Merge pull request #4 from dingquanyu/multimer-dataloader

created Multimer dataloader and datamodule classes

tests/test_data/alignments/3zee_A/mgnify_hits.sto

+# STOCKHOLM 1.0
+
+#=GS MGYP000252309144/2-40  DE [subseq from] PL=10 UP=0 BIOMES=0000000010100
+#=GS MGYP000179780280/51-90 DE [subseq from] PL=10 UP=0 BIOMES=0000000011000
+#=GS MGYP000502978124/9-85  DE [subseq from] PL=11 UP=0 BIOMES=0100000000000
+#=GS MGYP000308361322/5-70  DE [subseq from] PL=01 UP=0 BIOMES=0110000000000
+#=GS MGYP000223778335/1-28  DE [subseq from] PL=01 UP=0 BIOMES=0000000011000
+#=GS MGYP000036718232/2-50  DE [subseq from] PL=00 UP=0 BIOMES=0110000000000
+#=GS MGYP000262059246/1-65  DE [subseq from] PL=10 UP=0 BIOMES=0110000000000
+#=GS MGYP000027820786/2-40  DE [subseq from] PL=00 UP=0 BIOMES=0110000000000
+#=GS MGYP000267758348/2-40  DE [subseq from] PL=00 UP=0 BIOMES=0110000000000
+#=GS MGYP000218021762/13-50 DE [subseq from] PL=01 UP=0 BIOMES=0000000011000
+#=GS MGYP000076495019/22-59 DE [subseq from] PL=01 UP=0 BIOMES=0101000000000
+
+query                          SEFKVTVCFGRTRVVVPCGDGRMKVFSLIQQAVTRYRKAVAKDPNYWIQVHRLEHGDGGILDLDDILCDVADDKDRLVAVFDEQ
+MGYP000252309144/2-40          ---KVTVCFGRTRVVVPCGDGHMKVFSLIQQAVTRYRKAIAK------------------------------------------
+MGYP000179780280/51-90         --MKVTVCFGRTRVVVPCGDGHMKVFSLIQQAVTRYRKAIAK------------------------------------------
+MGYP000502978124/9-85          -------LFNTVKIVVPCGDGEKTVRELTQLATIRYKKATGKPRLSWVSVHSLKAKEGGILDPDDRLVDVCDDREQLIAYYDEE
+MGYP000308361322/5-70          ------------------SDGELSVRELTQLATTRYKKATGKARLSWVSVHSLKAKEGGILDPDDRLVDVCDDREQLIAFYDEE
+MGYP000223778335/1-28          -------------------------------------------------MHRLEHGDGGILDLDDILCDVADDKDRV-------
+MGYP000036718232/2-50          ---KVTVCFDRVRVIVPCGDGDLLVKELTEKAVLRYKKATGKVSCEWIQESR--------------------------------
+MGYP000262059246/1-65          ------------------GDGDISVRELTNLATVRYKKAIGKPLGFYVSVLSLKSYEGGILDPDDCVADVCDDREQLQALFDD-
+MGYP000027820786/2-40          ---KVTVCFDSVRVIVPCGNGDLTVCELIERAVSRYRKATNK------------------------------------------
+MGYP000267758348/2-40          ---KVTVCFDAVRVIVPCGNGELTVTELIERAVSRYRKATNK------------------------------------------
+MGYP000218021762/13-50         --MKVTVCFGRTGIVVPCKEGQLRVGELTQQALQRYLKTR--------------------------------------------
+MGYP000076495019/22-59         --MKVTVCFGKTGIVVPCKEGQLRVRELTQQALQRYLKTR--------------------------------------------
+#=GC RF                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
+//

