Mercurial > repos > jackcurragh > trips_viz_create_annotation

changeset 2:d70696d3341e draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author jackcurragh
date Sun, 17 Apr 2022 08:45:11 +0000
parents f089034be679
children f1c72ed4b32c
files trips_create_annotation/create_annotation_sqlite.py trips_create_annotation/test-data/notinfasta.csv trips_create_annotation/test-data/test_org.sqlite trips_create_annotation/test-data/test_organism.sqlite trips_create_annotation/trips_create_annotation.xml
diffstat 4 files changed, 1377 insertions(+), 6 deletions(-) [+]
line wrap: on
line diff
--- a/trips_create_annotation/create_annotation_sqlite.py	Wed Apr 13 10:58:41 2022 +0000
+++ b/trips_create_annotation/create_annotation_sqlite.py	Sun Apr 17 08:45:11 2022 +0000
@@ -32,7 +32,7 @@
 
 
 # old_exons = SqliteDict(
-#     "/home/DATA/www/tripsviz/tripsviz/trips_annotations/mus_musculus/transcriptomic_to_genomic.sqlite"
+#     "/home/data2/www/tripsviz/tripsviz/trips_annotations/mus_musculus/transcriptomic_to_genomic.sqlite"
 # )
 
 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/trips_create_annotation/test-data/notinfasta.csv	Sun Apr 17 08:45:11 2022 +0000
@@ -0,0 +1,1371 @@
+TGGCCD1
+TGGCCD1
+TGGCCD1
+SNR63
+SNR63
+SNR63
+TKUUUD
+TKUUUD
+TKUUUD
+TKUUUD
+TAAGCD
+TAAGCD
+TAAGCD
+TTAGUD
+TTAGUD
+TTAGUD
+TSAGAD1
+TSAGAD1
+TSAGAD1
+TVUACD
+TVUACD
+TVUACD
+TLUAAD
+TLUAAD
+TLUAAD
+TQUUGD1
+TQUUGD1
+TQUUGD1
+SNR47
+SNR47
+SNR47
+TRUCUD
+TRUCUD
+TRUCUD
+TDGUCD
+TDGUCD
+TDGUCD
+TRACGD
+TRACGD
+TRACGD
+TQUUGD2
+TQUUGD2
+TQUUGD2
+TIAAUD
+TIAAUD
+TIAAUD
+YDR134C
+YDR134C
+YDR134C
+TQUUGD3
+TQUUGD3
+TQUUGD3
+TIUAUD
+TIUAUD
+TIUAUD
+TIUAUD
+TYGUAD
+TYGUAD
+TYGUAD
+TYGUAD
+TSAGAD2
+TSAGAD2
+TSAGAD2
+TGGCCD2
+TGGCCD2
+TGGCCD2
+TECUCD
+TECUCD
+TECUCD
+TVCACD
+TVCACD
+TVCACD
+TFGAAD
+TFGAAD
+TFGAAD
+TFGAAD
+TXXXXD
+TXXXXD
+TXXXXD
+TMCAUD
+TMCAUD
+TMCAUD
+TKCUUD1
+TKCUUD1
+TKCUUD1
+TGCCCD
+TGCCCD
+TGCCCD
+TSAGAD3
+TSAGAD3
+TSAGAD3
