removed unused alignment files

e2193f77 · Geoffrey Yu · 08afe382 · 08afe382 · 08afe382 · 08afe382
Commit e2193f77 authored Aug 03, 2023 by Geoffrey Yu
20 changed files
--- a/tests/test_data/alignments/1hf9_A/bfd_uniclust_hits.a3m
+++ b/tests/test_data/alignments/1hf9_A/bfd_uniclust_hits.a3m
--- a/tests/test_data/alignments/1hf9_A/hmm_output.sto
+++ b/tests/test_data/alignments/1hf9_A/hmm_output.sto
--- a/tests/test_data/alignments/1hf9_A/mgnify_hits.sto
+++ b/tests/test_data/alignments/1hf9_A/mgnify_hits.sto
-# STOCKHOLM 1.0
-
-#=GS MGYP000184479417/51-87   DE [subseq from] PL=10 UP=0 BIOMES=0000000010100
-#=GS MGYP001032527956/9-36    DE [subseq from] PL=11 UP=0 BIOMES=0000000000001
-#=GS MGYP001032527956/100-127 DE [subseq from] PL=11 UP=0 BIOMES=0000000000001
-#=GS MGYP001032527956/130-155 DE [subseq from] PL=11 UP=0 BIOMES=0000000000001
-#=GS MGYP001032527956/177-204 DE [subseq from] PL=11 UP=0 BIOMES=0000000000001
-
-query                            ALKKHHENEISHHAKEIERLQKEIERHKQSIKKLKQSEDDD
-MGYP000184479417/51-87           ALKKHHEEEIVHHKKEIERLQKEIERHKQKIKMLKHD----
-MGYP001032527956/9-36            -------SKISEMTNEISRLNSEIENYKQQIESLN------
-MGYP001032527956/100-127         -------NKINDLNNEISRLNSEIENYKQQIETLN------
-MGYP001032527956/130-155         ---------INDLTNEISRLNSEIENYKQQIETLN------
-MGYP001032527956/177-204         -------NKINDLNNEISRLNSEIDNYKQQIETLN------
-#=GC RF                          xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
-//
--- a/tests/test_data/alignments/1hf9_A/uniprot_hits.sto
+++ b/tests/test_data/alignments/1hf9_A/uniprot_hits.sto
--- a/tests/test_data/alignments/1hf9_A/uniref90_hits.sto
+++ b/tests/test_data/alignments/1hf9_A/uniref90_hits.sto
--- a/tests/test_data/alignments/1hf9_B/bfd_uniclust_hits.a3m
+++ b/tests/test_data/alignments/1hf9_B/bfd_uniclust_hits.a3m
--- a/tests/test_data/alignments/1hf9_B/hmm_output.sto
+++ b/tests/test_data/alignments/1hf9_B/hmm_output.sto
--- a/tests/test_data/alignments/1hf9_B/mgnify_hits.sto
+++ b/tests/test_data/alignments/1hf9_B/mgnify_hits.sto
-# STOCKHOLM 1.0
-
-#=GS MGYP000184479417/51-87   DE [subseq from] PL=10 UP=0 BIOMES=0000000010100
-#=GS MGYP001032527956/9-36    DE [subseq from] PL=11 UP=0 BIOMES=0000000000001
-#=GS MGYP001032527956/100-127 DE [subseq from] PL=11 UP=0 BIOMES=0000000000001
-#=GS MGYP001032527956/130-155 DE [subseq from] PL=11 UP=0 BIOMES=0000000000001
-#=GS MGYP001032527956/177-204 DE [subseq from] PL=11 UP=0 BIOMES=0000000000001
-
-query                            ALKKHHENEISHHAKEIERLQKEIERHKQSIKKLKQSEDDD
-MGYP000184479417/51-87           ALKKHHEEEIVHHKKEIERLQKEIERHKQKIKMLKHD----
-MGYP001032527956/9-36            -------SKISEMTNEISRLNSEIENYKQQIESLN------
