14:52 2021 +0000
b
b'@@ -0,0 +1,430 @@\n+>ENSMUST00000091291_musmusculus\n+ATGGG-CTTCGGGAGAGGATGTGAGACGACGG-----CTGTGCCATTGCT\n+GGTGGCCGTGGCCGCGTTGCTGGTGGGCACAGCCGGCCACCTGTACCCTG\n+GAGAGG--TGTG-CCCTGGTATGGACATCCGGAACAACC-TGACCAGGCT\n+ACATGAGCTGGAGAACTGCTCAGTCATTGAGGGCCATCTGCAGATCCTCC\n+TGATGTTCAAGACCAGACCCGAAGATTTCCGAGACCTCAGTTTCCCCAAA\n+CTCATCATGATCACAGATTACCTGCTTCTCTTCCGTGTCTATGGTCTGGA\n+AAGTCTGAAAGACCTCTTCCCAAATCTCACAGTCATCCGAGGCTCCCGTC\n+TCTTCTTCAACTATGCCCTGGTTATCTTCGAGATGGTCCACCTGAAGGAG\n+CTGGGGCTTTATAACCTCATGAACATCACCCGGGGCTCTGTCCGCATCGA\n+GAAGAATAATGAGCTCTGCTACCTGGCCACTATCGACTGGTCCCGTATCC\n+TGGATTCTGTGGAGGACAACTACATTGTACTGAACAAAGATGACAACGAG\n+GAATGTGGGGATGTCTGTCCAGGCACCGCCAAGGGCA-AGACCAA--CTG\n+TCCTGCCACTGTCATCAATGGGCAGTTTGTGGAACGGTGCTGGACACACA\n+GTCATTGTCAGAAAGTTTGCCCAACCATCTGTAAGTCACATGGCTGCACA\n+GCTGAAGGCCTGTGCTGCCACAAAGAGTGCCTGGGCAACTGTTCGGAACC\n+TGATGACCCCACCAAGTGTGTGGCCTGTCGCAACTTCTATCTGGATGGTC\n+AGTGTGTGGAGACCTGCCCGCCACCCTACTATCACTTCCAGGACTGGCGC\n+TGTGTGAACTTCAGCTTCTG--CCAAGACCTTCA-CTTCAAATGCAGGAA\n+CTCTCGGAAGCCTGGCTGCCACCAATACGTCATTCACAACAATAAGTGCA\n+TCCCCGAGTGCCCGTCTGGCTATACCATGAATTCCAGC---AACTTGATG\n+TGCACCCCATGTCTGGGACCCTGCCCTAAGGTCTGCCAA-ATCCTC-GAA\n+GGTG-AGAAGACCATTGATTCTGTGACATCTGCCCAGGAGCTCCGAGGCT\n+GCACTGTGATCAACGGTAGCCTGATCATCAACATCCGAGGGGGCAACAAC\n+CTGGCAGCTGAGCTGGAGGCTAACCTTGGCCTCATTGAAGAAATTTCGGG\n+ATTTCTAAAGATCCGCCGCTCCTATGCTCTGGTATCACTTTCTTTCTTCA\n+GGAAGCTACATCTGATTCGAGGAGAGACCTTGGAAATTGGGAACTATTCT\n+TTTTATGCCTTGGACAACCAGAACCTGAGGCAACTCTGGGACTGGAG-CA\n+AACACAACCTCACCATCACTCAGGGCAAGCTCTTCTTCCATTACAACCCG\n+AAACTCTGCTTGTCTGAAATTCACAAGATGGAAGAAGTCTCCGGAACTAA\n+GGGCCGTCAGGAGAGGAACGACATTGCCCTGAAGACCAATGGGGACCAGG\n+CATCGTGTGAAAATGAATTGCTTAAATTTTCTTTCATTCGGACATCTTTT\n+GACAAGATCCTGTTGAGGTGGGAACCCTACTGGCCCCCCGACTTCCGAGA\n+TCTCCTGGGATTCATGTTGTTCTACAAAGAGGCCCCTTATCAGAATGTGA\n+CAGAGTTTGATGGGCAGGATGCTTGTGGCTCCAACAGCTGGACTGTGGTG\n+GATATTGACCCGCCCCAGAGGTCCAACGACCCCAAGTCTCAGACCCCAAG\n+CCACCCTGGGTGGCTGAT-GCGGGGCCTCAAACCCTGGACCCAATACGCC\n+ATCTTTGTGAAGACCTTGG---TTACCTTCTCTGATGAACGGC-GGACCT\n+ATGGAGCCAAAAGTGATATCATCTATGTGCAAACAGATGCCACTAATCCT\n+TCTGTCCCCCTGGATCCCATATCAGTTTCTAATTCCTCATCTCAGATTAT\n+CTTAAAGTGGAAGCCCCCCTCTGACCCCAATGGCAACATCACACACTACC\n+TGGTGTACTGGGAGAGGCAAGCAGAGGACAGCGAGCTGTTTGAGCTGGAT\n+TATTGTCTCAAAGGGCTGA-AGCTCCCTTCACGGACCTGGTC---CCCAC\n+CCTTTGAGTCTGATGAT-T--CTCAGAAGCACAA-TCAGA-GT-GAGTA-\n+TGACGACTCGGCCAGTGAGTGC-TGCTCATGCCC-TAAGACTGACTCTCA\n+GATCCTGAAGGAGCTGGAGGAGTCTTCATTCAGGAAGACCTTCGAGGATT\n+ACCTGCACAACGTGGTTTTTGTCCCCAGGCCATCCCGAAAGCGAAGATCC\n+CTTGAAGAGGTGGGGAATGTGACA---GCCACCACACTCA-CACTTCCAG\n+ATTTCCCCAACGT-CTCCTCTACCATTGTGCCC-ACAAGTCAG-G-AGGA\n+GCACAGGCCATTTGAGA---AAGTGGTGAACAAGGAGTCACTTGTCATCT\n+CTGGCCTGAGACACTTCACTGGGTACCGCATTGAGCTGCAGGCATGCAAT\n+CAAGATTCCCCAGAT-GAGAGGTGCAGTGTGGCTGCCTACGTCAGTGCCC\n+GGACCATGCCTGAAGCTAAGGCAGATGACATCGTTGGCCCTGTGACTCAT\n+GAA---ATCTTTGAGAACAATGTTGTACACTTAATGTGGCAAGAGCCAAA\n+GGAACCTAATGGTCTGATTGTGCTATATGAAGTGAGCTATCGCCGATATG\n+GTGATGAGGAG-CTGCACCTCTGTGTCTCCCGGAAGCATTTTGCCCTGGA\n+GCGGGGCTGCAGGCTGCGAGGGCTCTCCCCAGGAAACTACAGTGTTCGAG\n+TCCGGGCTACCTCTCTGGCAGGAAATGGCTCCTGGACAGAACCCACCTAT\n+TTTTATGTGACTGAT-TATTTAGATGTCCCATCAAA-TATTGCCAAAATT\n+ATCATTGGACCCCTCATCTTTGTCTTCCTCTTCAGTGTTG--TGATTGGA\n+-AGTAT---TTATCTATTTCTGAGAAAGAGG-----CAGCCGGATGGGCC\n+AATGGGACCACTGTATGCATCTTCAAACCCTGAGTACCT-CAGTGCCAGT\n+GATGTGTTTCCATCTTCTGTGTACGTGCCGGACGAGTGGGAGGTGCCTCG\n+AGAGAAGATCACCCTTCTTCGAGAGCTGGGGCAGGGATCCTTTGGTATGG\n+TGTATGAAGGCAATGC-CAAGGATA--TCATCAAGGGTGAGGCAGAGACC\n+CGTGTTGCGGTTAAGACTGTCAATGAGTCAGCCAGTCTTCGAGAACGGAT\n+CGAGTTCCTCAATGAGGCATCAGTCATGAAGGGATTCACCTGCCATCATG\n+TGGTCCGCCTTCTTGGGGTGGTATCCAAAGGACAGCCAACGCTGGTAGTG\n+ATGGAATTGATGGCTCATGGAGACCTGAAAAGTCACCTCCGTTCTCTGAG\n+GCCAGATGCTGA---GAATAACCCAGGCCGCCCTCCCCCTACCTTGCAAG\n+AAATGATTCAGATGACAGCAGAAATTGCTGATGGCATGGCATACTTGAAC\n+GCCAAGAAGTTTGTGCACCGGGACCTGGCAGCTCGAAACTGCATGGTTGC\n+CCATGATTTTACTGTCAAAATTGGAGACTTTGGAATGACAAGGGACATCT\n+ACGAGACAGATTACTATCGGAAAGGGGGCAAGGGACTGCTTCCTGTGAGG\n+TGGATGTCACCTGAGTCCCTGAAGGATGGAGTCTTTACTGCTTCTTCTGA\n+TATGTGGTCCTTTGGGGTGGTCCTTTGGGAAATCACTAGCCTGGCTGAGC\n+AACCTTATCAAGGCCTGTCTAATGAACAGGTGTTGAAGTTTGTCATG'..b'GGAT\n+ATTGGGCTTTACAACCTGAGGAACATTACTCGGGGGGCCATCAGGATTGA\n+GAAAAATGCTGACCTCTGTTACCTCTCCACTGTGGACTGGTCCCTGATCC\n+TGGATGCGGTGTCCAATAACTACATTGTGGGGAATAA-GCCCCCA--AAG\n+GAATGTGGGGACCTGTGTCCAGGGACCATGGAGGAGA-AGCCGAT--GTG\n+TGAGAAGACCACCATCAACAATGAGTACAACTACCGCTGCTGGACCACAA\n+ACCGCTGCCAGAAAATGTGCCCGAGCACGTGTGGGAAGCGGGCGTGCACC\n+GAGAACAACGAGTGCTGCCACCCCGAGTGCCTGGGCAGCTGCAGCGCGCC\n+TGACAACGACACGGCCTGTGTAGCTTGCCGCCACTACTACTATGCCGGTG\n+TCTGTGTGCCTGCCTGCCCGCCCAACACCTACAGGTTTGAGGGCTGGCGC\n+TGTGTGGACCGTGACTTCTGCGCCAACATCCTCAGCGCCGAGAGCAGCGA\n+CTC---------------CGAGGGGTTTGTGATCCACGACGGCGAGTGCA\n+TGCAGGAGTGCCCCTCGGGCTTCATCCGCAACGGCAGCCAGAGCATGTAC\n+TGCATCCCTTGTGAAGGTCCTTGCCCGAAGGTCTGTG---AGGAAGAAAA\n+GAAAACAAAGACCATTGATTCTGTTACTTCTGCTCAGATGCTCCAAGGAT\n+GCACCATCTTCAAGGGCAATTTGCTCATTAACATCCGACGGGGGAATAAC\n+ATTGCTTCAGAGCTGGAGAACTTCATGGGGCTCATCGAGGTGGTGACGGG\n+CTACGTGAAGATCCGCCATTCTCATGCCTTGGTCTCCTTGTCCTTCCTAA\n+AAAACCTTCGCCTCATCTTAGGAGAGGAGCAGCTAGAAGGGAATTACTCC\n+TTCTACGTCCTCGACAACCAGAACTTGCAGCAACTATGGGACTGGGA-CC\n+ACCGCAACCTGACCATCAAAGCAGGGAAAATGTACTTTGCTTTCAATCCC\n+AAATTATGTGTTTCCGAAATTTACCGCATGGAGGAAGTGACGGGGACTAA\n+AGGGCGCCAAAGCAAAGGGGACATAAACACCAGGAACAACGGGGAGAGAG\n+CCTCCTGTGAAAGTGACGTCCTGCATTTCACCTCCACCACCACGTCGAAG\n+AATCGCATCATCATAACCTGGCACCGGTACCGGCCCCCTGACTACAGGGA\n+TCTCATCAGCTTCACCGTTTACTACAAGGAAGCACCCTTTAAGAATGTCA\n+CGGAGTATGATGGGCAGGACGCCTGCGGCTCCAACAGCTGGAACATGGTG\n+GACGTGGACCTCCCGCCCAA---CAAGGACG--------TGGAGCC----\n+-----CGGCAT-CTTACT-ACATGGGCTGAAGCCCTGGACTCAGTACGCC\n+GTTTACGTCAAGGCTGTGACCCTCACCATGG-TGGAGAATGACCATATCC\n+GTGGGGCCAAGAGTGAGATCTTGTACATTCGCACCAATGCTTCAGTTCCT\n+TCCATTCCCTTGGACGTTCTTTCAGCATCGAACTCCTCTTCTCAGTTAAT\n+CGTGAAGTGGAACCCTCCCTCTCTGCCCAACGGCAACCTGAGTTACTACA\n+TTGTGCGCTGGCAGCGGCAGCCTCAGGACGGCTACCTTTACCGGCACAAT\n+TACTGCTCCAAAGA-CAA--AATCCCCATCAGGAAGTATGCCGACGGCA-\n+CCATCGACATTGAGGAGGTCACAGAGAACCCCAAGACTGAGGT-GTGTGG\n+TGGGGAGAA---AGGGCCTTGC-TGCGCCTGCCC-CAAAACTGAAGCCGA\n+GAAGCAGGCCGAGAAGGAGGAGGCTGAATACCGCAAAGTCTTTGAGAATT\n+TCCTGCACAACTCCATCTTCGTGCCCAGACCTGAAAGGAAGCGGAGAGAT\n+GTCATGCAAGTGGCCAACACCACCATGTCCAGCCGAAGCAGGAACACCAC\n+GGC-CGCAGACAC-CTACAACATCACCGACCCGGAAGAGCTGGAGACAGA\n+GTACCCTTTCTTTGAGAGCAGAGTGGATAACAAGGAGAGAACTGTGATTT\n+CTAACCTTCGGCCTTTCACATTGTACCGCATCGATATCCACAGCTGCAAC\n+CACGAGGCT-GAGAAGCTGGGCTGCAGCGCCTCCAACTTTGTCTTTGCAA\n+GGACTATGCCCGCAGAAGGAGCAGATGACATTCCTGGGCCAGTGACCTGG\n+GAGCCAAGGCCTGAAAAC---TCCATCTTTTTAAAGTGGCCGGAACCTGA\n+GAATCCCAATGGATTGATTCTAATGTATGAAATAAAATACGGATCACAA-\n+--GTTGAGGAT-CAGCGAGAATGTGTGTCCAGACAGGAATACAGGAAGTA\n+TGGAGGGGCCAAGCTAAACCGGCTAAACCCGGGGAACTACACAGCCCGGA\n+TTCAGGCCACATCTCTCTCTGGGAATGGGTCGTGGACAGATCCTGTGTTC\n+TTCTATGTCCAGGCC-AA----AACAGGATATGAAAACTTCATCCATCTG\n+ATCATCGCTCTGCCCG---TCGCTGTCCTGTTGATCGTGGGAGGGTTGGT\n+GATTATGCTGTACGTCTTCCATAGAAAGAGAAATAACAGCAGGCTGGG-G\n+AATGG-AGTGCTGTATGCCTCTGTGAACCCGGAGTACTT-CAGCGCTGCT\n+GAT---------------GTGTACGTTCCCGATGAGTGGGAGGTGGCTCG\n+GGAGAAGATCACCATGAGCCGGGAACTTGGGCAGGGGTCCTTTGGGATGG\n+TCTATGAAGGAGTTGC-CAAGGGTG--TGGTGAAAGATGAACCTGAAACC\n+AGAGTGGCCATTAAAACAGTGAACGAGGCCGCAAGCATGCGTGAAAGGAT\n+TGAGTTTCTCAACGAAGCTTCTGTGATGAAGGAGTTCAATTGTCACCATG\n+TGGTGCGATTGCTGGGTGTGGTGTCCCAAGGCCAGCCAACACTGGTCATC\n+ATGGAACTGATGACACGGGGCGATCTCAAAAGTTATCTCCGGTCTCTGAG\n+GCCAGAAATGGA---GAATAATCCAGTCCTAGCACCTCCAAGCCTGAGCA\n+AGATGATTCAGATGGCCGGAGAGATTGCAGACGGCATGGCATACCTCAAC\n+GCCAATAAGTTCGTCCACAGAGACCTTGCTGCCCGGAATTGCATGGTAGC\n+CGAAGATTTCACAGTCAAAATCGGAGATTTTGGTATGACGCGAGATATCT\n+ATGAGACAGACTATTACCGGAAAGGAGGGAAAGGGCTGCTGCCCGTGCGC\n+TGGATGTCTCCCGAGTCCCTCAAGGATGGAGTCTTCACCACTTACTCGGA\n+CGTCTGGTCCTTCGGGGTCGTCCTCTGGGAGATCGCCACACTGGCCGAGC\n+AGCCCTACCAGGGCTTGTCCAACGAGCAAGTCCTTCGCTTCGTCATGGAG\n+GGCGGCCTTCTGGACAAGCCAGACAACTGTCCCGACATGCTGTTTGAACT\n+GATGCGCATGTGCTGGCAGTATAACCCCAAGATGAGGCCTTCCTTCCTGG\n+AGATCATCAGCAGCATCAAAGAGGAGATGGAGCCTGGCTTCCGGGAGGTC\n+TCCTTCTACTACAGCGAGGAGAACAAGCTGCCCGAGCCGGAGGAGCTGGA\n+----CCT------------GGAGCCAGAGAACATGGAGAGCGTCCCCCTG\n+GACCCCTCGGC---------CTCCCTGCCACTGCCCGACAGACACTCAGG\n+ACACAAGGCCGAGAACGGCCCCGGCCCTGGGGTGCTGGTCCTCCGCGCCA\n+GCTTCGACGAGAGACAG-CCGTACGCACACATGAACGGGGGCCGCAAGAA\n+CGAGCGGGCCTTGCCGCTGCCCCAGTCTTCGACCTGCTGA\n'