tests/test_data/alignments/4i6p_A/mgnify_hits.sto

+# STOCKHOLM 1.0
+
+#=GS MGYP000179780280/48-90 DE [subseq from] PL=10 UP=0 BIOMES=0000000011000
+#=GS MGYP000502978124/9-85  DE [subseq from] PL=11 UP=0 BIOMES=0100000000000
+#=GS MGYP000252309144/2-40  DE [subseq from] PL=10 UP=0 BIOMES=0000000010100
+#=GS MGYP000308361322/5-70  DE [subseq from] PL=01 UP=0 BIOMES=0110000000000
+#=GS MGYP000223778335/1-29  DE [subseq from] PL=01 UP=0 BIOMES=0000000011000
+#=GS MGYP000036718232/2-50  DE [subseq from] PL=00 UP=0 BIOMES=0110000000000
+#=GS MGYP000262059246/1-65  DE [subseq from] PL=10 UP=0 BIOMES=0110000000000
+#=GS MGYP000027820786/2-40  DE [subseq from] PL=00 UP=0 BIOMES=0110000000000
+#=GS MGYP000267758348/2-40  DE [subseq from] PL=00 UP=0 BIOMES=0110000000000
+#=GS MGYP000076495019/18-59 DE [subseq from] PL=01 UP=0 BIOMES=0101000000000
+#=GS MGYP000218021762/10-50 DE [subseq from] PL=01 UP=0 BIOMES=0000000011000
+
+query                          GPGSEFKVTVCFGRTRVVVPCGDGRMKVFSLIQQAVTRYRKAVAKDPNYWIQVHRLEHGDGGILDLDDILCDVADDKDRLVAVFDEQD
+MGYP000179780280/48-90         --GGGMKVTVCFGRTRVVVPCGDGHMKVFSLIQQAVTRYRKAIAK-------------------------------------------
+MGYP000502978124/9-85          ----------LFNTVKIVVPCGDGEKTVRELTQLATIRYKKATGKPRLSWVSVHSLKAKEGGILDPDDRLVDVCDDREQLIAYYDEE-
+MGYP000252309144/2-40          ------KVTVCFGRTRVVVPCGDGHMKVFSLIQQAVTRYRKAIAK-------------------------------------------
+MGYP000308361322/5-70          ---------------------SDGELSVRELTQLATTRYKKATGKARLSWVSVHSLKAKEGGILDPDDRLVDVCDDREQLIAFYDEE-
+MGYP000223778335/1-29          ----------------------------------------------------MHRLEHGDGGILDLDDILCDVADDKDRVS-------
+MGYP000036718232/2-50          ------KVTVCFDRVRVIVPCGDGDLLVKELTEKAVLRYKKATGKVSCEWIQESR---------------------------------
+MGYP000262059246/1-65          ---------------------GDGDISVRELTNLATVRYKKAIGKPLGFYVSVLSLKSYEGGILDPDDCVADVCDDREQLQALFDD--
+MGYP000027820786/2-40          ------KVTVCFDSVRVIVPCGNGDLTVCELIERAVSRYRKATNK-------------------------------------------
+MGYP000267758348/2-40          ------KVTVCFDAVRVIVPCGNGELTVTELIERAVSRYRKATNK-------------------------------------------
+MGYP000076495019/18-59         -PGARMKVTVCFGKTGIVVPCKEGQLRVRELTQQALQRYLKTR---------------------------------------------
+MGYP000218021762/10-50         --GGGMKVTVCFGRTGIVVPCKEGQLRVGELTQQALQRYLKTR---------------------------------------------
+#=GC RF                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
+//