-MGYP001032527956/100-127         -------NKINDLNNEISRLNSEIENYKQQIETLN------
-MGYP001032527956/130-155         ---------INDLTNEISRLNSEIENYKQQIETLN------
-MGYP001032527956/177-204         -------NKINDLNNEISRLNSEIDNYKQQIETLN------
-#=GC RF                          xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
-//
--- a/tests/test_data/alignments/1hf9_B/uniprot_hits.sto
+++ b/tests/test_data/alignments/1hf9_B/uniprot_hits.sto
--- a/tests/test_data/alignments/1hf9_B/uniref90_hits.sto
+++ b/tests/test_data/alignments/1hf9_B/uniref90_hits.sto
--- a/tests/test_data/alignments/1psm_A/bfd_uniclust_hits.a3m
+++ b/tests/test_data/alignments/1psm_A/bfd_uniclust_hits.a3m
->query
-EAYKKAKQASQDAEQAAKDAENASKEAEEAAKEAVNLK
->tr|A0A024VQI0|A0A024VQI0_PLAFA Uncharacterized protein OS=Plasmodium falciparum FCH/4 GN=PFFCH_02010 PE=4 SV=1
-EAYKKAKEASQDAEKAAEEAEKAAEQAEQASKDAEKLK
->tr|A0A151L2U9|A0A151L2U9_PLARE Merozoite surface protein 3 (Fragment) OS=Plasmodium reichenowi GN=PRSY57_0014700A PE=4 SV=1
-KAKKASEDAEKVKKASEDaekaakdAENASKEAEEAAQEAVKLK
->tr|O15855|O15855_PLAFA Merozoite surface protein 3 (Fragment) OS=Plasmodium falciparum GN=SPAM PE=4 SV=1
-KAKKASEDAEKAA-----ndAENASKEAEEAAKEAVNLK
->tr|W7JBM4|W7JBM4_PLAFA Uncharacterized protein OS=Plasmodium falciparum UGT5.1 GN=C923_03131 PE=4 SV=1
-KAKKASEDAGNASKEAE---EASCHKQNILY------
->tr|A0A1D8H334|A0A1D8H334_PLAFA Merozoite surface protein-3 (Fragment) OS=Plasmodium falciparum OX=5833 PE=4 SV=1 
------KKASEDAEKAANDAENASKEAEEASKEAVNLK
->tr|A0A2P9DFY8|A0A2P9DFY8_PLARE Merozoite surface protein 3 OS=Plasmodium reichenowi OX=5854 GN=PRG01_1033900 PE=4 SV=1
-DAYKKAKEAAEGAEKAAEEAEKAAEQAEQASKDAEKLK
->tr|A0A2P9GM08|A0A2P9GM08_9APIC Merozoite surface protein 3 OS=Plasmodium sp. DRC-Itaito OX=720590 GN=PBILCG01_1034200 PE=4 SV=1
-ETYKKVKQASQDAEQAAEKAEKAAKDAEQASKDAEKLK
->tr|A0A2S1Q7P9|A0A2S1Q7P9_PLAFA Merozoite surface protein 3 (Fragment) OS=Plasmodium falciparum OX=5833 PE=4 SV=1
-EAYKKAKQASQDAEQAAKDAEQAAKDAEQASKDAEKLK
->tr|A0A2P9C2Y3|A0A2P9C2Y3_9APIC Merozoite surface protein 3 OS=Plasmodium gaboni OX=647221 GN=PGABG01_1033300 PE=4 SV=1
---IIVKKEAQKAKEAAQTAEkekdisEN---AKNSAVSAKSSK
->tr|A0A060RU34|A0A060RU34_PLARE Merozoite surface protein 3 OS=Plasmodium reichenowi OX=5854 GN=MSP3 PE=4 SV=1
---LKAKKASEDAEKA---AEdaeNASKEAEEAAQEAVKLK
->tr|W4J2M7|W4J2M7_PLAFP Uncharacterized protein OS=Plasmodium falciparum (isolate Palo Alto / Uganda) OX=57270 GN=PFUGPA_01621 PE=4 SV=1
---LKAKKASEDAGNAS-------KEAEEASWFRVQ--
--- a/tests/test_data/alignments/1psm_A/hmm_output.sto
+++ b/tests/test_data/alignments/1psm_A/hmm_output.sto
--- a/tests/test_data/alignments/1psm_A/mgnify_hits.sto