+TKCUUD2
+TKCUUD2
+TKCUUD2
+SNR13
+SNR13
+SNR13
+TLCAAD
+TLCAAD
+TLCAAD
+TLCAAD
+SNR84
+SNR84
+SNR84
+YOL153C
+YOL153C
+YOL153C
+TGUCCO
+TGUCCO
+TGUCCO
+TTAGUO1
+TTAGUO1
+TTAGUO1
+SNR58
+SNR58
+SNR58
+TGGCCO1
+TGGCCO1
+TGGCCO1
+TNGUUO1
+TNGUUO1
+TNGUUO1
+SNR81
+SNR81
+SNR81
+SNR50
+SNR50
+SNR50
+TSGCUO
+TSGCUO
+TSGCUO
+TSGCUO
+TGGCCO2
+TGGCCO2
+TGGCCO2
+TYGUAO
+TYGUAO
+TYGUAO
+TYGUAO
+TPUGGO1
+TPUGGO1
+TPUGGO1
+TPUGGO1
+TRACGO
+TRACGO
+TRACGO
+TTAGUO2
+TTAGUO2
+TTAGUO2
+SNR9
+SNR9
+SNR9
+SNR62
+SNR62
+SNR62
+TKUUUO
+TKUUUO
+TKUUUO
+TKUUUO
+TPUGGO2
+TPUGGO2
+TPUGGO2
+TPUGGO2
+TNGUUO2
+TNGUUO2
+TNGUUO2
+TDGUCO
+TDGUCO
+TDGUCO
+TGCCCO
+TGCCCO
+TGCCCO
+TVAACO
+TVAACO
+TVAACO
+SNR36
+SNR36
+SNR36
+TMCAUO1
+TMCAUO1
+TMCAUO1
+SNR35
+SNR35
+SNR35
+SNR17A
+SNR17A
+SNR17A
+SNR17A
+SNR8
+SNR8
+SNR8
+SNR31
+SNR31
+SNR31
+SNR5
+SNR5
+SNR5
+TAUGCO
+TAUGCO
+TAUGCO
+TMCAUO2
+TMCAUO2
+TMCAUO2
+TPUGGO3
+TPUGGO3
+TPUGGO3
+TPUGGO3
+TVAACG3
+TVAACG3
+TVAACG3
+THGUGG1
+THGUGG1
+THGUGG1
+TKUUUG1
+TKUUUG1
+TKUUUG1
+TKUUUG1
+TKCUUG1
+TKCUUG1
+TKCUUG1
+TKCUUG2
+TKCUUG2
+TKCUUG2
+TLCAAG1
+TLCAAG1
+TLCAAG1
+TLCAAG1
+TWCCAG1
+TWCCAG1
+TWCCAG1
+TWCCAG1
+SNR82
+SNR82
+SNR82
+THGUGG2
+THGUGG2
+THGUGG2
+TEUUCG1
+TEUUCG1
+TEUUCG1
+SNR10
+SNR10
+SNR10
+SNR39
+SNR39
+SNR39
+SNR39B
+SNR39B
+SNR39B
+TEUUCG2
+TEUUCG2
+TEUUCG2
+TRUCUG1
+TRUCUG1
+TRUCUG1
+TVAACG1
+TVAACG1
+TVAACG1
+TLCAAG2
+TLCAAG2
+TLCAAG2
+TLCAAG2
+TFGAAG
+TFGAAG
+TFGAAG
+TFGAAG
+TDGUCG1
+TDGUCG1
+TDGUCG1
+TEUUCG3
+TEUUCG3
+TEUUCG3
+TDGUCG2
+TDGUCG2
+TDGUCG2
+SNR46
+SNR46
+SNR46
+TSAGAG
+TSAGAG
+TSAGAG
+SNR48
+SNR48
+SNR48
+TTUGUG1
+TTUGUG1
+TTUGUG1
+TLGAGG
+TLGAGG
+TLGAGG
+TKUUUG2
+TKUUUG2
+TKUUUG2
+TKUUUG2
+TCGCAG
+TCGCAG
+TCGCAG
+TNGUUG
+TNGUUG
+TNGUUG
+TRUCUG3
+TRUCUG3
+TRUCUG3
+TIAAUG
+TIAAUG
+TIAAUG
+TAAGCG
+TAAGCG
+TAAGCG
+TGUCCG
+TGUCCG
+TGUCCG
+TAUGCG
+TAUGCG
+TAUGCG
+TVAACG2
+TVAACG2
+TVAACG2
+TRUCUG2
+TRUCUG2
+TRUCUG2
+TGGCCG1
+TGGCCG1
+TGGCCG1
+TLCAAG3
+TLCAAG3
+TLCAAG3
+TLCAAG3