b
diff -r 0a189243186d -r ae69d14b6fbf test-data/output3.fasta_seq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output3.fasta_seq Thu Jan 14 12:14:52 2021 +0000
b
b'@@ -0,0 +1,415 @@\n+>ENSMUST00000091291_musmusculus\n+ATGGGCTTCGGGAGAGGATGTGAGACGACGGCTGTGCCATTGCTGGTGGC\n+CGTGGCCGCGTTGCTGGTGGGCACAGCCGGCCACCTGTACCCTGGAGAGG\n+TGTGCCCTGGTATGGACATCCGGAACAACCTGACCAGGCTACATGAGCTG\n+GAGAACTGCTCAGTCATTGAGGGCCATCTGCAGATCCTCCTGATGTTCAA\n+GACCAGACCCGAAGATTTCCGAGACCTCAGTTTCCCCAAACTCATCATGA\n+TCACAGATTACCTGCTTCTCTTCCGTGTCTATGGTCTGGAAAGTCTGAAA\n+GACCTCTTCCCAAATCTCACAGTCATCCGAGGCTCCCGTCTCTTCTTCAA\n+CTATGCCCTGGTTATCTTCGAGATGGTCCACCTGAAGGAGCTGGGGCTTT\n+ATAACCTCATGAACATCACCCGGGGCTCTGTCCGCATCGAGAAGAATAAT\n+GAGCTCTGCTACCTGGCCACTATCGACTGGTCCCGTATCCTGGATTCTGT\n+GGAGGACAACTACATTGTACTGAACAAAGATGACAACGAGGAATGTGGGG\n+ATGTCTGTCCAGGCACCGCCAAGGGCAAGACCAACTGTCCTGCCACTGTC\n+ATCAATGGGCAGTTTGTGGAACGGTGCTGGACACACAGTCATTGTCAGAA\n+AGTTTGCCCAACCATCTGTAAGTCACATGGCTGCACAGCTGAAGGCCTGT\n+GCTGCCACAAAGAGTGCCTGGGCAACTGTTCGGAACCTGATGACCCCACC\n+AAGTGTGTGGCCTGTCGCAACTTCTATCTGGATGGTCAGTGTGTGGAGAC\n+CTGCCCGCCACCCTACTATCACTTCCAGGACTGGCGCTGTGTGAACTTCA\n+GCTTCTGCCAAGACCTTCACTTCAAATGCAGGAACTCTCGGAAGCCTGGC\n+TGCCACCAATACGTCATTCACAACAATAAGTGCATCCCCGAGTGCCCGTC\n+TGGCTATACCATGAATTCCAGCAACTTGATGTGCACCCCATGTCTGGGAC\n+CCTGCCCTAAGGTCTGCCAAATCCTCGAAGGTGAGAAGACCATTGATTCT\n+GTGACATCTGCCCAGGAGCTCCGAGGCTGCACTGTGATCAACGGTAGCCT\n+GATCATCAACATCCGAGGGGGCAACAACCTGGCAGCTGAGCTGGAGGCTA\n+ACCTTGGCCTCATTGAAGAAATTTCGGGATTTCTAAAGATCCGCCGCTCC\n+TATGCTCTGGTATCACTTTCTTTCTTCAGGAAGCTACATCTGATTCGAGG\n+AGAGACCTTGGAAATTGGGAACTATTCTTTTTATGCCTTGGACAACCAGA\n+ACCTGAGGCAACTCTGGGACTGGAGCAAACACAACCTCACCATCACTCAG\n+GGCAAGCTCTTCTTCCATTACAACCCGAAACTCTGCTTGTCTGAAATTCA\n+CAAGATGGAAGAAGTCTCCGGAACTAAGGGCCGTCAGGAGAGGAACGACA\n+TTGCCCTGAAGACCAATGGGGACCAGGCATCGTGTGAAAATGAATTGCTT\n+AAATTTTCTTTCATTCGGACATCTTTTGACAAGATCCTGTTGAGGTGGGA\n+ACCCTACTGGCCCCCCGACTTCCGAGATCTCCTGGGATTCATGTTGTTCT\n+ACAAAGAGGCCCCTTATCAGAATGTGACAGAGTTTGATGGGCAGGATGCT\n+TGTGGCTCCAACAGCTGGACTGTGGTGGATATTGACCCGCCCCAGAGGTC\n+CAACGACCCCAAGTCTCAGACCCCAAGCCACCCTGGGTGGCTGATGCGGG\n+GCCTCAAACCCTGGACCCAATACGCCATCTTTGTGAAGACCTTGGTTACC\n+TTCTCTGATGAACGGCGGACCTATGGAGCCAAAAGTGATATCATCTATGT\n+GCAAACAGATGCCACTAATCCTTCTGTCCCCCTGGATCCCATATCAGTTT\n+CTAATTCCTCATCTCAGATTATCTTAAAGTGGAAGCCCCCCTCTGACCCC\n+AATGGCAACATCACACACTACCTGGTGTACTGGGAGAGGCAAGCAGAGGA\n+CAGCGAGCTGTTTGAGCTGGATTATTGTCTCAAAGGGCTGAAGCTCCCTT\n+CACGGACCTGGTCCCCACCCTTTGAGTCTGATGATTCTCAGAAGCACAAT\n+CAGAGTGAGTATGACGACTCGGCCAGTGAGTGCTGCTCATGCCCTAAGAC\n+TGACTCTCAGATCCTGAAGGAGCTGGAGGAGTCTTCATTCAGGAAGACCT\n+TCGAGGATTACCTGCACAACGTGGTTTTTGTCCCCAGGCCATCCCGAAAG\n+CGAAGATCCCTTGAAGAGGTGGGGAATGTGACAGCCACCACACTCACACT\n+TCCAGATTTCCCCAACGTCTCCTCTACCATTGTGCCCACAAGTCAGGAGG\n+AGCACAGGCCATTTGAGAAAGTGGTGAACAAGGAGTCACTTGTCATCTCT\n+GGCCTGAGACACTTCACTGGGTACCGCATTGAGCTGCAGGCATGCAATCA\n+AGATTCCCCAGATGAGAGGTGCAGTGTGGCTGCCTACGTCAGTGCCCGGA\n+CCATGCCTGAAGCTAAGGCAGATGACATCGTTGGCCCTGTGACTCATGAA\n+ATCTTTGAGAACAATGTTGTACACTTAATGTGGCAAGAGCCAAAGGAACC\n+TAATGGTCTGATTGTGCTATATGAAGTGAGCTATCGCCGATATGGTGATG\n+AGGAGCTGCACCTCTGTGTCTCCCGGAAGCATTTTGCCCTGGAGCGGGGC\n+TGCAGGCTGCGAGGGCTCTCCCCAGGAAACTACAGTGTTCGAGTCCGGGC\n+TACCTCTCTGGCAGGAAATGGCTCCTGGACAGAACCCACCTATTTTTATG\n+TGACTGATTATTTAGATGTCCCATCAAATATTGCCAAAATTATCATTGGA\n+CCCCTCATCTTTGTCTTCCTCTTCAGTGTTGTGATTGGAAGTATTTATCT\n+ATTTCTGAGAAAGAGGCAGCCGGATGGGCCAATGGGACCACTGTATGCAT\n+CTTCAAACCCTGAGTACCTCAGTGCCAGTGATGTGTTTCCATCTTCTGTG\n+TACGTGCCGGACGAGTGGGAGGTGCCTCGAGAGAAGATCACCCTTCTTCG\n+AGAGCTGGGGCAGGGATCCTTTGGTATGGTGTATGAAGGCAATGCCAAGG\n+ATATCATCAAGGGTGAGGCAGAGACCCGTGTTGCGGTTAAGACTGTCAAT\n+GAGTCAGCCAGTCTTCGAGAACGGATCGAGTTCCTCAATGAGGCATCAGT\n+CATGAAGGGATTCACCTGCCATCATGTGGTCCGCCTTCTTGGGGTGGTAT\n+CCAAAGGACAGCCAACGCTGGTAGTGATGGAATTGATGGCTCATGGAGAC\n+CTGAAAAGTCACCTCCGTTCTCTGAGGCCAGATGCTGAGAATAACCCAGG\n+CCGCCCTCCCCCTACCTTGCAAGAAATGATTCAGATGACAGCAGAAATTG\n+CTGATGGCATGGCATACTTGAACGCCAAGAAGTTTGTGCACCGGGACCTG\n+GCAGCTCGAAACTGCATGGTTGCCCATGATTTTACTGTCAAAATTGGAGA\n+CTTTGGAATGACAAGGGACATCTACGAGACAGATTACTATCGGAAAGGGG\n+GCAAGGGACTGCTTCCTGTGAGGTGGATGTCACCTGAGTCCCTGAAGGAT\n+GGAGTCTTTACTGCTTCTTCTGATATGTGGTCCTTTGGGGTGGTCCTTTG\n+GGAAATCACTAGCCTGGCTGAGCAACCTTATCAAGGCCTGTCTAATGAAC\n+AGGTGTTGAAGTTTGTCATGGATGGAGGCTATCTGGATCCCCCTGATAAC\n+TGTCCAGAGAGACTCACTGACCTGATGCGCATGTGCTGGCAGTTCAA'..b'+ACTTGCTGCTGTTCCGAGTGGCTGGCCTCGAGAGCCTCGGAGACCTCTTC\n+CCCAACCTCACGGTCATCCGCGGCTGGAAACTCTTCTACAACTACGCCCT\n+GGTCATCTTCGAGATGACCAATCTCAAGGATATTGGGCTTTACAACCTGA\n+GGAACATTACTCGGGGGGCCATCAGGATTGAGAAAAATGCTGACCTCTGT\n+TACCTCTCCACTGTGGACTGGTCCCTGATCCTGGATGCGGTGTCCAATAA\n+CTACATTGTGGGGAATAAGCCCCCAAAGGAATGTGGGGACCTGTGTCCAG\n+GGACCATGGAGGAGAAGCCGATGTGTGAGAAGACCACCATCAACAATGAG\n+TACAACTACCGCTGCTGGACCACAAACCGCTGCCAGAAAATGTGCCCGAG\n+CACGTGTGGGAAGCGGGCGTGCACCGAGAACAACGAGTGCTGCCACCCCG\n+AGTGCCTGGGCAGCTGCAGCGCGCCTGACAACGACACGGCCTGTGTAGCT\n+TGCCGCCACTACTACTATGCCGGTGTCTGTGTGCCTGCCTGCCCGCCCAA\n+CACCTACAGGTTTGAGGGCTGGCGCTGTGTGGACCGTGACTTCTGCGCCA\n+ACATCCTCAGCGCCGAGAGCAGCGACTCCGAGGGGTTTGTGATCCACGAC\n+GGCGAGTGCATGCAGGAGTGCCCCTCGGGCTTCATCCGCAACGGCAGCCA\n+GAGCATGTACTGCATCCCTTGTGAAGGTCCTTGCCCGAAGGTCTGTGAGG\n+AAGAAAAGAAAACAAAGACCATTGATTCTGTTACTTCTGCTCAGATGCTC\n+CAAGGATGCACCATCTTCAAGGGCAATTTGCTCATTAACATCCGACGGGG\n+GAATAACATTGCTTCAGAGCTGGAGAACTTCATGGGGCTCATCGAGGTGG\n+TGACGGGCTACGTGAAGATCCGCCATTCTCATGCCTTGGTCTCCTTGTCC\n+TTCCTAAAAAACCTTCGCCTCATCTTAGGAGAGGAGCAGCTAGAAGGGAA\n+TTACTCCTTCTACGTCCTCGACAACCAGAACTTGCAGCAACTATGGGACT\n+GGGACCACCGCAACCTGACCATCAAAGCAGGGAAAATGTACTTTGCTTTC\n+AATCCCAAATTATGTGTTTCCGAAATTTACCGCATGGAGGAAGTGACGGG\n+GACTAAAGGGCGCCAAAGCAAAGGGGACATAAACACCAGGAACAACGGGG\n+AGAGAGCCTCCTGTGAAAGTGACGTCCTGCATTTCACCTCCACCACCACG\n+TCGAAGAATCGCATCATCATAACCTGGCACCGGTACCGGCCCCCTGACTA\n+CAGGGATCTCATCAGCTTCACCGTTTACTACAAGGAAGCACCCTTTAAGA\n+ATGTCACGGAGTATGATGGGCAGGACGCCTGCGGCTCCAACAGCTGGAAC\n+ATGGTGGACGTGGACCTCCCGCCCAACAAGGACGTGGAGCCCGGCATCTT\n+ACTACATGGGCTGAAGCCCTGGACTCAGTACGCCGTTTACGTCAAGGCTG\n+TGACCCTCACCATGGTGGAGAATGACCATATCCGTGGGGCCAAGAGTGAG\n+ATCTTGTACATTCGCACCAATGCTTCAGTTCCTTCCATTCCCTTGGACGT\n+TCTTTCAGCATCGAACTCCTCTTCTCAGTTAATCGTGAAGTGGAACCCTC\n+CCTCTCTGCCCAACGGCAACCTGAGTTACTACATTGTGCGCTGGCAGCGG\n+CAGCCTCAGGACGGCTACCTTTACCGGCACAATTACTGCTCCAAAGACAA\n+AATCCCCATCAGGAAGTATGCCGACGGCACCATCGACATTGAGGAGGTCA\n+CAGAGAACCCCAAGACTGAGGTGTGTGGTGGGGAGAAAGGGCCTTGCTGC\n+GCCTGCCCCAAAACTGAAGCCGAGAAGCAGGCCGAGAAGGAGGAGGCTGA\n+ATACCGCAAAGTCTTTGAGAATTTCCTGCACAACTCCATCTTCGTGCCCA\n+GACCTGAAAGGAAGCGGAGAGATGTCATGCAAGTGGCCAACACCACCATG\n+TCCAGCCGAAGCAGGAACACCACGGCCGCAGACACCTACAACATCACCGA\n+CCCGGAAGAGCTGGAGACAGAGTACCCTTTCTTTGAGAGCAGAGTGGATA\n+ACAAGGAGAGAACTGTGATTTCTAACCTTCGGCCTTTCACATTGTACCGC\n+ATCGATATCCACAGCTGCAACCACGAGGCTGAGAAGCTGGGCTGCAGCGC\n+CTCCAACTTTGTCTTTGCAAGGACTATGCCCGCAGAAGGAGCAGATGACA\n+TTCCTGGGCCAGTGACCTGGGAGCCAAGGCCTGAAAACTCCATCTTTTTA\n+AAGTGGCCGGAACCTGAGAATCCCAATGGATTGATTCTAATGTATGAAAT\n+AAAATACGGATCACAAGTTGAGGATCAGCGAGAATGTGTGTCCAGACAGG\n+AATACAGGAAGTATGGAGGGGCCAAGCTAAACCGGCTAAACCCGGGGAAC\n+TACACAGCCCGGATTCAGGCCACATCTCTCTCTGGGAATGGGTCGTGGAC\n+AGATCCTGTGTTCTTCTATGTCCAGGCCAAAACAGGATATGAAAACTTCA\n+TCCATCTGATCATCGCTCTGCCCGTCGCTGTCCTGTTGATCGTGGGAGGG\n+TTGGTGATTATGCTGTACGTCTTCCATAGAAAGAGAAATAACAGCAGGCT\n+GGGGAATGGAGTGCTGTATGCCTCTGTGAACCCGGAGTACTTCAGCGCTG\n+CTGATGTGTACGTTCCCGATGAGTGGGAGGTGGCTCGGGAGAAGATCACC\n+ATGAGCCGGGAACTTGGGCAGGGGTCCTTTGGGATGGTCTATGAAGGAGT\n+TGCCAAGGGTGTGGTGAAAGATGAACCTGAAACCAGAGTGGCCATTAAAA\n+CAGTGAACGAGGCCGCAAGCATGCGTGAAAGGATTGAGTTTCTCAACGAA\n+GCTTCTGTGATGAAGGAGTTCAATTGTCACCATGTGGTGCGATTGCTGGG\n+TGTGGTGTCCCAAGGCCAGCCAACACTGGTCATCATGGAACTGATGACAC\n+GGGGCGATCTCAAAAGTTATCTCCGGTCTCTGAGGCCAGAAATGGAGAAT\n+AATCCAGTCCTAGCACCTCCAAGCCTGAGCAAGATGATTCAGATGGCCGG\n+AGAGATTGCAGACGGCATGGCATACCTCAACGCCAATAAGTTCGTCCACA\n+GAGACCTTGCTGCCCGGAATTGCATGGTAGCCGAAGATTTCACAGTCAAA\n+ATCGGAGATTTTGGTATGACGCGAGATATCTATGAGACAGACTATTACCG\n+GAAAGGAGGGAAAGGGCTGCTGCCCGTGCGCTGGATGTCTCCCGAGTCCC\n+TCAAGGATGGAGTCTTCACCACTTACTCGGACGTCTGGTCCTTCGGGGTC\n+GTCCTCTGGGAGATCGCCACACTGGCCGAGCAGCCCTACCAGGGCTTGTC\n+CAACGAGCAAGTCCTTCGCTTCGTCATGGAGGGCGGCCTTCTGGACAAGC\n+CAGACAACTGTCCCGACATGCTGTTTGAACTGATGCGCATGTGCTGGCAG\n+TATAACCCCAAGATGAGGCCTTCCTTCCTGGAGATCATCAGCAGCATCAA\n+AGAGGAGATGGAGCCTGGCTTCCGGGAGGTCTCCTTCTACTACAGCGAGG\n+AGAACAAGCTGCCCGAGCCGGAGGAGCTGGACCTGGAGCCAGAGAACATG\n+GAGAGCGTCCCCCTGGACCCCTCGGCCTCCCTGCCACTGCCCGACAGACA\n+CTCAGGACACAAGGCCGAGAACGGCCCCGGCCCTGGGGTGCTGGTCCTCC\n+GCGCCAGCTTCGACGAGAGACAGCCGTACGCACACATGAACGGGGGCCGC\n+AAGAACGAGCGGGCCTTGCCGCTGCCCCAGTCTTCGACCTGCTGA\n'
b
diff -r 0a189243186d -r ae69d14b6fbf test-data/output3.msf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output3.msf Thu Jan 14 12:14:52 2021 +0000
b
b'@@ -0,0 +1,610 @@\n+PileUp\n+\n+\n+\n+   MSF: 4240  Type: N    Check:    72   .. \n+\n+ Name: ENSMUST00000091291_musmusculus oo  Len: 4240  Check:  4481  Weight:  1.000\n+ Name: ENSCAFT00000026349_canisfamiliaris oo  Len: 4240  Check:  6017  Weight:  1.000\n+ Name: ENSMUST00000005671_homosapiens oo  Len: 4240  Check:  1338  Weight:  1.000\n+ Name: ENSRNOT00000019267_rattusnorvegicus oo  Len: 4240  Check:  6549  Weight:  1.000\n+ Name: ENSPTRT00000013802_pantroglodytes oo  Len: 4240  Check:  1687  Weight:  1.000\n+\n+//\n+\n+\n+\n+ENSMUST00000091291_musmusculus           ATGGG.CTTC GGGAGAGGAT GTGAGACGAC GG.....CTG TGCCATTGCT \n+ENSCAFT00000026349_canisfamiliaris       ATGGCAGT.. .GCCCAGT.. CTGTGCCCAT GG.GTCGC.A TGC..CTGCT \n+ENSMUST00000005671_homosapiens           ATGAA.GTCT GGCTCCGGAG GAGGGTCCCC GACCTCGCTG TGG..GGGCT \n+ENSRNOT00000019267_rattusnorvegicus      ATGAA.GTCT GGCTCCGGAG GAGGGTCCCC GACCTCGCTG TGG..GGGCT \n+ENSPTRT00000013802_pantroglodytes        ATGAA.GTCT GGCTCCGGAG GAGGGTCCCC GACCTCGCTG TGG..GGGCT \n+\n+\n+ENSMUST00000091291_musmusculus           GGTGGCCGTG GCCGCGTTGC TGGTGGGCAC AGCCGGCCAC CTGTACCCTG \n+ENSCAFT00000026349_canisfamiliaris       GGTGATCCTC CTCTCCTTGG GATTTGGCCT GGAC...... ......ACAC \n+ENSMUST00000005671_homosapiens           CGTGTTTCTC TCCGCCGCGC TC.TCTCTCT GGCCGA...C .....GAGTG \n+ENSRNOT00000019267_rattusnorvegicus      CGTGTTTCTC TCCGCCGCGC TC.TCGCTCT GGCCGA...C .....GAGTG \n+ENSPTRT00000013802_pantroglodytes        CCTGTTTCTC TCCGCCGCGC TC.TCGCTCT GGCCGA...C .....GAGTG \n+\n+\n+ENSMUST00000091291_musmusculus           GAGAGG..TG TG.CCCTGGT ATGGACATCC GGAACAACC. TGACCAGGCT \n+ENSCAFT00000026349_canisfamiliaris       TAGAGG..TG TG.CCCCAGC CTGGACATCC GCTCAGAGGT GGCGG.AGCT \n+ENSMUST00000005671_homosapiens           GAGAAATCTG TGGGCCCGGC ATTGACATCC GCAACGACTA TCAGC.AGCT \n+ENSRNOT00000019267_rattusnorvegicus      GAGAAATTTG TGGGCCCGGC ATTGACATCC GCAACGACTA TCAGC.AGCT \n+ENSPTRT00000013802_pantroglodytes        GAGAAATCTG CGGGCCAGGC ATCGACATCC GCAACGACTA TCAGC.AGCT \n+\n+\n+ENSMUST00000091291_musmusculus           ACATGAGCTG GAGAACTGCT CAGTCATTGA GGGCCATCTG CAGATCCTCC \n+ENSCAFT00000026349_canisfamiliaris       GCGCCGGCTG GAGAACTGCA GCGTGGTGGA GGGCCATCTG CAGATCCTGC \n+ENSMUST00000005671_homosapiens           GAAGCGCCTG GAAAACTGCA CGGTGATCGA GGGCTTCCTC CACATCCTGC \n+ENSRNOT00000019267_rattusnorvegicus      GAAGCGCCTG GAAAACTGCA CGGTGATCGA GGGCTTCCTC CACATCCTGC \n+ENSPTRT00000013802_pantroglodytes        GAAGCGCCTG GAGAACTGCA CGGTGATCGA GGGCTACCTC CACATCCTGC \n+\n+\n+ENSMUST00000091291_musmusculus           TGATGTTCAA GACCAGACCC GAAGATTTCC GAGACCTCAG TTTCCCCAAA \n+ENSCAFT00000026349_canisfamiliaris       TCATGTTCAC GGCCACGGGC GAGGACTTCC GCGGCCTCAG CTTCCCGCGC \n+ENSMUST00000005671_homosapiens           TCATCTCCAA GG......CC GAGGACTACC GAAGCTACCG CTTCCCCAAG \n+ENSRNOT00000019267_rattusnorvegicus      TCATCTCCAA GG......CC GAGGACTACC GAAGCTACCG CTTCCCCAAG \n+ENSPTRT00000013802_pantroglodytes        TCATCTCCAA GG......CC GAGGACTACC GCAGCTACCG CTTCCCCAAG \n+\n+\n+ENSMUST00000091291_musmusculus           CTCATCATGA TCACAGATTA CCTGCTTCTC TTCCGTGTCT ATGGTCTGGA \n+ENSCAFT00000026349_canisfamiliaris       CTCACTCAGG TCACTGACTA CCTGCTGCTC TTCCGCGTGT ATGGCCTGGA \n+ENSMUST00000005671_homosapiens           CTCACCGTCA TCACTGAGTA CTTGCTGCTC TTCCGAGTCG CTGGCCTCGA \n+ENSRNOT00000019267_rattusnorvegicus      CTCACGGTCA TCACCGAGTA CTTGCTGCTG TTTCGAGTGG CCGGCCTCGA \n+ENSPTRT00000013802_pantroglodytes        CTCACGGTCA TTACCGAGTA CTTGCTGCTG TTCCGAGTGG CTGGCCTCGA \n+\n+\n+ENSMUST00000091291_musmusculus           AAGTCTGAAA GACCTCTTCC CAAATCTCAC AGTCATCCGA GGCTCCCGTC \n+ENSCAFT00000026349_canisfamiliaris       GAGCCTGCGG GACCTCTTCC CCAACCTCGC GGTCGTGCGT GGCGCCCGCC \n+ENSMUST00000005671_homosapiens           GAGCCTGGGA GACCTCTTCC CCAACCTCAC AGTCATCCGT GGCTGGAAAC \n+ENSRNOT00000019267_rattusnorvegicus      GAGCCTGGGA GACCTCTTCC CGAACCTCAC AGTCATCCGT GGCTGGAAAC \n+ENSPTRT00000013802_pantroglodytes        GAGCCTCGGA GACCTCTTCC CCAACCTCAC GGTCATCCGC GGCTGGAAAC \n+\n+\n+ENSMUST00000091291_mus'..b' \n+ENSPTRT00000013802_pantroglodytes        GGCGGCCTTC TGGACAAGCC AGACAACTGT CCCGACATGC TGTTTGAACT \n+\n+\n+ENSMUST00000091291_musmusculus           GATGCGCATG TGCTGGCAGT TCAACCCCAA GATGAGGCCA ACCTTCCTGG \n+ENSCAFT00000026349_canisfamiliaris       GATGAGCCGC TGCTGGCAGC AGAACCCACG CCTGCGGCCC ACCTTCACCC \n+ENSMUST00000005671_homosapiens           TATGCGCATG TGCTGGCAGT ATAACCCCAA GATGCGGCCC TCCTTCCTGG \n+ENSRNOT00000019267_rattusnorvegicus      TATGCGCATG TGCTGGCAGT ACAACCCCAA GATGCGGCCC TCCTTCCTGG \n+ENSPTRT00000013802_pantroglodytes        GATGCGCATG TGCTGGCAGT ATAACCCCAA GATGAGGCCT TCCTTCCTGG \n+\n+\n+ENSMUST00000091291_musmusculus           AAATCGTCAA CCTGCTCAAG GATGACCTCC ACCCCAGCTT TCCAGAAGTT \n+ENSCAFT00000026349_canisfamiliaris       ACATCCTGGA CAGCATTCGG GGGGAACTGC GGCCCTCTTT CCGCCTCTTT \n+ENSMUST00000005671_homosapiens           AGATCATCGG CAGCATCAAG GATGAGATGG AGCCCAGCTT CCAGGAGGTC \n+ENSRNOT00000019267_rattusnorvegicus      AGATCATCGG AAGCATCAAG GATGAGATGG AGCCCAGTTT CCAGGAGGTC \n+ENSPTRT00000013802_pantroglodytes        AGATCATCAG CAGCATCAAA GAGGAGATGG AGCCTGGCTT CCGGGAGGTC \n+\n+\n+ENSMUST00000091291_musmusculus           TCCTTCTTCT ACAGCGAGGA GAACAAGGCT CCTGAGAGTG AGGAGCTGGA \n+ENSCAFT00000026349_canisfamiliaris       TCCTTCTATT ACAGCCCAGA GTG....... ......CCAG GGGAGCCAGG \n+ENSMUST00000005671_homosapiens           TCCTTCTACT ACAGCGAGGA GAACAAGCCT CCCGAGCCAG AGGAGCTGGA \n+ENSRNOT00000019267_rattusnorvegicus      TCCTTCTACT ACAGCGAGGA GAACAAGCCT CCAGAGCCGG AGGAGCTGGA \n+ENSPTRT00000013802_pantroglodytes        TCCTTCTACT ACAGCGAGGA GAACAAGCTG CCCGAGCCGG AGGAGCTGGA \n+\n+\n+ENSMUST00000091291_musmusculus           ....GAT... .........G GAGTTTGAAG ACATGGAGAA TGTCCCGTTG \n+ENSCAFT00000026349_canisfamiliaris       GGGCCCT... .........G CTGCCTAATG CC........ .........A \n+ENSMUST00000005671_homosapiens           ....GAT... .........G GAGCCTGAGA ACATGGAGAG CGTCCCACTG \n+ENSRNOT00000019267_rattusnorvegicus      ....GATGGA GCTGGAGCTG GAGCCCGAGA ACATGGAGAG CGTCCCGCTG \n+ENSPTRT00000013802_pantroglodytes        ....CCT... .........G GAGCCAGAGA ACATGGAGAG CGTCCCCCTG \n+\n+\n+ENSMUST00000091291_musmusculus           GATCGTTC.. .......... ....CTCTCA CTGTCAGAGA GAA...GAG. \n+ENSCAFT00000026349_canisfamiliaris       AACCCAA... .......... CTCCCTACCA .......... .A........ \n+ENSMUST00000005671_homosapiens           GACCCTTCGG CCTCCTCAGC CTCCCTGCCT CTGCCTGAAA GACACTCAGG \n+ENSRNOT00000019267_rattusnorvegicus      GACCCTTCGG CCTCCTCAGC CTCCCTGCCT CTGCCTGAAA GACACTCAGG \n+ENSPTRT00000013802_pantroglodytes        GACCCCTCGG C......... CTCCCTGCCA CTGCCCGACA GACACTCAGG \n+\n+\n+ENSMUST00000091291_musmusculus           GCTGGGGGCC GGGAGGGA.. .GGGTCCTCA ....CTGAGC ATCAAACGGA \n+ENSCAFT00000026349_canisfamiliaris       .......CCC CAGAAGGG.. ...GCTC... .........C CTC....... \n+ENSMUST00000005671_homosapiens           ACACAAGGCT GAGAATGGCC CGGGCCCTGG CGTGCTCGTT CTCCGCGCCA \n+ENSRNOT00000019267_rattusnorvegicus      ACACAAGGCT GAGAACGG.. ....CCCTGG CGTGCTGGTT CTCCGTGCCA \n+ENSPTRT00000013802_pantroglodytes        ACACAAGGCC GAGAACGGCC CCGGCCCTGG GGTGCTGGTC CTCCGCGCCA \n+\n+\n+ENSMUST00000091291_musmusculus           CCTATGATGA .ACACATCCC CTATACCCAC ATGAATGGGG GCAAGAAGAA \n+ENSCAFT00000026349_canisfamiliaris       .......... .AGACTG.C. ..ATGCCC.C A.AAATGGGG GTC....... \n+ENSMUST00000005671_homosapiens           GTTTTGATGA GAGACAG.CC TTACGCTCAC ATGAACGGGG GACGCGCCAA \n+ENSRNOT00000019267_rattusnorvegicus      GTTTTGATGA GAGACAG.CC TTACGCTCAC ATGAATGGGG GACGCGCCAA \n+ENSPTRT00000013802_pantroglodytes        GCTTCGACGA GAGACAG.CC GTACGCACAC ATGAACGGGG GCCGCAAGAA \n+\n+\n+ENSMUST00000091291_musmusculus           CGGACGTGTC CTTACCCTGC CAAGGTCAAA CCCTTCCTAA \n+ENSCAFT00000026349_canisfamiliaris       .......... C......... ..AGGGC... .....ACTGA \n+ENSMUST00000005671_homosapiens           CGAGAGGGCC TTGCCTCTGC CCCAGTCCTC GACCTGCTGA \n+ENSRNOT00000019267_rattusnorvegicus      CGAGAGGGCC TTGCCTCTGC CCCAGTCCTC AA...CCTGC \n+ENSPTRT00000013802_pantroglodytes        CGAGCGGGCC TTGCCGCTGC CCCAGTCTTC GACCTGCTGA \n+\n'
b
diff -r 0a189243186d -r ae69d14b6fbf test-data/output3.nhx
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output3.nhx Thu Jan 14 12:14:52 2021 +0000
b
@@ -0,0 +1,1 @@
+(((ENSCAFT00000026349_canisfamiliaris:0.07500,ENSMUST00000091291_musmusculus:0.07500):0.02000,ENSPTRT00000013802_pantroglodytes:0.04500):0.01500,ENSMUST00000005671_homosapiens:0.03000,ENSRNOT00000019267_rattusnorvegicus:0.03000);
\ No newline at end of file
b
diff -r 0a189243186d -r ae69d14b6fbf test-data/output3.phylip
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output3.phylip Thu Jan 14 12:14:52 2021 +0000
b
b'@@ -0,0 +1,429 @@\n+    5  4240\n+ENSMUST000 ATGGG-CTTC GGGAGAGGAT GTGAGACGAC GG-----CTG TGCCATTGCT GGTGGCCGTG\n+ENSCAFT000 ATGGCAGT-- -GCCCAGT-- CTGTGCCCAT GG-GTCGC-A TGC--CTGCT GGTGATCCTC\n+ENSMUST000 ATGAA-GTCT GGCTCCGGAG GAGGGTCCCC GACCTCGCTG TGG--GGGCT CGTGTTTCTC\n+ENSRNOT000 ATGAA-GTCT GGCTCCGGAG GAGGGTCCCC GACCTCGCTG TGG--GGGCT CGTGTTTCTC\n+ENSPTRT000 ATGAA-GTCT GGCTCCGGAG GAGGGTCCCC GACCTCGCTG TGG--GGGCT CCTGTTTCTC\n+\n+           GCCGCGTTGC TGGTGGGCAC AGCCGGCCAC CTGTACCCTG GAGAGG--TG TG-CCCTGGT\n+           CTCTCCTTGG GATTTGGCCT GGAC------ ------ACAC TAGAGG--TG TG-CCCCAGC\n+           TCCGCCGCGC TC-TCTCTCT GGCCGA---C -----GAGTG GAGAAATCTG TGGGCCCGGC\n+           TCCGCCGCGC TC-TCGCTCT GGCCGA---C -----GAGTG GAGAAATTTG TGGGCCCGGC\n+           TCCGCCGCGC TC-TCGCTCT GGCCGA---C -----GAGTG GAGAAATCTG CGGGCCAGGC\n+\n+           ATGGACATCC GGAACAACC- TGACCAGGCT ACATGAGCTG GAGAACTGCT CAGTCATTGA\n+           CTGGACATCC GCTCAGAGGT GGCGG-AGCT GCGCCGGCTG GAGAACTGCA GCGTGGTGGA\n+           ATTGACATCC GCAACGACTA TCAGC-AGCT GAAGCGCCTG GAAAACTGCA CGGTGATCGA\n+           ATTGACATCC GCAACGACTA TCAGC-AGCT GAAGCGCCTG GAAAACTGCA CGGTGATCGA\n+           ATCGACATCC GCAACGACTA TCAGC-AGCT GAAGCGCCTG GAGAACTGCA CGGTGATCGA\n+\n+           GGGCCATCTG CAGATCCTCC TGATGTTCAA GACCAGACCC GAAGATTTCC GAGACCTCAG\n+           GGGCCATCTG CAGATCCTGC TCATGTTCAC GGCCACGGGC GAGGACTTCC GCGGCCTCAG\n+           GGGCTTCCTC CACATCCTGC TCATCTCCAA GG------CC GAGGACTACC GAAGCTACCG\n+           GGGCTTCCTC CACATCCTGC TCATCTCCAA GG------CC GAGGACTACC GAAGCTACCG\n+           GGGCTACCTC CACATCCTGC TCATCTCCAA GG------CC GAGGACTACC GCAGCTACCG\n+\n+           TTTCCCCAAA CTCATCATGA TCACAGATTA CCTGCTTCTC TTCCGTGTCT ATGGTCTGGA\n+           CTTCCCGCGC CTCACTCAGG TCACTGACTA CCTGCTGCTC TTCCGCGTGT ATGGCCTGGA\n+           CTTCCCCAAG CTCACCGTCA TCACTGAGTA CTTGCTGCTC TTCCGAGTCG CTGGCCTCGA\n+           CTTCCCCAAG CTCACGGTCA TCACCGAGTA CTTGCTGCTG TTTCGAGTGG CCGGCCTCGA\n+           CTTCCCCAAG CTCACGGTCA TTACCGAGTA CTTGCTGCTG TTCCGAGTGG CTGGCCTCGA\n+\n+           AAGTCTGAAA GACCTCTTCC CAAATCTCAC AGTCATCCGA GGCTCCCGTC TCTTCTTCAA\n+           GAGCCTGCGG GACCTCTTCC CCAACCTCGC GGTCGTGCGT GGCGCCCGCC TCTTCCTGGG\n+           GAGCCTGGGA GACCTCTTCC CCAACCTCAC AGTCATCCGT GGCTGGAAAC TCTTCTACAA\n+           GAGCCTGGGA GACCTCTTCC CGAACCTCAC AGTCATCCGT GGCTGGAAAC TCTTCTACAA\n+           GAGCCTCGGA GACCTCTTCC CCAACCTCAC GGTCATCCGC GGCTGGAAAC TCTTCTACAA\n+\n+           CTATGCCCTG GTTATCTTCG AGATGGTCCA CCTGAAGGAG CTGGGGCTTT ATAACCTCAT\n+           TTATGCGCTG GTGGTCTACG AGATGCCGCA CCTGCGGGAC GTGGGGCTGC CGGCGCTGGG\n+           CTACGCACTG GTCATCTTCG AGATGACCAA TCTCAAGGAT ATTGGGCTTT ATAATCTGAG\n+           TTACGCACTG GTCATCTTCG AGATGACCAA TCTCAAGGAT ATTGGGCTTT ATAATCTGAG\n+           CTACGCCCTG GTCATCTTCG AGATGACCAA TCTCAAGGAT ATTGGGCTTT ACAACCTGAG\n+\n+           GAACATCACC CGGGGCTCTG TCCGCATCGA GAAGAATAAT GAGCTCTGCT ACCTGGCCAC\n+           GGCCGTGCTG CGTGGGGCCG TGCGGGTGGA GAAGAACCAG GAGCTCTGTC ATCTCTCCAC\n+           GAACATTACT CGGGGGGCCA TCAGGATTGA GAAGAACGCC GACCTCTGTT ACCTCTCCAC\n+           GAACATTACT CGGGGGGCCA TCAGGATTGA GAAAAACGCT GACCTCTGTT ACCTCTCCAC\n+           GAACATTACT CGGGGGGCCA TCAGGATTGA GAAAAATGCT GACCTCTGTT ACCTCTCCAC\n+\n+           TATCGACTGG TCCCGTATCC TGGATTCTGT GGAGGACAAC TACATTGTAC TGAACAAAGA\n+           CATCGACTGG GGGCTGCTGC AGCCCTCGCC CAGCGCCAAC CACATCGTGG GCAACAA-GC\n+           CATAGACTGG TCTCTCATCT TGGATGCGGT GTCCAATAAC TACATTGTGG GGAACAA-GC\n+           CATAGACTGG TCTCTCATCT TGGATGCGGT GTCCAATAAC TACATTGTGG GGAACAA-GC\n+           TGTGGACTGG TCCCTGATCC TGGATGCGGT GTCCAATAAC TACATTGTGG GGAATAA-GC\n+\n+           TGACAACGAG GAATGTGGGG ATGTCTGTCC AGGCACCGCC AAGGGCA-AG ACCAA--CTG\n+           TGCGT--GAG GAGTGTGCCG ACGTGTGCCC TGGTGTGCTG GGTGCCACCG GCCAGCCCTG\n+           CCCCG--AAG GAATGTGGGG ACCTGTGTCC AGGGACATTG