+++ b/tests/test_data/alignments/1psm_A/mgnify_hits.sto
-# STOCKHOLM 1.0
-
-#=GS MGYP000005532851/48-76   DE [subseq from] PL=00 UP=0 BIOMES=0110000000000
-#=GS MGYP000005532851/81-108  DE [subseq from] PL=00 UP=0 BIOMES=0110000000000
-#=GS MGYP000005532851/110-139 DE [subseq from] PL=00 UP=0 BIOMES=0110000000000
-#=GS MGYP000091056102/48-76   DE [subseq from] PL=01 UP=0 BIOMES=0110000000000
-#=GS MGYP000091056102/81-108  DE [subseq from] PL=01 UP=0 BIOMES=0110000000000
-#=GS MGYP000091056102/110-139 DE [subseq from] PL=01 UP=0 BIOMES=0110000000000
-#=GS MGYP000091056102/174-199 DE [subseq from] PL=01 UP=0 BIOMES=0110000000000
-#=GS MGYP000091056102/252-279 DE [subseq from] PL=01 UP=0 BIOMES=0110000000000
-
-query                            EAYKKAKQASQDAEQAAKDAENASKEAEEAAKEAVNLK
-MGYP000005532851/48-76           -----AKQASLDAKQASVDAKHESVVAKQASLEA----
-MGYP000005532851/81-108          ---VVAKQASVDAKQASVDAKHESVVAKQAS-------
-MGYP000005532851/110-139         ----VAKQASLDAKQASLDAKQASLDAKQASVDA----
-MGYP000091056102/48-76           -----AKQASLDAKQASVDAKHESVVAKQASLEA----
-MGYP000091056102/81-108          ---VVAKQASVDAKQASVDAKHESVVAKQAS-------
-MGYP000091056102/110-139         ----VAKQASLDAKQASLDAKQASLDAKQASVDA----
-MGYP000091056102/174-199         -----AKQASLDAKQASVDAKHESVVAKQAS-------
-MGYP000091056102/252-279         ------KQASVDAKQASVDAKQASVDAKQASVDA----
-#=GC RF                          xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
-//
--- a/tests/test_data/alignments/1psm_A/uniprot_hits.sto
+++ b/tests/test_data/alignments/1psm_A/uniprot_hits.sto
--- a/tests/test_data/alignments/1psm_A/uniref90_hits.sto
+++ b/tests/test_data/alignments/1psm_A/uniref90_hits.sto
-# STOCKHOLM 1.0
-
-#=GS UniRef90_Q9NIG6/58-95          DE [subseq from] Merozoite surface protein 3 (Fragment) n=1 Tax=Plasmodium falciparum TaxID=5833 RepID=Q9NIG6_PLAFA
-#=GS UniRef90_A0A024VYN0/90-127     DE [subseq from] Merozoite surface protein 3 n=52 Tax=Plasmodium falciparum TaxID=5833 RepID=A0A024VYN0_PLAFA
-#=GS UniRef90_UPI0019011389/487-495 DE [subseq from] potassium voltage-gated channel subfamily C member 1-like n=1 Tax=Salvelinus namaycush TaxID=8040 RepID=UPI0019011389
-#=GS UniRef90_O15863/57-94          DE [subseq from] Merozoite surface protein 3 (Fragment) n=10 Tax=Plasmodium falciparum TaxID=5833 RepID=O15863_PLAFA
-#=GS UniRef90_A0A6J8EZW5/149-173    DE [subseq from] Secreted protein n=1 Tax=Mytilus coruscus TaxID=42192 RepID=A0A6J8EZW5_MYTCO
-#=GS UniRef90_A0A8C3V826/99-123     DE [subseq from] Translation initiation factor IF-2 n=1 Tax=Catharus ustulatus TaxID=91951 RepID=A0A8C3V826_CATUS
-#=GS UniRef90_A0A8C3V826/170-202    DE [subseq from] Translation initiation factor IF-2 n=1 Tax=Catharus ustulatus TaxID=91951 RepID=A0A8C3V826_CATUS