+TKCUUG3
+TKCUUG3
+TKCUUG3
+TWCCAG2
+TWCCAG2
+TWCCAG2
+TWCCAG2
+TGGCCG2
+TGGCCG2
+TGGCCG2
+SNR7_L
+SNR7_L
+SNR7_L
+SNR7_S
+SNR7_S
+SNR7_S
+TTUGUG2
+TTUGUG2
+TTUGUG2
+TPUGGL
+TPUGGL
+TPUGGL
+TPUGGL
+YLL017W
+YLL017W
+YLL017W
+YLL016W
+YLL016W
+YLL016W
+TSAGAL
+TSAGAL
+TSAGAL
+SNR30
+SNR30
+SNR30
+TAUGCL
+TAUGCL
+TAUGCL
+SNR79
+SNR79
+SNR79
+SNR6
+SNR6
+SNR6
+TRACGL
+TRACGL
+TRACGL
+TDGUCL1
+TDGUCL1
+TDGUCL1
+TQUUGL
+TQUUGL
+TQUUGL
+RDN25_1
+RDN25_1
+RDN25_1
+RDN37_1
+RDN37_1
+RDN37_1
+RDN37_1
+RDN37_1
+RDN58_1
+RDN58_1
+RDN58_1
+RDN18_1
+RDN18_1
+RDN18_1
+RDN5_1
+RDN5_1
+RDN5_1
+RDN37_2
+RDN37_2
+RDN37_2
+RDN37_2
+RDN37_2
+RDN25_2
+RDN25_2
+RDN25_2
+RDN58_2
+RDN58_2
+RDN58_2
+RDN18_2
+RDN18_2
+RDN18_2
+RDN5_2
+RDN5_2
+RDN5_2
+RDN5_3
+RDN5_3
+RDN5_3
+RDN5_4
+RDN5_4
+RDN5_4
+RDN5_5
+RDN5_5
+RDN5_5
+RDN5_6
+RDN5_6
+RDN5_6
+TLUAGL1
+TLUAGL1
+TLUAGL1
+TLUAGL1
+TIUAUL
+TIUAUL
+TIUAUL
+TIUAUL
+TLCAAL
+TLCAAL
+TLCAAL
+TLCAAL
+TAAGCL
+TAAGCL
+TAAGCL
+TVAACL
+TVAACL
+TVAACL
+TLUAGL2
+TLUAGL2
+TLUAGL2
+TLUAGL2
+TIAAUL1
+TIAAUL1
+TIAAUL1
+TSGCUL
+TSGCUL
+TSGCUL
+TSGCUL
+TDGUCL2
+TDGUCL2
+TDGUCL2
+SNR61
+SNR61
+SNR61
+SNR55
+SNR55
+SNR55
+SNR57
+SNR57
+SNR57
+TEUUCL
+TEUUCL
+TEUUCL
+TRCCGL
+TRCCGL
+TRCCGL
+SNR44
+SNR44
+SNR44
+TKUUUL
+TKUUUL
+TKUUUL
+TKUUUL
+SNR34
+SNR34
+SNR34
+TLUAAL
+TLUAAL
+TLUAAL
+TNGUUL
+TNGUUL
+TNGUUL
+TIAAUL2
+TIAAUL2
+TIAAUL2
+YPL276W
+YPL276W
+YPL276W
+YPL275W
+YPL275W
+YPL275W
+TWCCAP
+TWCCAP
+TWCCAP
+TWCCAP
+SNR59
+SNR59
+SNR59
+TEUUCP
+TEUUCP
+TEUUCP
+SNR17B
+SNR17B
+SNR17B
+SNR17B
+TMCAUP
+TMCAUP
+TMCAUP
+TCGCAP1
+TCGCAP1
+TCGCAP1
+YPL060C_A
+YPL060C_A
+YPL060C_A
+TFGAAP1
+TFGAAP1
+TFGAAP1
+TFGAAP1
+TGGCCP1
+TGGCCP1
+TGGCCP1
+TKCUUP
+TKCUUP
+TKCUUP
+TFGAAP2
+TFGAAP2
+TFGAAP2
+TFGAAP2
+TSUGAP
+TSUGAP
+TSUGAP
+SNR51
+SNR51
+SNR51
+SNR70
+SNR70
+SNR70
+SNR41
+SNR41
+SNR41
+TTUGUP
+TTUGUP
+TTUGUP
+TKUUUP
+TKUUUP
+TKUUUP
+TKUUUP
+TCGCAP2
+TCGCAP2
+TCGCAP2
+TNGUUP
+TNGUUP
+TNGUUP
+TIAAUP1
+TIAAUP1