GAGGAGA-AG CCCAT--GTG\n+           CCCCA--AAG GAATGTGGGG ACCTGTGTCC AGGGACCTTG GAGGAGA-AG CCCAT--GTG\n+           CCCCA--AAG GAATGTGGGG ACCTGTGTCC AGGGACCATG GAGGAGA-AG CCGAT--GTG\n+\n+           TCCTGCCACT GTCATCAATG GGCAGTTTGT GGA'..b'TGCT GCCTGTGCGC TGGATGTCTC\n+           ACGAGACGGA CTACTACCGG AAAGGCGGGA AGGGCTTGCT GCCTGTGCGC TGGATGTCTC\n+           ATGAGACAGA CTATTACCGG AAAGGAGGGA AAGGGCTGCT GCCCGTGCGC TGGATGTCTC\n+\n+           CTGAGTCCCT GAAGGATGGA GTCTTTACTG CTTCTTCTGA TATGTGGTCC TTTGGGGTGG\n+           CCGAGTCCCT CAAAGATGGA ATCTTCACCA CACATTCGGA TGTTTGGTCC TTCGGGGTGG\n+           CCGAGTCCCT CAAGGATGGT GTCTTCACTA CTCATTCTGA TGTCTGGTCC TTCGGGGTCG\n+           CCGAGTCCCT CAAGGATGGC GTCTTCACCA CTCATTCCGA TGTCTGGTCC TTTGGGGTCG\n+           CCGAGTCCCT CAAGGATGGA GTCTTCACCA CTTACTCGGA CGTCTGGTCC TTCGGGGTCG\n+\n+           TCCTTTGGGA AATCACTAGC CTGGCTGAGC AACCTTATCA AGGCCTGTCT AATGAACAGG\n+           TGCTCTGGGA GATCGTGACC CTAGCTGAAC AGCCCTACCA GGGTTTATCC AACGAGCAGG\n+           TCCTCTGGGA GATCGCCACG CTGGCTGAGC AGCCCTACCA GGGCTTGTCC AACGAGCAAG\n+           TCCTCTGGGA GATCGCCACT CTGGCTGAGC AGCCGTACCA GGGCCTGTCC AACGAGCAAG\n+           TCCTCTGGGA GATCGCCACA CTGGCCGAGC AGCCCTACCA GGGCTTGTCC AACGAGCAAG\n+\n+           TGTTGAAGTT TGTCATGGAT GGAGGCTATC TGGATCCCCC TGATAACTGT CCAGAGAGAC\n+           TGCTCAAGTT TGTCATGGAT GGTGGGGTCC TGGAGGAGCT GGAGAGCTGT CCCCTTCAGC\n+           TTCTTCGTTT CGTCATGGAG GGTGGCCTTC TGGACAAGCC GGACAACTGC CCTGATATGC\n+           TTCTTCGTTT CGTCATGGAG GGCGGCCTTC TGGACAAGCC GGATAACTGC CCCGATATGC\n+           TCCTTCGCTT CGTCATGGAG GGCGGCCTTC TGGACAAGCC AGACAACTGT CCCGACATGC\n+\n+           TCACTGACCT GATGCGCATG TGCTGGCAGT TCAACCCCAA GATGAGGCCA ACCTTCCTGG\n+           TGCAAGAACT GATGAGCCGC TGCTGGCAGC AGAACCCACG CCTGCGGCCC ACCTTCACCC\n+           TGTTTGAACT TATGCGCATG TGCTGGCAGT ATAACCCCAA GATGCGGCCC TCCTTCCTGG\n+           TGTTTGAACT TATGCGCATG TGCTGGCAGT ACAACCCCAA GATGCGGCCC TCCTTCCTGG\n+           TGTTTGAACT GATGCGCATG TGCTGGCAGT ATAACCCCAA GATGAGGCCT TCCTTCCTGG\n+\n+           AAATCGTCAA CCTGCTCAAG GATGACCTCC ACCCCAGCTT TCCAGAAGTT TCCTTCTTCT\n+           ACATCCTGGA CAGCATTCGG GGGGAACTGC GGCCCTCTTT CCGCCTCTTT TCCTTCTATT\n+           AGATCATCGG CAGCATCAAG GATGAGATGG AGCCCAGCTT CCAGGAGGTC TCCTTCTACT\n+           AGATCATCGG AAGCATCAAG GATGAGATGG AGCCCAGTTT CCAGGAGGTC TCCTTCTACT\n+           AGATCATCAG CAGCATCAAA GAGGAGATGG AGCCTGGCTT CCGGGAGGTC TCCTTCTACT\n+\n+           ACAGCGAGGA GAACAAGGCT CCTGAGAGTG AGGAGCTGGA ----GAT--- ---------G\n+           ACAGCCCAGA GTG------- ------CCAG GGGAGCCAGG GGGCCCT--- ---------G\n+           ACAGCGAGGA GAACAAGCCT CCCGAGCCAG AGGAGCTGGA ----GAT--- ---------G\n+           ACAGCGAGGA GAACAAGCCT CCAGAGCCGG AGGAGCTGGA ----GATGGA GCTGGAGCTG\n+           ACAGCGAGGA GAACAAGCTG CCCGAGCCGG AGGAGCTGGA ----CCT--- ---------G\n+\n+           GAGTTTGAAG ACATGGAGAA TGTCCCGTTG GATCGTTC-- ---------- ----CTCTCA\n+           CTGCCTAATG CC-------- ---------A AACCCAA--- ---------- CTCCCTACCA\n+           GAGCCTGAGA ACATGGAGAG CGTCCCACTG GACCCTTCGG CCTCCTCAGC CTCCCTGCCT\n+           GAGCCCGAGA ACATGGAGAG CGTCCCGCTG GACCCTTCGG CCTCCTCAGC CTCCCTGCCT\n+           GAGCCAGAGA ACATGGAGAG CGTCCCCCTG GACCCCTCGG C--------- CTCCCTGCCA\n+\n+           CTGTCAGAGA GAA---GAG- GCTGGGGGCC GGGAGGGA-- -GGGTCCTCA ----CTGAGC\n+           ---------- -A-------- -------CCC CAGAAGGG-- ---GCTC--- ---------C\n+           CTGCCTGAAA GACACTCAGG ACACAAGGCT GAGAATGGCC CGGGCCCTGG CGTGCTCGTT\n+           CTGCCTGAAA GACACTCAGG ACACAAGGCT GAGAACGG-- ----CCCTGG CGTGCTGGTT\n+           CTGCCCGACA GACACTCAGG ACACAAGGCC GAGAACGGCC CCGGCCCTGG GGTGCTGGTC\n+\n+           ATCAAACGGA CCTATGATGA -ACACATCCC CTATACCCAC ATGAATGGGG GCAAGAAGAA\n+           CTC------- ---------- -AGACTG-C- --ATGCCC-C A-AAATGGGG GTC-------\n+           CTCCGCGCCA GTTTTGATGA GAGACAG-CC TTACGCTCAC ATGAACGGGG GACGCGCCAA\n+           CTCCGTGCCA GTTTTGATGA GAGACAG-CC TTACGCTCAC ATGAATGGGG GACGCGCCAA\n+           CTCCGCGCCA GCTTCGACGA GAGACAG-CC GTACGCACAC ATGAACGGGG GCCGCAAGAA\n+\n+           CGGACGTGTC CTTACCCTGC CAAGGTCAAA CCCTTCCTAA\n+           ---------- C--------- --AGGGC--- -----ACTGA\n+           CGAGAGGGCC TTGCCTCTGC CCCAGTCCTC GACCTGCTGA\n+           CGAGAGGGCC TTGCCTCTGC CCCAGTCCTC AA---CCTGC\n+           CGAGCGGGCC TTGCCGCTGC CCCAGTCTTC GACCTGCTGA\n+\n+\n+\n'
b
diff -r 0a189243186d -r ae69d14b6fbf test-data/output3.pir_aln
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output3.pir_aln Thu Jan 14 12:14:52 2021 +0000
b
b'@@ -0,0 +1,440 @@\n+>DL;ENSMUST00000091291_musmusculus\n+\n+ATGGG-CTTCGGGAGAGGATGTGAGACGACGG-----CTGTGCCATTGCT\n+GGTGGCCGTGGCCGCGTTGCTGGTGGGCACAGCCGGCCACCTGTACCCTG\n+GAGAGG--TGTG-CCCTGGTATGGACATCCGGAACAACC-TGACCAGGCT\n+ACATGAGCTGGAGAACTGCTCAGTCATTGAGGGCCATCTGCAGATCCTCC\n+TGATGTTCAAGACCAGACCCGAAGATTTCCGAGACCTCAGTTTCCCCAAA\n+CTCATCATGATCACAGATTACCTGCTTCTCTTCCGTGTCTATGGTCTGGA\n+AAGTCTGAAAGACCTCTTCCCAAATCTCACAGTCATCCGAGGCTCCCGTC\n+TCTTCTTCAACTATGCCCTGGTTATCTTCGAGATGGTCCACCTGAAGGAG\n+CTGGGGCTTTATAACCTCATGAACATCACCCGGGGCTCTGTCCGCATCGA\n+GAAGAATAATGAGCTCTGCTACCTGGCCACTATCGACTGGTCCCGTATCC\n+TGGATTCTGTGGAGGACAACTACATTGTACTGAACAAAGATGACAACGAG\n+GAATGTGGGGATGTCTGTCCAGGCACCGCCAAGGGCA-AGACCAA--CTG\n+TCCTGCCACTGTCATCAATGGGCAGTTTGTGGAACGGTGCTGGACACACA\n+GTCATTGTCAGAAAGTTTGCCCAACCATCTGTAAGTCACATGGCTGCACA\n+GCTGAAGGCCTGTGCTGCCACAAAGAGTGCCTGGGCAACTGTTCGGAACC\n+TGATGACCCCACCAAGTGTGTGGCCTGTCGCAACTTCTATCTGGATGGTC\n+AGTGTGTGGAGACCTGCCCGCCACCCTACTATCACTTCCAGGACTGGCGC\n+TGTGTGAACTTCAGCTTCTG--CCAAGACCTTCA-CTTCAAATGCAGGAA\n+CTCTCGGAAGCCTGGCTGCCACCAATACGTCATTCACAACAATAAGTGCA\n+TCCCCGAGTGCCCGTCTGGCTATACCATGAATTCCAGC---AACTTGATG\n+TGCACCCCATGTCTGGGACCCTGCCCTAAGGTCTGCCAA-ATCCTC-GAA\n+GGTG-AGAAGACCATTGATTCTGTGACATCTGCCCAGGAGCTCCGAGGCT\n+GCACTGTGATCAACGGTAGCCTGATCATCAACATCCGAGGGGGCAACAAC\n+CTGGCAGCTGAGCTGGAGGCTAACCTTGGCCTCATTGAAGAAATTTCGGG\n+ATTTCTAAAGATCCGCCGCTCCTATGCTCTGGTATCACTTTCTTTCTTCA\n+GGAAGCTACATCTGATTCGAGGAGAGACCTTGGAAATTGGGAACTATTCT\n+TTTTATGCCTTGGACAACCAGAACCTGAGGCAACTCTGGGACTGGAG-CA\n+AACACAACCTCACCATCACTCAGGGCAAGCTCTTCTTCCATTACAACCCG\n+AAACTCTGCTTGTCTGAAATTCACAAGATGGAAGAAGTCTCCGGAACTAA\n+GGGCCGTCAGGAGAGGAACGACATTGCCCTGAAGACCAATGGGGACCAGG\n+CATCGTGTGAAAATGAATTGCTTAAATTTTCTTTCATTCGGACATCTTTT\n+GACAAGATCCTGTTGAGGTGGGAACCCTACTGGCCCCCCGACTTCCGAGA\n+TCTCCTGGGATTCATGTTGTTCTACAAAGAGGCCCCTTATCAGAATGTGA\n+CAGAGTTTGATGGGCAGGATGCTTGTGGCTCCAACAGCTGGACTGTGGTG\n+GATATTGACCCGCCCCAGAGGTCCAACGACCCCAAGTCTCAGACCCCAAG\n+CCACCCTGGGTGGCTGAT-GCGGGGCCTCAAACCCTGGACCCAATACGCC\n+ATCTTTGTGAAGACCTTGG---TTACCTTCTCTGATGAACGGC-GGACCT\n+ATGGAGCCAAAAGTGATATCATCTATGTGCAAACAGATGCCACTAATCCT\n+TCTGTCCCCCTGGATCCCATATCAGTTTCTAATTCCTCATCTCAGATTAT\n+CTTAAAGTGGAAGCCCCCCTCTGACCCCAATGGCAACATCACACACTACC\n+TGGTGTACTGGGAGAGGCAAGCAGAGGACAGCGAGCTGTTTGAGCTGGAT\n+TATTGTCTCAAAGGGCTGA-AGCTCCCTTCACGGACCTGGTC---CCCAC\n+CCTTTGAGTCTGATGAT-T--CTCAGAAGCACAA-TCAGA-GT-GAGTA-\n+TGACGACTCGGCCAGTGAGTGC-TGCTCATGCCC-TAAGACTGACTCTCA\n+GATCCTGAAGGAGCTGGAGGAGTCTTCATTCAGGAAGACCTTCGAGGATT\n+ACCTGCACAACGTGGTTTTTGTCCCCAGGCCATCCCGAAAGCGAAGATCC\n+CTTGAAGAGGTGGGGAATGTGACA---GCCACCACACTCA-CACTTCCAG\n+ATTTCCCCAACGT-CTCCTCTACCATTGTGCCC-ACAAGTCAG-G-AGGA\n+GCACAGGCCATTTGAGA---AAGTGGTGAACAAGGAGTCACTTGTCATCT\n+CTGGCCTGAGACACTTCACTGGGTACCGCATTGAGCTGCAGGCATGCAAT\n+CAAGATTCCCCAGAT-GAGAGGTGCAGTGTGGCTGCCTACGTCAGTGCCC\n+GGACCATGCCTGAAGCTAAGGCAGATGACATCGTTGGCCCTGTGACTCAT\n+GAA---ATCTTTGAGAACAATGTTGTACACTTAATGTGGCAAGAGCCAAA\n+GGAACCTAATGGTCTGATTGTGCTATATGAAGTGAGCTATCGCCGATATG\n+GTGATGAGGAG-CTGCACCTCTGTGTCTCCCGGAAGCATTTTGCCCTGGA\n+GCGGGGCTGCAGGCTGCGAGGGCTCTCCCCAGGAAACTACAGTGTTCGAG\n+TCCGGGCTACCTCTCTGGCAGGAAATGGCTCCTGGACAGAACCCACCTAT\n+TTTTATGTGACTGAT-TATTTAGATGTCCCATCAAA-TATTGCCAAAATT\n+ATCATTGGACCCCTCATCTTTGTCTTCCTCTTCAGTGTTG--TGATTGGA\n+-AGTAT---TTATCTATTTCTGAGAAAGAGG-----CAGCCGGATGGGCC\n+AATGGGACCACTGTATGCATCTTCAAACCCTGAGTACCT-CAGTGCCAGT\n+GATGTGTTTCCATCTTCTGTGTACGTGCCGGACGAGTGGGAGGTGCCTCG\n+AGAGAAGATCACCCTTCTTCGAGAGCTGGGGCAGGGATCCTTTGGTATGG\n+TGTATGAAGGCAATGC-CAAGGATA--TCATCAAGGGTGAGGCAGAGACC\n+CGTGTTGCGGTTAAGACTGTCAATGAGTCAGCCAGTCTTCGAGAACGGAT\n+CGAGTTCCTCAATGAGGCATCAGTCATGAAGGGATTCACCTGCCATCATG\n+TGGTCCGCCTTCTTGGGGTGGTATCCAAAGGACAGCCAACGCTGGTAGTG\n+ATGGAATTGATGGCTCATGGAGACCTGAAAAGTCACCTCCGTTCTCTGAG\n+GCCAGATGCTGA---GAATAACCCAGGCCGCCCTCCCCCTACCTTGCAAG\n+AAATGATTCAGATGACAGCAGAAATTGCTGATGGCATGGCATACTTGAAC\n+GCCAAGAAGTTTGTGCACCGGGACCTGGCAGCTCGAAACTGCATGGTTGC\n+CCATGATTTTACTGTCAAAATTGGAGACTTTGGAATGACAAGGGACATCT\n+ACGAGACAGATTACTATCGGAAAGGGGGCAAGGGACTGCTTCCTGTGAGG\n+TGGATGTCACCTGAGTCCCTGAAGGATGGAGTCTTTACTGCTTCTTCTGA\n+TATGTGGTCCTTTGGGGTGGTCCTTTGGGAAATCACTAGCCTGGCTGAGC\n+AACCTTATCAAGGCCTGTCTAATGAACAGGTGTTGAAGTTTG'..b'T\n+ATTGGGCTTTACAACCTGAGGAACATTACTCGGGGGGCCATCAGGATTGA\n+GAAAAATGCTGACCTCTGTTACCTCTCCACTGTGGACTGGTCCCTGATCC\n+TGGATGCGGTGTCCAATAACTACATTGTGGGGAATAA-GCCCCCA--AAG\n+GAATGTGGGGACCTGTGTCCAGGGACCATGGAGGAGA-AGCCGAT--GTG\n+TGAGAAGACCACCATCAACAATGAGTACAACTACCGCTGCTGGACCACAA\n+ACCGCTGCCAGAAAATGTGCCCGAGCACGTGTGGGAAGCGGGCGTGCACC\n+GAGAACAACGAGTGCTGCCACCCCGAGTGCCTGGGCAGCTGCAGCGCGCC\n+TGACAACGACACGGCCTGTGTAGCTTGCCGCCACTACTACTATGCCGGTG\n+TCTGTGTGCCTGCCTGCCCGCCCAACACCTACAGGTTTGAGGGCTGGCGC\n+TGTGTGGACCGTGACTTCTGCGCCAACATCCTCAGCGCCGAGAGCAGCGA\n+CTC---------------CGAGGGGTTTGTGATCCACGACGGCGAGTGCA\n+TGCAGGAGTGCCCCTCGGGCTTCATCCGCAACGGCAGCCAGAGCATGTAC\n+TGCATCCCTTGTGAAGGTCCTTGCCCGAAGGTCTGTG---AGGAAGAAAA\n+GAAAACAAAGACCATTGATTCTGTTACTTCTGCTCAGATGCTCCAAGGAT\n+GCACCATCTTCAAGGGCAATTTGCTCATTAACATCCGACGGGGGAATAAC\n+ATTGCTTCAGAGCTGGAGAACTTCATGGGGCTCATCGAGGTGGTGACGGG\n+CTACGTGAAGATCCGCCATTCTCATGCCTTGGTCTCCTTGTCCTTCCTAA\n+AAAACCTTCGCCTCATCTTAGGAGAGGAGCAGCTAGAAGGGAATTACTCC\n+TTCTACGTCCTCGACAACCAGAACTTGCAGCAACTATGGGACTGGGA-CC\n+ACCGCAACCTGACCATCAAAGCAGGGAAAATGTACTTTGCTTTCAATCCC\n+AAATTATGTGTTTCCGAAATTTACCGCATGGAGGAAGTGACGGGGACTAA\n+AGGGCGCCAAAGCAAAGGGGACATAAACACCAGGAACAACGGGGAGAGAG\n+CCTCCTGTGAAAGTGACGTCCTGCATTTCACCTCCACCACCACGTCGAAG\n+AATCGCATCATCATAACCTGGCACCGGTACCGGCCCCCTGACTACAGGGA\n+TCTCATCAGCTTCACCGTTTACTACAAGGAAGCACCCTTTAAGAATGTCA\n+CGGAGTATGATGGGCAGGACGCCTGCGGCTCCAACAGCTGGAACATGGTG\n+GACGTGGACCTCCCGCCCAA---CAAGGACG--------TGGAGCC----\n+-----CGGCAT-CTTACT-ACATGGGCTGAAGCCCTGGACTCAGTACGCC\n+GTTTACGTCAAGGCTGTGACCCTCACCATGG-TGGAGAATGACCATATCC\n+GTGGGGCCAAGAGTGAGATCTTGTACATTCGCACCAATGCTTCAGTTCCT\n+TCCATTCCCTTGGACGTTCTTTCAGCATCGAACTCCTCTTCTCAGTTAAT\n+CGTGAAGTGGAACCCTCCCTCTCTGCCCAACGGCAACCTGAGTTACTACA\n+TTGTGCGCTGGCAGCGGCAGCCTCAGGACGGCTACCTTTACCGGCACAAT\n+TACTGCTCCAAAGA-CAA--AATCCCCATCAGGAAGTATGCCGACGGCA-\n+CCATCGACATTGAGGAGGTCACAGAGAACCCCAAGACTGAGGT-GTGTGG\n+TGGGGAGAA---AGGGCCTTGC-TGCGCCTGCCC-CAAAACTGAAGCCGA\n+GAAGCAGGCCGAGAAGGAGGAGGCTGAATACCGCAAAGTCTTTGAGAATT\n+TCCTGCACAACTCCATCTTCGTGCCCAGACCTGAAAGGAAGCGGAGAGAT\n+GTCATGCAAGTGGCCAACACCACCATGTCCAGCCGAAGCAGGAACACCAC\n+GGC-CGCAGACAC-CTACAACATCACCGACCCGGAAGAGCTGGAGACAGA\n+GTACCCTTTCTTTGAGAGCAGAGTGGATAACAAGGAGAGAACTGTGATTT\n+CTAACCTTCGGCCTTTCACATTGTACCGCATCGATATCCACAGCTGCAAC\n+CACGAGGCT-GAGAAGCTGGGCTGCAGCGCCTCCAACTTTGTCTTTGCAA\n+GGACTATGCCCGCAGAAGGAGCAGATGACATTCCTGGGCCAGTGACCTGG\n+GAGCCAAGGCCTGAAAAC---TCCATCTTTTTAAAGTGGCCGGAACCTGA\n+GAATCCCAATGGATTGATTCTAATGTATGAAATAAAATACGGATCACAA-\n+--GTTGAGGAT-CAGCGAGAATGTGTGTCCAGACAGGAATACAGGAAGTA\n+TGGAGGGGCCAAGCTAAACCGGCTAAACCCGGGGAACTACACAGCCCGGA\n+TTCAGGCCACATCTCTCTCTGGGAATGGGTCGTGGACAGATCCTGTGTTC\n+TTCTATGTCCAGGCC-AA----AACAGGATATGAAAACTTCATCCATCTG\n+ATCATCGCTCTGCCCG---TCGCTGTCCTGTTGATCGTGGGAGGGTTGGT\n+GATTATGCTGTACGTCTTCCATAGAAAGAGAAATAACAGCAGGCTGGG-G\n+AATGG-AGTGCTGTATGCCTCTGTGAACCCGGAGTACTT-CAGCGCTGCT\n+GAT---------------GTGTACGTTCCCGATGAGTGGGAGGTGGCTCG\n+GGAGAAGATCACCATGAGCCGGGAACTTGGGCAGGGGTCCTTTGGGATGG\n+TCTATGAAGGAGTTGC-CAAGGGTG--TGGTGAAAGATGAACCTGAAACC\n+AGAGTGGCCATTAAAACAGTGAACGAGGCCGCAAGCATGCGTGAAAGGAT\n+TGAGTTTCTCAACGAAGCTTCTGTGATGAAGGAGTTCAATTGTCACCATG\n+TGGTGCGATTGCTGGGTGTGGTGTCCCAAGGCCAGCCAACACTGGTCATC\n+ATGGAACTGATGACACGGGGCGATCTCAAAAGTTATCTCCGGTCTCTGAG\n+GCCAGAAATGGA---GAATAATCCAGTCCTAGCACCTCCAAGCCTGAGCA\n+AGATGATTCAGATGGCCGGAGAGATTGCAGACGGCATGGCATACCTCAAC\n+GCCAATAAGTTCGTCCACAGAGACCTTGCTGCCCGGAATTGCATGGTAGC\n+CGAAGATTTCACAGTCAAAATCGGAGATTTTGGTATGACGCGAGATATCT\n+ATGAGACAGACTATTACCGGAAAGGAGGGAAAGGGCTGCTGCCCGTGCGC\n+TGGATGTCTCCCGAGTCCCTCAAGGATGGAGTCTTCACCACTTACTCGGA\n+CGTCTGGTCCTTCGGGGTCGTCCTCTGGGAGATCGCCACACTGGCCGAGC\n+AGCCCTACCAGGGCTTGTCCAACGAGCAAGTCCTTCGCTTCGTCATGGAG\n+GGCGGCCTTCTGGACAAGCCAGACAACTGTCCCGACATGCTGTTTGAACT\n+GATGCGCATGTGCTGGCAGTATAACCCCAAGATGAGGCCTTCCTTCCTGG\n+AGATCATCAGCAGCATCAAAGAGGAGATGGAGCCTGGCTTCCGGGAGGTC\n+TCCTTCTACTACAGCGAGGAGAACAAGCTGCCCGAGCCGGAGGAGCTGGA\n+----CCT------------GGAGCCAGAGAACATGGAGAGCGTCCCCCTG\n+GACCCCTCGGC---------CTCCCTGCCACTGCCCGACAGACACTCAGG\n+ACACAAGGCCGAGAACGGCCCCGGCCCTGGGGTGCTGGTCCTCCGCGCCA\n+GCTTCGACGAGAGACAG-CCGTACGCACACATGAACGGGGGCCGCAAGAA\n+CGAGCGGGCCTTGCCGCTGCCCCAGTCTTCGACCTGCTGA\n+*\n'
b
diff -r 0a189243186d -r ae69d14b6fbf test-data/output3.pir_seq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output3.pir_seq Thu Jan 14 12:14:52 2021 +0000
b
b'@@ -0,0 +1,425 @@\n+>DL;ENSMUST00000091291_musmusculus\n+\n+ATGGGCTTCGGGAGAGGATGTGAGACGACGGCTGTGCCATTGCTGGTGGC\n+CGTGGCCGCGTTGCTGGTGGGCACAGCCGGCCACCTGTACCCTGGAGAGG\n+TGTGCCCTGGTATGGACATCCGGAACAACCTGACCAGGCTACATGAGCTG\n+GAGAACTGCTCAGTCATTGAGGGCCATCTGCAGATCCTCCTGATGTTCAA\n+GACCAGACCCGAAGATTTCCGAGACCTCAGTTTCCCCAAACTCATCATGA\n+TCACAGATTACCTGCTTCTCTTCCGTGTCTATGGTCTGGAAAGTCTGAAA\n+GACCTCTTCCCAAATCTCACAGTCATCCGAGGCTCCCGTCTCTTCTTCAA\n+CTATGCCCTGGTTATCTTCGAGATGGTCCACCTGAAGGAGCTGGGGCTTT\n+ATAACCTCATGAACATCACCCGGGGCTCTGTCCGCATCGAGAAGAATAAT\n+GAGCTCTGCTACCTGGCCACTATCGACTGGTCCCGTATCCTGGATTCTGT\n+GGAGGACAACTACATTGTACTGAACAAAGATGACAACGAGGAATGTGGGG\n+ATGTCTGTCCAGGCACCGCCAAGGGCAAGACCAACTGTCCTGCCACTGTC\n+ATCAATGGGCAGTTTGTGGAACGGTGCTGGACACACAGTCATTGTCAGAA\n+AGTTTGCCCAACCATCTGTAAGTCACATGGCTGCACAGCTGAAGGCCTGT\n+GCTGCCACAAAGAGTGCCTGGGCAACTGTTCGGAACCTGATGACCCCACC\n+AAGTGTGTGGCCTGTCGCAACTTCTATCTGGATGGTCAGTGTGTGGAGAC\n+CTGCCCGCCACCCTACTATCACTTCCAGGACTGGCGCTGTGTGAACTTCA\n+GCTTCTGCCAAGACCTTCACTTCAAATGCAGGAACTCTCGGAAGCCTGGC\n+TGCCACCAATACGTCATTCACAACAATAAGTGCATCCCCGAGTGCCCGTC\n+TGGCTATACCATGAATTCCAGCAACTTGATGTGCACCCCATGTCTGGGAC\n+CCTGCCCTAAGGTCTGCCAAATCCTCGAAGGTGAGAAGACCATTGATTCT\n+GTGACATCTGCCCAGGAGCTCCGAGGCTGCACTGTGATCAACGGTAGCCT\n+GATCATCAACATCCGAGGGGGCAACAACCTGGCAGCTGAGCTGGAGGCTA\n+ACCTTGGCCTCATTGAAGAAATTTCGGGATTTCTAAAGATCCGCCGCTCC\n+TATGCTCTGGTATCACTTTCTTTCTTCAGGAAGCTACATCTGATTCGAGG\n+AGAGACCTTGGAAATTGGGAACTATTCTTTTTATGCCTTGGACAACCAGA\n+ACCTGAGGCAACTCTGGGACTGGAGCAAACACAACCTCACCATCACTCAG\n+GGCAAGCTCTTCTTCCATTACAACCCGAAACTCTGCTTGTCTGAAATTCA\n+CAAGATGGAAGAAGTCTCCGGAACTAAGGGCCGTCAGGAGAGGAACGACA\n+TTGCCCTGAAGACCAATGGGGACCAGGCATCGTGTGAAAATGAATTGCTT\n+AAATTTTCTTTCATTCGGACATCTTTTGACAAGATCCTGTTGAGGTGGGA\n+ACCCTACTGGCCCCCCGACTTCCGAGATCTCCTGGGATTCATGTTGTTCT\n+ACAAAGAGGCCCCTTATCAGAATGTGACAGAGTTTGATGGGCAGGATGCT\n+TGTGGCTCCAACAGCTGGACTGTGGTGGATATTGACCCGCCCCAGAGGTC\n+CAACGACCCCAAGTCTCAGACCCCAAGCCACCCTGGGTGGCTGATGCGGG\n+GCCTCAAACCCTGGACCCAATACGCCATCTTTGTGAAGACCTTGGTTACC\n+TTCTCTGATGAACGGCGGACCTATGGAGCCAAAAGTGATATCATCTATGT\n+GCAAACAGATGCCACTAATCCTTCTGTCCCCCTGGATCCCATATCAGTTT\n+CTAATTCCTCATCTCAGATTATCTTAAAGTGGAAGCCCCCCTCTGACCCC\n+AATGGCAACATCACACACTACCTGGTGTACTGGGAGAGGCAAGCAGAGGA\n+CAGCGAGCTGTTTGAGCTGGATTATTGTCTCAAAGGGCTGAAGCTCCCTT\n+CACGGACCTGGTCCCCACCCTTTGAGTCTGATGATTCTCAGAAGCACAAT\n+CAGAGTGAGTATGACGACTCGGCCAGTGAGTGCTGCTCATGCCCTAAGAC\n+TGACTCTCAGATCCTGAAGGAGCTGGAGGAGTCTTCATTCAGGAAGACCT\n+TCGAGGATTACCTGCACAACGTGGTTTTTGTCCCCAGGCCATCCCGAAAG\n+CGAAGATCCCTTGAAGAGGTGGGGAATGTGACAGCCACCACACTCACACT\n+TCCAGATTTCCCCAACGTCTCCTCTACCATTGTGCCCACAAGTCAGGAGG\n+AGCACAGGCCATTTGAGAAAGTGGTGAACAAGGAGTCACTTGTCATCTCT\n+GGCCTGAGACACTTCACTGGGTACCGCATTGAGCTGCAGGCATGCAATCA\n+AGATTCCCCAGATGAGAGGTGCAGTGTGGCTGCCTACGTCAGTGCCCGGA\n+CCATGCCTGAAGCTAAGGCAGATGACATCGTTGGCCCTGTGACTCATGAA\n+ATCTTTGAGAACAATGTTGTACACTTAATGTGGCAAGAGCCAAAGGAACC\n+TAATGGTCTGATTGTGCTATATGAAGTGAGCTATCGCCGATATGGTGATG\n+AGGAGCTGCACCTCTGTGTCTCCCGGAAGCATTTTGCCCTGGAGCGGGGC\n+TGCAGGCTGCGAGGGCTCTCCCCAGGAAACTACAGTGTTCGAGTCCGGGC\n+TACCTCTCTGGCAGGAAATGGCTCCTGGACAGAACCCACCTATTTTTATG\n+TGACTGATTATTTAGATGTCCCATCAAATATTGCCAAAATTATCATTGGA\n+CCCCTCATCTTTGTCTTCCTCTTCAGTGTTGTGATTGGAAGTATTTATCT\n+ATTTCTGAGAAAGAGGCAGCCGGATGGGCCAATGGGACCACTGTATGCAT\n+CTTCAAACCCTGAGTACCTCAGTGCCAGTGATGTGTTTCCATCTTCTGTG\n+TACGTGCCGGACGAGTGGGAGGTGCCTCGAGAGAAGATCACCCTTCTTCG\n+AGAGCTGGGGCAGGGATCCTTTGGTATGGTGTATGAAGGCAATGCCAAGG\n+ATATCATCAAGGGTGAGGCAGAGACCCGTGTTGCGGTTAAGACTGTCAAT\n+GAGTCAGCCAGTCTTCGAGAACGGATCGAGTTCCTCAATGAGGCATCAGT\n+CATGAAGGGATTCACCTGCCATCATGTGGTCCGCCTTCTTGGGGTGGTAT\n+CCAAAGGACAGCCAACGCTGGTAGTGATGGAATTGATGGCTCATGGAGAC\n+CTGAAAAGTCACCTCCGTTCTCTGAGGCCAGATGCTGAGAATAACCCAGG\n+CCGCCCTCCCCCTACCTTGCAAGAAATGATTCAGATGACAGCAGAAATTG\n+CTGATGGCATGGCATACTTGAACGCCAAGAAGTTTGTGCACCGGGACCTG\n+GCAGCTCGAAACTGCATGGTTGCCCATGATTTTACTGTCAAAATTGGAGA\n+CTTTGGAATGACAAGGGACATCTACGAGACAGATTACTATCGGAAAGGGG\n+GCAAGGGACTGCTTCCTGTGAGGTGGATGTCACCTGAGTCCCTGAAGGAT\n+GGAGTCTTTACTGCTTCTTCTGATATGTGGTCCTTTGGGGTGGTCCTTTG\n+GGAAATCACTAGCCTGGCTGAGCAACCTTATCAAGGCCTGTCTAATGAAC\n+AGGTGTTGAAGTTTGTCATGGATGGAGGCTATCTGGATCCCCCTGATAAC\n+TGTCCAGAGAGACTCACTGACCTGATGCGCATGTGCTGGCAG'..b'TTGCTGCTGTTCCGAGTGGCTGGCCTCGAGAGCCTCGGAGACCTCTTC\n+CCCAACCTCACGGTCATCCGCGGCTGGAAACTCTTCTACAACTACGCCCT\n+GGTCATCTTCGAGATGACCAATCTCAAGGATATTGGGCTTTACAACCTGA\n+GGAACATTACTCGGGGGGCCATCAGGATTGAGAAAAATGCTGACCTCTGT\n+TACCTCTCCACTGTGGACTGGTCCCTGATCCTGGATGCGGTGTCCAATAA\n+CTACATTGTGGGGAATAAGCCCCCAAAGGAATGTGGGGACCTGTGTCCAG\n+GGACCATGGAGGAGAAGCCGATGTGTGAGAAGACCACCATCAACAATGAG\n+TACAACTACCGCTGCTGGACCACAAACCGCTGCCAGAAAATGTGCCCGAG\n+CACGTGTGGGAAGCGGGCGTGCACCGAGAACAACGAGTGCTGCCACCCCG\n+AGTGCCTGGGCAGCTGCAGCGCGCCTGACAACGACACGGCCTGTGTAGCT\n+TGCCGCCACTACTACTATGCCGGTGTCTGTGTGCCTGCCTGCCCGCCCAA\n+CACCTACAGGTTTGAGGGCTGGCGCTGTGTGGACCGTGACTTCTGCGCCA\n+ACATCCTCAGCGCCGAGAGCAGCGACTCCGAGGGGTTTGTGATCCACGAC\n+GGCGAGTGCATGCAGGAGTGCCCCTCGGGCTTCATCCGCAACGGCAGCCA\n+GAGCATGTACTGCATCCCTTGTGAAGGTCCTTGCCCGAAGGTCTGTGAGG\n+AAGAAAAGAAAACAAAGACCATTGATTCTGTTACTTCTGCTCAGATGCTC\n+CAAGGATGCACCATCTTCAAGGGCAATTTGCTCATTAACATCCGACGGGG\n+GAATAACATTGCTTCAGAGCTGGAGAACTTCATGGGGCTCATCGAGGTGG\n+TGACGGGCTACGTGAAGATCCGCCATTCTCATGCCTTGGTCTCCTTGTCC\n+TTCCTAAAAAACCTTCGCCTCATCTTAGGAGAGGAGCAGCTAGAAGGGAA\n+TTACTCCTTCTACGTCCTCGACAACCAGAACTTGCAGCAACTATGGGACT\n+GGGACCACCGCAACCTGACCATCAAAGCAGGGAAAATGTACTTTGCTTTC\n+AATCCCAAATTATGTGTTTCCGAAATTTACCGCATGGAGGAAGTGACGGG\n+GACTAAAGGGCGCCAAAGCAAAGGGGACATAAACACCAGGAACAACGGGG\n+AGAGAGCCTCCTGTGAAAGTGACGTCCTGCATTTCACCTCCACCACCACG\n+TCGAAGAATCGCATCATCATAACCTGGCACCGGTACCGGCCCCCTGACTA\n+CAGGGATCTCATCAGCTTCACCGTTTACTACAAGGAAGCACCCTTTAAGA\n+ATGTCACGGAGTATGATGGGCAGGACGCCTGCGGCTCCAACAGCTGGAAC\n+ATGGTGGACGTGGACCTCCCGCCCAACAAGGACGTGGAGCCCGGCATCTT\n+ACTACATGGGCTGAAGCCCTGGACTCAGTACGCCGTTTACGTCAAGGCTG\n+TGACCCTCACCATGGTGGAGAATGACCATATCCGTGGGGCCAAGAGTGAG\n+ATCTTGTACATTCGCACCAATGCTTCAGTTCCTTCCATTCCCTTGGACGT\n+TCTTTCAGCATCGAACTCCTCTTCTCAGTTAATCGTGAAGTGGAACCCTC\n+CCTCTCTGCCCAACGGCAACCTGAGTTACTACATTGTGCGCTGGCAGCGG\n+CAGCCTCAGGACGGCTACCTTTACCGGCACAATTACTGCTCCAAAGACAA\n+AATCCCCATCAGGAAGTATGCCGACGGCACCATCGACATTGAGGAGGTCA\n+CAGAGAACCCCAAGACTGAGGTGTGTGGTGGGGAGAAAGGGCCTTGCTGC\n+GCCTGCCCCAAAACTGAAGCCGAGAAGCAGGCCGAGAAGGAGGAGGCTGA\n+ATACCGCAAAGTCTTTGAGAATTTCCTGCACAACTCCATCTTCGTGCCCA\n+GACCTGAAAGGAAGCGGAGAGATGTCATGCAAGTGGCCAACACCACCATG\n+TCCAGCCGAAGCAGGAACACCACGGCCGCAGACACCTACAACATCACCGA\n+CCCGGAAGAGCTGGAGACAGAGTACCCTTTCTTTGAGAGCAGAGTGGATA\n+ACAAGGAGAGAACTGTGATTTCTAACCTTCGGCCTTTCACATTGTACCGC\n+ATCGATATCCACAGCTGCAACCACGAGGCTGAGAAGCTGGGCTGCAGCGC\n+CTCCAACTTTGTCTTTGCAAGGACTATGCCCGCAGAAGGAGCAGATGACA\n+TTCCTGGGCCAGTGACCTGGGAGCCAAGGCCTGAAAACTCCATCTTTTTA\n+AAGTGGCCGGAACCTGAGAATCCCAATGGATTGATTCTAATGTATGAAAT\n+AAAATACGGATCACAAGTTGAGGATCAGCGAGAATGTGTGTCCAGACAGG\n+AATACAGGAAGTATGGAGGGGCCAAGCTAAACCGGCTAAACCCGGGGAAC\n+TACACAGCCCGGATTCAGGCCACATCTCTCTCTGGGAATGGGTCGTGGAC\n+AGATCCTGTGTTCTTCTATGTCCAGGCCAAAACAGGATATGAAAACTTCA\n+TCCATCTGATCATCGCTCTGCCCGTCGCTGTCCTGTTGATCGTGGGAGGG\n+TTGGTGATTATGCTGTACGTCTTCCATAGAAAGAGAAATAACAGCAGGCT\n+GGGGAATGGAGTGCTGTATGCCTCTGTGAACCCGGAGTACTTCAGCGCTG\n+CTGATGTGTACGTTCCCGATGAGTGGGAGGTGGCTCGGGAGAAGATCACC\n+ATGAGCCGGGAACTTGGGCAGGGGTCCTTTGGGATGGTCTATGAAGGAGT\n+TGCCAAGGGTGTGGTGAAAGATGAACCTGAAACCAGAGTGGCCATTAAAA\n+CAGTGAACGAGGCCGCAAGCATGCGTGAAAGGATTGAGTTTCTCAACGAA\n+GCTTCTGTGATGAAGGAGTTCAATTGTCACCATGTGGTGCGATTGCTGGG\n+TGTGGTGTCCCAAGGCCAGCCAACACTGGTCATCATGGAACTGATGACAC\n+GGGGCGATCTCAAAAGTTATCTCCGGTCTCTGAGGCCAGAAATGGAGAAT\n+AATCCAGTCCTAGCACCTCCAAGCCTGAGCAAGATGATTCAGATGGCCGG\n+AGAGATTGCAGACGGCATGGCATACCTCAACGCCAATAAGTTCGTCCACA\n+GAGACCTTGCTGCCCGGAATTGCATGGTAGCCGAAGATTTCACAGTCAAA\n+ATCGGAGATTTTGGTATGACGCGAGATATCTATGAGACAGACTATTACCG\n+GAAAGGAGGGAAAGGGCTGCTGCCCGTGCGCTGGATGTCTCCCGAGTCCC\n+TCAAGGATGGAGTCTTCACCACTTACTCGGACGTCTGGTCCTTCGGGGTC\n+GTCCTCTGGGAGATCGCCACACTGGCCGAGCAGCCCTACCAGGGCTTGTC\n+CAACGAGCAAGTCCTTCGCTTCGTCATGGAGGGCGGCCTTCTGGACAAGC\n+CAGACAACTGTCCCGACATGCTGTTTGAACTGATGCGCATGTGCTGGCAG\n+TATAACCCCAAGATGAGGCCTTCCTTCCTGGAGATCATCAGCAGCATCAA\n+AGAGGAGATGGAGCCTGGCTTCCGGGAGGTCTCCTTCTACTACAGCGAGG\n+AGAACAAGCTGCCCGAGCCGGAGGAGCTGGACCTGGAGCCAGAGAACATG\n+GAGAGCGTCCCCCTGGACCCCTCGGCCTCCCTGCCACTGCCCGACAGACA\n+CTCAGGACACAAGGCCGAGAACGGCCCCGGCCCTGGGGTGCTGGTCCTCC\n+GCGCCAGCTTCGACGAGAGACAGCCGTACGCACACATGAACGGGGGCCGC\n+AAGAACGAGCGGGCCTTGCCGCTGCCCCAGTCTTCGACCTGCTGA\n+*\n'
b
diff -r 0a189243186d -r ae69d14b6fbf test-data/output3.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output3.txt Thu Jan 14 12:14:52 2021 +0000
b