-#=GS UniRef90_O15854/44-77          DE [subseq from] Merozoite surface protein 3 (Fragment) n=2 Tax=Plasmodium falciparum TaxID=5833 RepID=O15854_PLAFA
-#=GS UniRef90_A0A401U021/46-73      DE [subseq from] CG2 omega repeat (Fragment) n=1 Tax=Chiloscyllium punctatum TaxID=137246 RepID=A0A401U021_CHIPU
-#=GS UniRef90_UPI001F20CBA7/9-40    DE [subseq from] hypothetical protein n=1 Tax=Niallia circulans TaxID=1397 RepID=UPI001F20CBA7
-#=GS UniRef90_UPI001F20CBA7/36-61   DE [subseq from] hypothetical protein n=1 Tax=Niallia circulans TaxID=1397 RepID=UPI001F20CBA7
-#=GS UniRef90_UPI001F20CBA7/64-88   DE [subseq from] hypothetical protein n=1 Tax=Niallia circulans TaxID=1397 RepID=UPI001F20CBA7
-#=GS UniRef90_A0A1D8H334/1-33       DE [subseq from] Merozoite surface protein-3 (Fragment) n=1 Tax=Plasmodium falciparum TaxID=5833 RepID=A0A1D8H334_PLAFA
-#=GS UniRef90_A0A3M0JR79/4-33       DE [subseq from] Protein Wnt n=22 Tax=Neognathae TaxID=8825 RepID=A0A3M0JR79_HIRRU
-#=GS UniRef90_A0A3M0JR79/40-67      DE [subseq from] Protein Wnt n=22 Tax=Neognathae TaxID=8825 RepID=A0A3M0JR79_HIRRU
-#=GS UniRef90_A0A3M0JR79/67-98      DE [subseq from] Protein Wnt n=22 Tax=Neognathae TaxID=8825 RepID=A0A3M0JR79_HIRRU
-#=GS UniRef90_A0A3M0JR79/95-124     DE [subseq from] Protein Wnt n=22 Tax=Neognathae TaxID=8825 RepID=A0A3M0JR79_HIRRU
-#=GS UniRef90_A0A159SN41/45-78      DE [subseq from] Merozoite surface protein 3 (Fragment) n=2 Tax=Plasmodium falciparum TaxID=5833 RepID=A0A159SN41_PLAFA
-#=GS UniRef90_A0A159SLY0/58-95      DE [subseq from] Merozoite surface protein 3 (Fragment) n=2 Tax=Plasmodium falciparum TaxID=5833 RepID=A0A159SLY0_PLAFA
-
-query                                  EAYKKAKQASQDAEQAAKDAENASKEAEEAAKEAVNLK
-UniRef90_Q9NIG6/58-95                  EAYKKAKQASQDAEQAAKDAENASKEAEEAAKEAVNLK
-UniRef90_A0A024VYN0/90-127             EAYKKAKQASQDAEQAAKDAENASKEAEEAAKEAVNLK
-UniRef90_UPI0019011389/487-495         ------------------------KDARQVIKD-----
-UniRef90_O15863/57-94                  EAYKKAKQASQDAEQAAKDAEQAAKDAEQASKDAEKLK
-UniRef90_A0A6J8EZW5/149-173            -------QACKDLGQACKDLEQACKDIGQACK------
-UniRef90_A0A8C3V826/99-123             -AVRDAPNAVRDAPNAVRDAPNAVRD------------
-UniRef90_A0A8C3V826/170-202            --VRDAPKAVRDAPNAVRDAPNAVRDAPNAVRDAP---
-UniRef90_O15854/44-77                  ----KAKKASEDAEKAANDAENASKEAEEAAKEAVNLK
-UniRef90_A0A401U021/46-73              --------GNKDSDNGTKDSDNGTKDSDNGTKESDN--
-UniRef90_UPI001F20CBA7/9-40            --RKDVEMARKDVEVARKDVEVARKDVEVASKDA----
-UniRef90_UPI001F20CBA7/36-61           --------ASKDAEVASKDAEVASKDAEVASKDV----
