Merge pull request #6 from cobeylab/multi-way

Multi way

README.md

@@ -86,19 +86,19 @@ With your configuration file set up to your liking, run the container with the f
 
 
 ```
-docker run -v ${flu_strain_compare_path}:/app flu_strain_compare python3 src/<SCRIPT NAME>.py
+docker run -v ${flu_strain_compare_path}:/app flu_strain_compare python3 src/<SCRIPT NAME>.py configuration/config.json
 ```
 
 ### Singularity
 
 ```
-singularity exec --bind ${flu_strain_compare_path}:/app ubuntu-pymol-biopython_latest.sif python3 src/<SCRIPT NAME>.py
+singularity exec --bind ${flu_strain_compare_path}:/app ubuntu-pymol-biopython_latest.sif python3 src/<SCRIPT NAME>.py configuration/config.json
 ```
 
 ### Native
 
 ```
-python src/<SCRIPT NAME>.py
+python src/<SCRIPT NAME>.py configuration/config.json
 ```
 
 `<SCRIPT NAME>` should either be `make_comparison_figure` or `make_movie`
@@ -108,7 +108,7 @@ Example:
 
 ```
 # from repo root
-singularity exec --bind /home/youruser/flu_strain_compare:/app ubuntu_pymol_biopython.sif python3 src/make_movie.py
+singularity exec --bind /home/youruser/flu_strain_compare:/app ubuntu_pymol_biopython.sif python3 src/make_movie.py configuration/config.json
 ```
 
 ## Outputs

configuration/config.json

@@ -1,8 +1,9 @@
 {
         "seq_file": "sample_input/H3_cell_vaccines.fasta",
-        "q1_id": "EPI1752480",
-        "q2_id": "EPI1928379",
+        "reference_id": "A/Cambodia/e0826360/2020",
+        "comparison_ids": ["A/Michigan/15/2021", "A/Victoria/361/2011", "A/Minnesota/41/2019", "A/Darwin/6/2021"],
         "seq_lineage": "H3",
         "numbering_scheme": "H3",
-        "output_dir": "figures"
+        "output_dir": "figures",
+        "reference_mode": false
 }