tests/test_data/alignments/4i6p_B/mgnify_hits.sto

+# STOCKHOLM 1.0
+
+#=GS MGYP000179780280/48-90 DE [subseq from] PL=10 UP=0 BIOMES=0000000011000
+#=GS MGYP000502978124/9-85  DE [subseq from] PL=11 UP=0 BIOMES=0100000000000
+#=GS MGYP000252309144/2-40  DE [subseq from] PL=10 UP=0 BIOMES=0000000010100
+#=GS MGYP000308361322/5-70  DE [subseq from] PL=01 UP=0 BIOMES=0110000000000
+#=GS MGYP000223778335/1-29  DE [subseq from] PL=01 UP=0 BIOMES=0000000011000
+#=GS MGYP000036718232/2-50  DE [subseq from] PL=00 UP=0 BIOMES=0110000000000
+#=GS MGYP000262059246/1-65  DE [subseq from] PL=10 UP=0 BIOMES=0110000000000
+#=GS MGYP000027820786/2-40  DE [subseq from] PL=00 UP=0 BIOMES=0110000000000
+#=GS MGYP000267758348/2-40  DE [subseq from] PL=00 UP=0 BIOMES=0110000000000
+#=GS MGYP000076495019/18-59 DE [subseq from] PL=01 UP=0 BIOMES=0101000000000
+#=GS MGYP000218021762/10-50 DE [subseq from] PL=01 UP=0 BIOMES=0000000011000
+
+query                          GPGSEFKVTVCFGRTRVVVPCGDGRMKVFSLIQQAVTRYRKAVAKDPNYWIQVHRLEHGDGGILDLDDILCDVADDKDRLVAVFDEQD
+MGYP000179780280/48-90         --GGGMKVTVCFGRTRVVVPCGDGHMKVFSLIQQAVTRYRKAIAK-------------------------------------------
+MGYP000502978124/9-85          ----------LFNTVKIVVPCGDGEKTVRELTQLATIRYKKATGKPRLSWVSVHSLKAKEGGILDPDDRLVDVCDDREQLIAYYDEE-
+MGYP000252309144/2-40          ------KVTVCFGRTRVVVPCGDGHMKVFSLIQQAVTRYRKAIAK-------------------------------------------
+MGYP000308361322/5-70          ---------------------SDGELSVRELTQLATTRYKKATGKARLSWVSVHSLKAKEGGILDPDDRLVDVCDDREQLIAFYDEE-
+MGYP000223778335/1-29          ----------------------------------------------------MHRLEHGDGGILDLDDILCDVADDKDRVS-------
+MGYP000036718232/2-50          ------KVTVCFDRVRVIVPCGDGDLLVKELTEKAVLRYKKATGKVSCEWIQESR---------------------------------
+MGYP000262059246/1-65          ---------------------GDGDISVRELTNLATVRYKKAIGKPLGFYVSVLSLKSYEGGILDPDDCVADVCDDREQLQALFDD--
+MGYP000027820786/2-40          ------KVTVCFDSVRVIVPCGNGDLTVCELIERAVSRYRKATNK-------------------------------------------
+MGYP000267758348/2-40          ------KVTVCFDAVRVIVPCGNGELTVTELIERAVSRYRKATNK-------------------------------------------
+MGYP000076495019/18-59         -PGARMKVTVCFGKTGIVVPCKEGQLRVRELTQQALQRYLKTR---------------------------------------------
+MGYP000218021762/10-50         --GGGMKVTVCFGRTGIVVPCKEGQLRVGELTQQALQRYLKTR---------------------------------------------
+#=GC RF                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
+//