-UniRef90_UPI001F20CBA7/64-88           --------ASKDVEVASKDVEVASKDVEVARKD-----
-UniRef90_A0A1D8H334/1-33               -----AKKASEDAEKAANDAENASKEAEEASKEAVNLK
-UniRef90_A0A3M0JR79/4-33               ---RSAEQISEDAEQISEDAEQISKVAEQISEV-----
-UniRef90_A0A3M0JR79/40-67              ----DAEQISEDAEQISEDAEQISKVAEQISK------
-UniRef90_A0A3M0JR79/67-98              ---KVAEQISEDAEQISEDAEQISKDAEQISKDAE---
-UniRef90_A0A3M0JR79/95-124             ---KDAEQISEDAGQISEDAEQISEDAEQISSL-----
-UniRef90_A0A159SN41/45-78              ----KAKKASEDAEKAANDAENASKEAEEAAKEAVNLK
-UniRef90_A0A159SLY0/58-95              EAYKKAKQASQDAEQAAKDAEQAAKDAEQASKDAEKLK
-#=GC RF                                xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
-//
--- a/tests/test_data/alignments/2crb_A/bfd_uniclust_hits.a3m
+++ b/tests/test_data/alignments/2crb_A/bfd_uniclust_hits.a3m
--- a/tests/test_data/alignments/2crb_A/hmm_output.sto
+++ b/tests/test_data/alignments/2crb_A/hmm_output.sto
--- a/tests/test_data/alignments/2crb_A/mgnify_hits.sto
+++ b/tests/test_data/alignments/2crb_A/mgnify_hits.sto
-# STOCKHOLM 1.0
-
-#=GS MGYP000613015979/52-138  DE [subseq from] PL=11 UP=0 BIOMES=0000000011000
-#=GS MGYP000356782790/15-100  DE [subseq from] PL=01 UP=0 BIOMES=1000000000000
-#=GS MGYP000745946800/67-150  DE [subseq from] PL=00 UP=0 BIOMES=0000000011000
-#=GS MGYP000365627167/34-120  DE [subseq from] PL=01 UP=0 BIOMES=1000000000000
-#=GS MGYP000326981611/4-88    DE [subseq from] PL=00 UP=0 BIOMES=0000000011000
-#=GS MGYP000438079158/44-95   DE [subseq from] PL=10 UP=0 BIOMES=0000000010100
-#=GS MGYP000660499351/22-69   DE [subseq from] PL=00 UP=0 BIOMES=1000000000000
-#=GS MGYP000054740637/2-50    DE [subseq from] PL=00 UP=0 BIOMES=0000000010100
-#=GS MGYP000111717601/1-44    DE [subseq from] PL=00 UP=0 BIOMES=0000000011000
-#=GS MGYP000888755554/1-44    DE [subseq from] PL=00 UP=0 BIOMES=0000000011000
-#=GS MGYP000294730968/1-44    DE [subseq from] PL=00 UP=0 BIOMES=0000000010100
-#=GS MGYP000492638681/46-75   DE [subseq from] PL=00 UP=0 BIOMES=0000000000001
-#=GS MGYP001120896613/151-179 DE [subseq from] PL=01 UP=0 BIOMES=0101000000000
-#=GS MGYP000299282490/49-75   DE [subseq from] PL=00 UP=0 BIOMES=0000101000000
-#=GS MGYP000665431927/41-61   DE [subseq from] PL=10 UP=0 BIOMES=0110000000000
-#=GS MGYP000236921234/89-111  DE [subseq from] PL=01 UP=0 BIOMES=0110000000000
-#=GS MGYP000139113544/297-357 DE [subseq from] PL=01 UP=0 BIOMES=0000000011000
-#=GS MGYP000139113544/476-542 DE [subseq from] PL=01 UP=0 BIOMES=0000000011000
-
-query                            GSSGSSGMEGPLNLAHQQSRRADRLLAAGKYEEAISCHRKATTYLSEAMKLTESEQAHLSLELQRDSHMKQLLLIQERWKRA-KREERLKAHSGPSSG