sample_input/H3_cell_vaccines.fasta

@@ -1,4 +1,4 @@
->EPI1885402 | A/Darwin/6/2021 | 2021-03-16 | HA | S2 | A / H3N2 | EPI_ISL_3534319
+>A/Darwin/6/2021 | 2021-03-16 | HA | S2 | A / H3N2 | EPI_ISL_3534319
 MKTIIALSNILCLVFAQKIPGNDNSTATLCLGHHAVPNGTIVKTITNDRIEVTNATELVQNSSIGEICGSPHQILDGGNC
 TLIDALLGDPQCDGFQNKEWDLFVERSRANSNCYPYDVPDYASLRSLVASSGTLEFKNESFNWTGVKQNGTSSACIRGSS
 SSFFSRLNWLTSLNNIYPAQNVTMPNKEQFDKLYIWGVHHPDTDKNQISLFAQSSGRITVSTKRSQQAVIPNIGSRPRIR
@@ -7,7 +7,7 @@ CPRYVKQSTLKLATGMRNVPEKQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEGRGQAADLKSTQAAIDQINGKLNRL
 IGKTNEKFHQIEKEFSEVEGRVQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTKKQLRENAEDMGN
 GCFKIYHKCDNACIGSIRNETYDHNVYRDEALNNRFQIKGVELKSGYKDWILWISFAMSCFLLCIALLGFIMWACQKGNI
 RCNICI
->EPI1752480 | A/Tasmania/503/2020 | 2020-02-16 | HA | SIAT1 | A / H3N2 | EPI_ISL_483574
+>A/Tasmania/503/2020 | 2020-02-16 | HA | SIAT1 | A / H3N2 | EPI_ISL_483574
 MKTIIALSYILCLVFAQKIPGNDNSTATLCLGHHAVPNGTIVKTITNDRIEVTNATELVQNSSIGEICDSPHQILDGGNC
 TLIDALLGDPQCDGFQNKEWDLFVERSRANSNCYPYDVPDYASLRSLVASSGTLEFKNESFNWTGVKQNGTSSACIRGSS
 SSFFSRLNWLTHLNYTYPALNVTMPNKEQFDKLYIWGVHHPSTDKDQISLFAQPSGRITVSTKRSQQAVIPNIGSRPRIR
@@ -16,7 +16,7 @@ CPRYVKQSTLKLATGMRNVPEKQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEGRGQAADLKSTQAAIDQINGKLNRL
 IGKTNEKFHQIEKEFSEVEGRVQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTKKQLRENAEDMGN
 GCFKIYHKCDNACIGSIRNETYDHNVYRDEALNNRFQIKGVELKSGYKDWILWISFAMSCFLLCIALLGFIMWACQKGNI
 RCNICI
->EPI1843589 | A/Cambodia/e0826360/2020 | 2020-07-16 | HA | SIAT2 | A / H3N2 | EPI_ISL_944639
+>A/Cambodia/e0826360/2020 | 2020-07-16 | HA | SIAT2 | A / H3N2 | EPI_ISL_944639
 MKTIIALSYILCLVFAQKIPGNDNSTATLCLGHHAVPNGTIVKTITNDRIEVTNATELVQNSSIGEICDSPHQILDGGNC
 TLIDALLGDPQCDGFQNKEWDLFVERSRANSNCYPYDVPDYASLRSLVASSGTLEFKNESFNWTGVKQNGTSSACIRGSS
 SSFFSRLNWLTHLNYTYPALNVTMPNNEQFDKLYIWGVHHPSTDKDQISLFAQPSGRITVSTKRSQQAVIPNIGSRPRIR
@@ -25,7 +25,7 @@ CPRYVKQSTLKLATGMRNVPEKQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEGRGQAADLKSTQAAIDQINGKLNRL
 IGKTNEKFHQIEKEFSEVEGRVQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTKKQLRENAEDMGN
 GCFKIYHKCDNACIGSIRNETYDHNVYRDEALNNRFQIKGVELKSGYKDWILWISFAMSCFLLCIALLGFIMWACQKGNI
 RCNICI
->EPI1548699 | A/Minnesota/41/2019 | 2019-05-25 | HA | S1 | A / H3N2 | EPI_ISL_378110
+>A/Minnesota/41/2019 | 2019-05-25 | HA | S1 | A / H3N2 | EPI_ISL_378110
 MKTIIALSYILCLVFTQKIPGNDNSTATLCLGHHAVPNGTIVKTITNDRIEVTNATELVQNSSIGEICDSPHQILDGGNC
 TLIDALLGDPQCDGFQNKKWDLFVERSRAYSNCYPYDVPDYASLRSLVASSGTLEFKNESFNWAGVTQNGKSFSCIRGSS