b'@@ -0,0 +1,585 @@\n+T-COFFEE, Version_13.45.0.4846264 (2020-10-15 17:52:11 - Revision 5becd5d - Build 620)\n+Cedric Notredame \n+CPU TIME:0 sec.\n+SCORE=891\n+*\n+ BAD AVG GOOD\n+*\n+ENSMUST00000091291_musmusculus        :  85\n+ENSCAFT00000026349_canisfamiliaris    :  85\n+ENSMUST00000005671_homosapiens        :  88\n+ENSRNOT00000019267_rattusnorvegicus   :  87\n+ENSPTRT00000013802_pantroglodytes     :  88\n+cons                                  :  89\n+\n+ENSMUST00000091291_musmusculus        99964-33222333333322333333332223-----33333211334444444444444\n+ENSCAFT00000026349_canisfamiliaris    88853122---2222222--222222322222-22223-2333--334444554544443\n+ENSMUST00000005671_homosapiens        99975-4433344443333333444444444333333434554--445555555554444\n+ENSRNOT00000019267_rattusnorvegicus   99975-4433344443333333333333333323333333443--344444454544444\n+ENSPTRT00000013802_pantroglodytes     99975-4433334433333333444444444333333434554--445555555444444\n+cons                                  998631322222222222222222333222222222232233300334444444443333\n+\n+\n+ENSMUST00000091291_musmusculus        3333222222221222222222222211121122223444555555--5554-5678899\n+ENSCAFT00000026349_canisfamiliaris    333322222222122222232222------------2233444444--5554-5677889\n+ENSMUST00000005671_homosapiens        433333333333-2222333333333---3-----3444455555544555545678899\n+ENSRNOT00000019267_rattusnorvegicus   433333333333-2222333433333---3-----3444445555544555545678899\n+ENSPTRT00000013802_pantroglodytes     433333333333-3333334444333---3-----3444455555544555545677999\n+cons                                  322222222221011112222222220002000002233344444433555434677899\n+\n+\n+ENSMUST00000091291_musmusculus        9999999999999998876-4444525888888888999999999999999999999999\n+ENSCAFT00000026349_canisfamiliaris    9999999999999888876444566-7999999999999999999999999889999999\n+ENSMUST00000005671_homosapiens        9999999999999999887555667-7899998899999999999999999999999999\n+ENSRNOT00000019267_rattusnorvegicus   9999999999999999887555667-7899998899999999999999999899999999\n+ENSPTRT00000013802_pantroglodytes     9999999999999999887555667-7899998899999999999999999899999999\n+cons                                  999999999999998887644455616899998889999999999999999899999999\n+\n+\n+ENSMUST00000091291_musmusculus        999999999999999999999999999898874444447999999999999999999999\n+ENSCAFT00000026349_canisfamiliaris    999999999999999999999999999888874444448999999999999999999999\n+ENSMUST00000005671_homosapiens        99999999999999999999999999889888------8899999999999999999999\n+ENSRNOT00000019267_rattusnorvegicus   99999999999999999999999999889888------8899999999999999999999\n+ENSPTRT00000013802_pantroglodytes     99999999999999999999999999889888------8899999999999999999999\n+cons                                  999999999999999999999999998888873222227899999999999999999999\n+\n+\n+ENSMUST00000091291_musmusculus        999999999999999999999999999999999999999999999999999999999999\n+ENSCAFT00000026349_canisfamiliaris    999999999999999888999999999999999999999999999999999999999999\n+ENSMUST00000005671_homosapiens        999999999999999999999999999999999999999999999999999999999999\n+ENSRNOT00000019267_rattusnorvegicus   999999999999999999999999999999999999999999999999999999999999\n+ENSPTRT00000013802_pantroglodytes     999999999999999999999999999999999999999999999999999999999999\n+cons                                  999999999999999998999999999999999999999999999999999999999999\n+\n+\n+ENSMUST00000091291_musmusculus        999999999999999999999999999999999999999999999999999999999999\n+ENSCAFT00000026349_canisfamiliaris    999999999999999999999999999999999999999999999999999999999999\n+ENSMUST00000005671_homosapiens        999999999999999999999999999999999999999999999999999999999999\n+ENSRNOT00000019267_rattusnorvegicus   999999999999999999999999999999999999999999999999999999999999\n+ENSPTRT00000013802_pantroglodytes     999999999999999999999999999999999999999999999999999999999999\n+cons                            '..b'6349_canisfamiliaris    999999999999999999999999999999999998887789999999999999999999\n+ENSMUST00000005671_homosapiens        999999999999999999999999999999999999988899999999999999999999\n+ENSRNOT00000019267_rattusnorvegicus   999999999999999999999999999999999999988899999999999999999999\n+ENSPTRT00000013802_pantroglodytes     999999999999999999999999999999999999988899999999999999999999\n+cons                                  999999999999999999999999999999999999988899999999999999999999\n+\n+\n+ENSMUST00000091291_musmusculus        999999999998878999999999999999999999887666666778899999999999\n+ENSCAFT00000026349_canisfamiliaris    999999999999889988999999999999999999877777677788899999999999\n+ENSMUST00000005671_homosapiens        999999999999889999999999999999999999987777777888999999999999\n+ENSRNOT00000019267_rattusnorvegicus   999999999999889999999999999999999999988777777888999999999999\n+ENSPTRT00000013802_pantroglodytes     999999999999889999999999999999999999987777777888999999999999\n+cons                                  999999999998888999999999999999999999887777777788999999999999\n+\n+\n+ENSMUST00000091291_musmusculus        9999998888877666666776767667676656666665----565------------4\n+ENSCAFT00000026349_canisfamiliaris    9999987666655-------------455555444443332222334------------3\n+ENSMUST00000005671_homosapiens        9999998888877666666666666667776666666555----565------------4\n+ENSRNOT00000019267_rattusnorvegicus   9999998888877666667666666667776667777666----5662222222222225\n+ENSPTRT00000013802_pantroglodytes     9999998888887666666776666677776656666555----666------------5\n+cons                                  999999878777656555666565566666555555544311113441111111001113\n+\n+\n+ENSMUST00000091291_musmusculus        44455566778876668776677666677788776443----------------333344\n+ENSCAFT00000026349_canisfamiliaris    444444443333-----------------35554333-------------3333444442\n+ENSMUST00000005671_homosapiens        445555666688767678666776766666776566544443322334434455555654\n+ENSRNOT00000019267_rattusnorvegicus   445556666788776688666766655666766566544333222334434455545554\n+ENSPTRT00000013802_pantroglodytes     55555676667877666566676565666677665544443---------3334555555\n+cons                                  444445555566666566655665555665665443322211111111112233333343\n+\n+\n+ENSMUST00000091291_musmusculus        4444444444442---233-233333344433443222---222333444----334444\n+ENSCAFT00000026349_canisfamiliaris    -----------2---------------23333334222-----2222------------2\n+ENSMUST00000005671_homosapiens        444454555565534444454343443455444444332222233334444454445544\n+ENSRNOT00000019267_rattusnorvegicus   44444455456543344444433333334533344333------3333332333445444\n+ENSPTRT00000013802_pantroglodytes     455455666554434444454454444455555544332223333344545655455544\n+cons                                  333333433342222223232222222233333332221111112223322233233332\n+\n+\n+ENSMUST00000091291_musmusculus        45444344566667777766-666655244566676655555678887766545667777\n+ENSCAFT00000026349_canisfamiliaris    233------------------444443-3---334433-33-46677655433-------\n+ENSMUST00000005671_homosapiens        454455666666666777675576655-54456676665556788988776656665567\n+ENSRNOT00000019267_rattusnorvegicus   444444555666666766564565555-44456666655555678887776656665567\n+ENSPTRT00000013802_pantroglodytes     444454656776667777765566665-44456676665555788888877656666756\n+cons                                  233333444555656666563455544133344555544445577887665545555556\n+\n+\n+ENSMUST00000091291_musmusculus        6876655544445656787544556654433333457998\n+ENSCAFT00000026349_canisfamiliaris    ----------3-----------33332--------36888\n+ENSMUST00000005671_homosapiens        7766555445556656897555556565554433467998\n+ENSRNOT00000019267_rattusnorvegicus   77656554455666578875555565545544---46887\n+ENSPTRT00000013802_pantroglodytes     6665655445567768997555556555554333467998\n+cons                                  6655544444445556786444444444433222346897\n+\n+\n+\n+\n+\n'