-MGYP000613015979/52-138          -----KVMEGPLNLAHQQSRRADRLLAAGKYEEAISCHKKAAAYLSEAMKLTQSEQAHLSLELQRDSHMKQLLLIQERWKRA-QREERLKAQQ-----
-MGYP000356782790/15-100          ------VMEGPLNLAHQQSRRADRLLAAGKYEEAISCHKKAAAYLSEAMKLTQSEQAHLSLELQRDSHMKQLLLIQERWKRA-QGEARLKAQQ-----
-MGYP000745946800/67-150          ------VMEGPLNLAHQQSRRADRLLAAGKYEEAISCHKKAAAYLSEAMKLTQSEQARLSLELQRDSHMKQLLLIQERWKRA-QREERLKA-------
-MGYP000365627167/34-120          -----EVMEGPLNLAHQQSRRADRLLAAGKYEEAISCHKKAAVYLSEAMKLTQSKQAHLSLELQRDSHMKQLLLIQERWKRA-QGEARLKAQQ-----
-MGYP000326981611/4-88            -------MEGPLNLAHQQSRRADRLLAAGKYEEAISCHKKAAAYLSEAMKLTQSEQARLSLELQRDSHMKQLLLIQERWKRP-QHEERLKAQQ-----
-MGYP000438079158/44-95           -----EVMEGPLNLAHQQSRRADHLLAAGKYEEAISCHKKAAVYLSEAMKLTQSEQV-----------------------------------------
-MGYP000660499351/22-69           --------NGSLNLAHQQSRRADRLLAAGKYEEAISCHKKAAAYLYEAMKLTQSEQ------------------------------------------
-MGYP000054740637/2-50            -------------------------------------------YLSEAMKLTQSKQAHLSLELQRDSHMKQLLLIQERWKRA-QGEARLKAQQ-----
-MGYP000111717601/1-44            ------------------------------------------------MKLTQSEQAHLSLELQRDSHMKQLLLIQERWKRA-QREERLKAQQ-----
-MGYP000888755554/1-44            ------------------------------------------------MKLTQSEQARLSLELQRDSHMKQLLLIQERWKRA-QREERLKAQQ-----
-MGYP000294730968/1-44            ------------------------------------------------MKLTQSKQAHLSLELQRDSHMKQLLLIQERWKRP-QHEERLKAQQ-----
-MGYP000492638681/46-75           ------------NNAKFYSRLAATLSALEKYEEAIDCYQKAI--------------------------------------------------------
-MGYP001120896613/151-179         -------------AAHVWNSKGDALANLGKYEEAIECYDKAI--------------------------------------------------------
-MGYP000299282490/49-75           ---------------YLLNKKGDNLSRLGKFEEAIECYDKAI--------------------------------------------------------
-MGYP000665431927/41-61           -----------------------ILQALGKYEEAIACYDKVITF------------------------------------------------------
-MGYP000236921234/89-111          ---------------------GKILEALGKYEEAIACYDKVITF------------------------------------------------------
-MGYP000139113544/297-357         ----------------REYQKALKLMTDEKYEEAIKAFEVLNNYSDSATKISECNTAILEREYQKAL--K--LMMDEKYEE-----------------
-MGYP000139113544/476-542         -------------------QKATRLMEDEKYEDAIQAFEALNSYSDSTTKISECKTAILEKEYQKA--LK--LMMDEKYEEAIKAFEALN--------
-#=GC RF                          xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx
-//
--- a/tests/test_data/alignments/2crb_A/uniprot_hits.sto
+++ b/tests/test_data/alignments/2crb_A/uniprot_hits.sto
--- a/tests/test_data/alignments/2crb_A/uniref90_hits.sto
+++ b/tests/test_data/alignments/2crb_A/uniref90_hits.sto