 SSFFSRLNWLTHLNYTYPALNVTMPNKEQFDKLYIWGVHHPGTDKDQISLYAQSSGRITVSTKRSQQAVIPNIGSRPRIR
@@ -34,7 +34,7 @@ CPRYVKQSTLKLATGMRNVPEKQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEGRGQAADLKSTQAAIDQINGKLNRL
 IGKTNEKFHQIEKEFSEVEGRVQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTKKQLRENAEDMGN
 GCFKIYHKCDNACIGSIRNETYDHNVYRDEALNNRFQIKGVELKSGYKDWILWISFAISCFLLCVALLGFIMWACQKGNI
 RCNICI
->EPI1409001 | A/Hong Kong/45/2019 | 2018-12-24 | HA | S2 | A / H3N2 | EPI_ISL_349926
+>A/Hong Kong/45/2019 | 2018-12-24 | HA | S2 | A / H3N2 | EPI_ISL_349926
 MKTIIALSYILCLGFTQKIPGNDNSTATLCLGHHAVPNGTIVKTITNDRIEVTNATELVQNSSIGEICDSPHQILDGGNC
 TLIDALLGDPQCDGFQNKKWDLFVERSRAYSNCYPYDVPDYASLRSLVASSGTLEFKNESFNWAGVTQNGKSFSCIRGSS
 SSFFSRLNWLTHLNYTYPALNVTMPNKEQFDKLYIWGVHHPGTDKDQISLYAQSSGRITVSTKRSQQAVIPNIGSRPRIR
@@ -43,7 +43,7 @@ CPRYVKQNTLKLATGMRNVPEKQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEGRGQAADLKSTQAAIDQINGKLNRL
 IGKTNEKFHQIEKEFSEVEGRVQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTKKQLRENAEDMGN
 GCFKIYHKCDNACIGSIRNETYDHNVYRDEALNNRFQIKGVELKSGYKDWILWISFAISCFLLCVALLGFIMWACQKGNI
 RCNICI
->EPI1174043 | A/Kansas/14/2017 | 2017-12-14 | HA | S1 | A / H3N2 | EPI_ISL_298310
+>A/Kansas/14/2017 | 2017-12-14 | HA | S1 | A / H3N2 | EPI_ISL_298310
 MKTIIALSCILCLVFAQKIPGNDNSTATLCLGHHAVPNGTIVKTITNDRIEVTNATELVQNSSIGEICDSPHQILDGENC
 TLIDALLGDPQCDGFQNKKWDLFVERNKAYSNCYPYDVPDYASLRSLVASSGTLEFNNESFNWAGVTQNGTSSSCIRGSK
 SSFFSRLNWLTHLNSKYPALNVTMPNNEQFDKLYIWGVHHPGTDKDQISLYAQSSGRITVSTKRSQQAVIPNIGSRPRIR
@@ -52,7 +52,7 @@ CPRYVKQSTLKLATGMRNVPERQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEGRGQAADLKSTQAAIDQINGKLNRL
 IGKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTKKQLRENAEDMGN
 GCFKIYHKCDNACMGSIRNGTYDHNVYRDEALNNRFQIKGVELKSGYKDWILWISFAISCFLLCVALLGFIMWACQKGNI
 RCNICI
->EPI1106235 | A/Singapore/INFIMH-16-0019/2016 | 2016-06-14 | HA | C1S3 | A / H3N2 | EPI_ISL_285898
+>A/Singapore/INFIMH-16-0019/2016 | 2016-06-14 | HA | C1S3 | A / H3N2 | EPI_ISL_285898
 MKTIIALSYILCLVFAQKIPGNDNSTATLCLGHHAVPNGTIVKTITNDRIEVTNATELVQNSSIGEICDSPHQILDGENC
 TLIDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEFKNESFNWTGVTQNGTSSACIRGSS
 SSFFSRLNWLTHLNYTYPALNVTMPNKEQFDKLYIWGVHHPGTDKDQIFLYAQSSGRITVSTKRSQQAVIPNIGSRPRIR
@@ -61,7 +61,7 @@ CPRYVKHSTLKLATGMRNVPEKQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEGRGQAADLKSTQAAIDQINGKLNRL
 IGKTNEKFHQIEKEFSEVEGRVQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTKKQLRENAEDMGN
 GCFKIYHKCDNACIESIRNETYDHNVYRDEALNNRFQIKGVELKSGYKDWILWISFAISCFLLCVALLGFIMWACQKGNI
 RCNICI
->EPI539576 | A/Hong Kong/4801/2014 | 2014-02-26 | HA | SIAT1 | A / H3N2 | EPI_ISL_165554
+>A/Hong Kong/4801/2014 | 2014-02-26 | HA | SIAT1 | A / H3N2 | EPI_ISL_165554
 MKTIIALSYILCLVFAQKIPGNDNSTATLCLGHHAVPNGTIVKTITNDRIEVTNATELVQNSSIGEICDSPHQILDGENC
 TLIDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEFNNESFNWTGVTQNGTSSACIRRSS
 SSFFSRLNWLTHLNYTYPALNVTMPNNEQFDKLYIWGVHHPGTDKDQIFLYAQSSGRITVSTKRSQQAVIPNIGSRPRIR
@@ -70,7 +70,7 @@ CPRYVKHSTLKLATGMRNVPEKQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEGRGQAADLKSTQAAIDQINGKLNRL
 IGKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTKKQLRENAEDMGN
 GCFKIYHKCDNACIGSIRNGTYDHNVYRDEALNNRFQIKGVELKSGYKDWILWISFAISCFLLCVALLGFIMWACQKGNI
 RCNICI
->EPI530687 | A/Switzerland/9715293/2013 | 2013-12-06 | HA | SIAT2 | A / H3N2 | EPI_ISL_162149
+>A/Switzerland/9715293/2013 | 2013-12-06 | HA | SIAT2 | A / H3N2 | EPI_ISL_162149
 MKTIIALSYILCLVFAQKLPGNDNSTATLCLGHHAVPNGTIVKTITNDRIEVTNATELVQNSSIGEICDSPHQILDGENC
 TLIDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEFNNESFNWAGVTQNGTSSSCIRGSN
 SSFFSRLNWLTHLNSKYPALNVTMPNNEQFDKLYIWGVHHPGTDKDQIFLYAQSSGRITVSTKRSQQAVIPNIGSRPRIR
@@ -79,7 +79,7 @@ CPRYVKQSTLKLATGMRNVPERQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEGRGQAADLKSTQAAIDQINGKLNRL
 IGKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTKKQLRENAEDMGN
 GCFKIYHKCDNACIGSIRNGTYDHDVYRDEALNNRFQIKGVELKSGYKDWILWISFAISCFLLCVALLGFIMWACQKGNI
 RCNICI
->EPI349103 | A/Victoria/361/2011 | 2011-10-24 | HA | MDCK1 | A / H3N2 | EPI_ISL_101506
+>A/Victoria/361/2011 | 2011-10-24 | HA | MDCK1 | A / H3N2 | EPI_ISL_101506
 MKTIIALSHILCLVFAQKLPGNDNSTATLCLGHHAVPNGTIVKTITNDQIEVTNATELVQNSSIGEICDSPHQILDGENC
 TLIDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEFNNESFNWTGVTQNGTSSACIRRSN
 NSFFSRLNWLTHLNFKYPALNVTMPNNEQFDKLYIWGVHHPGTDKDQIFLYAQSSGRITVSTKRSQQAVIPNIGSRPRIR
@@ -88,7 +88,7 @@ CPRYVKQSTLKLATGMRNVPEKQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEGRGQAADLKSTQAAIDQINGKLNRL
 IGKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTKKQLRENAEDMGN
 GCFKIYHKCDNACIGSIRNGTYDHDVYRDEALNNRFQIKGVELKSGYKDWILWISFAISCFLLCVALLGFIMWACQKGNI
 RCNICI
->EPI1928379 | A/Michigan/15/2021 | 2021-10-28 | HA | S1 | A / H3N2 | EPI_ISL_6600759
+>A/Michigan/15/2021 | 2021-10-28 | HA | S1 | A / H3N2 | EPI_ISL_6600759
 MKTIIALSNILCLVFAQKIPGNDNSTATLCLGHHAVPNGTIVKTITNDRIEVTNATELVQNSSIGEICGSPHQILDGGNC
 TLIDALLGDPQCDGFQNKEWDLFVERSRANSNCYPYDVPGYASLRSLVASSGTLEFKNESFNWTGVKQNGTSSACIRGSS
 SSFFSRLNWLTSINNIYPAQNVTMPNKEQFDKLYIWGVHHPDTDKNQISLFAQSSGRITVSTKRSQQAVIPNIGSRPRIR