tests/test_data/alignments/4zey_A/mgnify_hits.sto

+# STOCKHOLM 1.0
+
+#=GS MGYP000613015979/54-136  DE [subseq from] PL=11 UP=0 BIOMES=0000000011000
+#=GS MGYP000745946800/68-150  DE [subseq from] PL=00 UP=0 BIOMES=0000000011000
+#=GS MGYP000356782790/16-98   DE [subseq from] PL=01 UP=0 BIOMES=1000000000000
+#=GS MGYP000326981611/4-86    DE [subseq from] PL=00 UP=0 BIOMES=0000000011000
+#=GS MGYP000365627167/36-118  DE [subseq from] PL=01 UP=0 BIOMES=1000000000000
+#=GS MGYP000438079158/46-95   DE [subseq from] PL=10 UP=0 BIOMES=0000000010100
+#=GS MGYP000660499351/22-69   DE [subseq from] PL=00 UP=0 BIOMES=1000000000000
+#=GS MGYP000054740637/2-48    DE [subseq from] PL=00 UP=0 BIOMES=0000000010100
+#=GS MGYP000111717601/1-42    DE [subseq from] PL=00 UP=0 BIOMES=0000000011000
+#=GS MGYP000888755554/1-42    DE [subseq from] PL=00 UP=0 BIOMES=0000000011000
+#=GS MGYP000294730968/1-42    DE [subseq from] PL=00 UP=0 BIOMES=0000000010100
+#=GS MGYP001120896613/151-179 DE [subseq from] PL=01 UP=0 BIOMES=0101000000000
+#=GS MGYP000492638681/47-75   DE [subseq from] PL=00 UP=0 BIOMES=0000000000001
+#=GS MGYP000299282490/51-75   DE [subseq from] PL=00 UP=0 BIOMES=0000101000000
+#=GS MGYP001099220598/40-68   DE [subseq from] PL=01 UP=0 BIOMES=0101000000000
+#=GS MGYP001057540932/31-51   DE [subseq from] PL=11 UP=0 BIOMES=0110000000000
+
+query                            GMEGPLNLAHQQSRRADRLLAAGKYEEAISCHKKAAAYLSEAMKLTQSEQAHLSLELQRDSHMKQLLLIQERWKRAQREERLKA
+MGYP000613015979/54-136          -MEGPLNLAHQQSRRADRLLAAGKYEEAISCHKKAAAYLSEAMKLTQSEQAHLSLELQRDSHMKQLLLIQERWKRAQREERLKA
+MGYP000745946800/68-150          -MEGPLNLAHQQSRRADRLLAAGKYEEAISCHKKAAAYLSEAMKLTQSEQARLSLELQRDSHMKQLLLIQERWKRAQREERLKA
+MGYP000356782790/16-98           -MEGPLNLAHQQSRRADRLLAAGKYEEAISCHKKAAAYLSEAMKLTQSEQAHLSLELQRDSHMKQLLLIQERWKRAQGEARLKA
+MGYP000326981611/4-86            -MEGPLNLAHQQSRRADRLLAAGKYEEAISCHKKAAAYLSEAMKLTQSEQARLSLELQRDSHMKQLLLIQERWKRPQHEERLKA
+MGYP000365627167/36-118          -MEGPLNLAHQQSRRADRLLAAGKYEEAISCHKKAAVYLSEAMKLTQSKQAHLSLELQRDSHMKQLLLIQERWKRAQGEARLKA
+MGYP000438079158/46-95           -MEGPLNLAHQQSRRADHLLAAGKYEEAISCHKKAAVYLSEAMKLTQSEQV---------------------------------
+MGYP000660499351/22-69           --NGSLNLAHQQSRRADRLLAAGKYEEAISCHKKAAAYLYEAMKLTQSEQ----------------------------------
+MGYP000054740637/2-48            -------------------------------------YLSEAMKLTQSKQAHLSLELQRDSHMKQLLLIQERWKRAQGEARLKA
+MGYP000111717601/1-42            ------------------------------------------MKLTQSEQAHLSLELQRDSHMKQLLLIQERWKRAQREERLKA
+MGYP000888755554/1-42            ------------------------------------------MKLTQSEQARLSLELQRDSHMKQLLLIQERWKRAQREERLKA
+MGYP000294730968/1-42            ------------------------------------------MKLTQSKQAHLSLELQRDSHMKQLLLIQERWKRPQHEERLKA
+MGYP001120896613/151-179         -------AAHVWNSKGDALANLGKYEEAIECYDKAI------------------------------------------------
+MGYP000492638681/47-75           -------NAKFYSRLAATLSALEKYEEAIDCYQKAI------------------------------------------------
+MGYP000299282490/51-75           -----------LNKKGDNLSRLGKFEEAIECYDKAI------------------------------------------------
+MGYP001099220598/40-68           -------AAHVWNSKGDALANLGKYEEAIECYDKAI------------------------------------------------
+MGYP001057540932/31-51           -----------------ILQALGKYEEAIACYDKVIAF----------------------------------------------
+#=GC RF                          xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
+//