Stabilize clade assignment

For each clade, include the earliest 3 samples within that clade that are at
least 5000 bp long. Hopefully, this should be enough to stabilize the clade
assignment.

Snakefile

@@ -107,7 +107,8 @@ rule filter:
     input:
         sequences = "data/sequences_{serotype}.fasta",
         metadata = "results/wrangled_metadata_{serotype}.tsv",
-        exclude = files.dropped_strains
+        exclude = files.dropped_strains,
+        include_strains = "config/include_{serotype}.txt"
     output:
         sequences = "results/filtered_{serotype}.fasta"
     params:
@@ -120,6 +121,7 @@ rule filter:
             --sequences {input.sequences} \
             --metadata {input.metadata} \
             --exclude {input.exclude} \
+            --include {input.include_strains} \
             --output {output.sequences} \
             --group-by {params.group_by} \
             --sequences-per-group {params.sequences_per_group} \

config/include_all.txt

@@ -0,0 +1,54 @@
+OR389282 # 1944-XX-XX DENV1/I
+OR389293 # 1964-XX-XX DENV1/I
+AY732483 # 1981-XX-XX DENV1/I
+KM204119 # 1944-XX-XX DENV1/II
+OR389281 # 1944-XX-XX DENV1/II
+EU848545 # 1944-XX-XX DENV1/II
+KF289073 # 1956-XX-XX DENV1/III
+AY732474 # 1980-XX-XX DENV1/III
+AY732476 # 1980-XX-XX DENV1/III
+MW945952 # 1974-XX-XX DENV1/IV
+OK469344 # 1975-XX-XX DENV1/IV
+OK605753 # 1983-XX-XX DENV1/IV
+JQ922544 # 1963-XX-XX DENV1/V
+OR389283 # 1963-XX-XX DENV1/V
+OR389284 # 1970-XX-XX DENV1/V
+OK469346 # 1981-XX-XX DENV2/AA
+KF955363 # 1986-XX-XX DENV2/AA
+EU482568 # 1986-XX-XX DENV2/AA
+NC_001474 # 1964-XX-XX DENV2/AI
+GQ868591 # 1964-XX-XX DENV2/AI
+AJ487271 # 1974-XX-XX DENV2/AI
+KM204118 # 1944-XX-XX DENV2/AII
+MW945433 # 1944-XX-XX DENV2/AII
+EU854293 # 1944-XX-XX DENV2/AII
+JX966380 # 1969-XX-XX DENV2/AM
+GQ868600 # 1969-XX-XX DENV2/AM
+HM582099 # 1971-XX-XX DENV2/AM
+OR389318 # 1969-XX-XX DENV2/C
+MW946478 # 1974-XX-XX DENV2/C
+GQ398258 # 1975-XX-XX DENV2/C
+OR389309 # 1959-XX-XX DENV2/S
+JQ922552 # 1960-XX-XX DENV2/S
+OR389310 # 1963-XX-XX DENV2/S
+OM258630 # 1953-XX-XX DENV3/I
+MW945427 # 1963-XX-XX DENV3/I
+MW946955 # 1978-XX-XX DENV3/I
+OK469355 # 1973-XX-XX DENV3/II
+DQ863638 # 1973-XX-XX DENV3/II
+GQ868593 # 1973-XX-XX DENV3/II
+JQ922555 # 1966-XX-XX DENV3/III
+OR389336 # 1966-XX-XX DENV3/III
+OR389337 # 1970-XX-XX DENV3/III
+KU050695 # 1956-XX-XX DENV3/IV
+JQ922554 # 1963-XX-XX DENV3/IV
+KM190937 # 1964-XX-XX DENV3/IV
+KR011349 # 1956-08-28 DENV4/I
+GQ868594 # 1956-XX-XX DENV4/I
+OR389348 # 1961-XX-XX DENV4/I
+KF907503 # 1953-XX-XX DENV4/II
+OR389347 # 1961-XX-XX DENV4/II
+MW945636 # 1973-XX-XX DENV4/II
+MW945552 # 1973-XX-XX DENV4/S
+OR389042 # 1973-XX-XX DENV4/S
+JF262780 # 1973-XX-XX DENV4/S

config/include_denv1.txt

@@ -0,0 +1,15 @@
+OR389282 # 1944-XX-XX DENV1/I
+OR389293 # 1964-XX-XX DENV1/I
+AY732483 # 1981-XX-XX DENV1/I
+KM204119 # 1944-XX-XX DENV1/II
+OR389281 # 1944-XX-XX DENV1/II
+EU848545 # 1944-XX-XX DENV1/II
+KF289073 # 1956-XX-XX DENV1/III
+AY732474 # 1980-XX-XX DENV1/III
+AY732476 # 1980-XX-XX DENV1/III
+MW945952 # 1974-XX-XX DENV1/IV
+OK469344 # 1975-XX-XX DENV1/IV
+OK605753 # 1983-XX-XX DENV1/IV
+JQ922544 # 1963-XX-XX DENV1/V
+OR389283 # 1963-XX-XX DENV1/V
+OR389284 # 1970-XX-XX DENV1/V

config/include_denv2.txt

@@ -0,0 +1,18 @@
+OK469346 # 1981-XX-XX DENV2/AA
+KF955363 # 1986-XX-XX DENV2/AA
+EU482568 # 1986-XX-XX DENV2/AA
+NC_001474 # 1964-XX-XX DENV2/AI
+GQ868591 # 1964-XX-XX DENV2/AI
+AJ487271 # 1974-XX-XX DENV2/AI
+KM204118 # 1944-XX-XX DENV2/AII
+MW945433 # 1944-XX-XX DENV2/AII
+EU854293 # 1944-XX-XX DENV2/AII
+JX966380 # 1969-XX-XX DENV2/AM
+GQ868600 # 1969-XX-XX DENV2/AM
+HM582099 # 1971-XX-XX DENV2/AM
+OR389318 # 1969-XX-XX DENV2/C
+MW946478 # 1974-XX-XX DENV2/C
+GQ398258 # 1975-XX-XX DENV2/C
+OR389309 # 1959-XX-XX DENV2/S
+JQ922552 # 1960-XX-XX DENV2/S
+OR389310 # 1963-XX-XX DENV2/S

config/include_denv3.txt

@@ -0,0 +1,12 @@
+OM258630 # 1953-XX-XX DENV3/I
+MW945427 # 1963-XX-XX DENV3/I
+MW946955 # 1978-XX-XX DENV3/I
+OK469355 # 1973-XX-XX DENV3/II
+DQ863638 # 1973-XX-XX DENV3/II
+GQ868593 # 1973-XX-XX DENV3/II
+JQ922555 # 1966-XX-XX DENV3/III
+OR389336 # 1966-XX-XX DENV3/III
+OR389337 # 1970-XX-XX DENV3/III
+KU050695 # 1956-XX-XX DENV3/IV
+JQ922554 # 1963-XX-XX DENV3/IV
+KM190937 # 1964-XX-XX DENV3/IV

config/include_denv4.txt

@@ -0,0 +1,9 @@
+KR011349 # 1956-08-28 DENV4/I
+GQ868594 # 1956-XX-XX DENV4/I
+OR389348 # 1961-XX-XX DENV4/I
+KF907503 # 1953-XX-XX DENV4/II
+OR389347 # 1961-XX-XX DENV4/II
+MW945636 # 1973-XX-XX DENV4/II
+MW945552 # 1973-XX-XX DENV4/S
+OR389042 # 1973-XX-XX DENV4/S
+JF262780 # 1973-XX-XX DENV4/S