+TIAAUP1
+SNR45
+SNR45
+SNR45
+TAAGCP
+TAAGCP
+TAAGCP
+TGGCCP2
+TGGCCP2
+TGGCCP2
+TIAAUP2
+TIAAUP2
+TIAAUP2
+SNR85
+SNR85
+SNR85
+TRUCUM2
+TRUCUM2
+TRUCUM2
+SNR54
+SNR54
+SNR54
+TYGUAM1
+TYGUAM1
+TYGUAM1
+TYGUAM1
+TGGCCM
+TGGCCM
+TGGCCM
+TPUGGM
+TPUGGM
+TPUGGM
+TPUGGM
+TSAGAM
+TSAGAM
+TSAGAM
+TEUUCM
+TEUUCM
+TEUUCM
+SNR78
+SNR78
+SNR78
+SNR77
+SNR77
+SNR77
+SNR76
+SNR76
+SNR76
+SNR75
+SNR75
+SNR75
+SNR74
+SNR74
+SNR74
+SNR73
+SNR73
+SNR73
+SNR72
+SNR72
+SNR72
+TAAGCM1
+TAAGCM1
+TAAGCM1
+TFGAAM
+TFGAAM
+TFGAAM
+TFGAAM
+THGUGM
+THGUGM
+THGUGM
+TVAACM1
+TVAACM1
+TVAACM1
+TWCCAM
+TWCCAM
+TWCCAM
+TWCCAM
+TVAACM2
+TVAACM2
+TVAACM2
+TDGUCM
+TDGUCM
+TDGUCM
+TKCUUM
+TKCUUM
+TKCUUM
+SNR24
+SNR24
+SNR24
+TLCAAM
+TLCAAM
+TLCAAM
+TLCAAM
+TMCAUM
+TMCAUM
+TMCAUM
+TVAACM3
+TVAACM3
+TVAACM3
+SNR83
+SNR83
+SNR83
+SNR11
+SNR11
+SNR11
+RNA170
+RNA170
+RNA170
+TRUCUM1
+TRUCUM1
+TRUCUM1
+SNR86
+SNR86
+SNR86
+TAAGCM2
+TAAGCM2
+TAAGCM2
+TQCUGM
+TQCUGM
+TQCUGM
+TYGUAM2
+TYGUAM2
+TYGUAM2
+TYGUAM2
+TLUAAB1
+TLUAAB1
+TLUAAB1
+TFGAAB
+TFGAAB
+TFGAAB
+TFGAAB
+SNR56
+SNR56
+SNR56
+TIAAUB
+TIAAUB
+TIAAUB
+TGGCCB
+TGGCCB
+TGGCCB
+TSAGAB
+TSAGAB
+TSAGAB
+TTAGUB
+TTAGUB
+TTAGUB
+SNR161
+SNR161
+SNR161
+TLC1
+TLC1
+TLC1
+TVUACB
+TVUACB
+TVUACB
+TLUAAB2
+TLUAAB2
+TLUAAB2
+TQUUGB
+TQUUGB
+TQUUGB
+TRUCUB
+TRUCUB
+TRUCUB
+TDGUCB
+TDGUCB
+TDGUCB
+TCGCAB
+TCGCAB
+TCGCAB
+TEUUCB
+TEUUCB
+TEUUCB
+LSR1
+LSR1
+LSR1
+SNR40
+SNR40
+SNR40
+TGUCCN
+TGUCCN
+TGUCCN
+TNGUUN1
+TNGUUN1
+TNGUUN1
+TTAGUN1
+TTAGUN1
+TTAGUN1
+SNR19
+SNR19
+SNR19
+TFGAAN
+TFGAAN
+TFGAAN
+TFGAAN
+TLCAAN
+TLCAAN
+TLCAAN
+TLCAAN
+TDGUCN
+TDGUCN
+TDGUCN
+YNL054W_B
+YNL054W_B
+YNL054W_B
+YNL054W_B
+TPUGGN1
+TPUGGN1
+TPUGGN1
+TPUGGN1
+TTAGUN2
+TTAGUN2
+TTAGUN2
+TPUGGN2
+TPUGGN2
+TPUGGN2
+TPUGGN2
+TIAAUN1
+TIAAUN1
+TIAAUN1
+NME1
+NME1
+NME1
+SNR66
+SNR66
+SNR66
+TIAAUN2
+TIAAUN2
+TIAAUN2
+TPAGGN
+TPAGGN
+TPAGGN
+TNGUUN2
+TNGUUN2
+TNGUUN2
+SNR49
+SNR49
+SNR49
+SNR191
+SNR191
+SNR191
+TLUAAN
+TLUAAN
+TLUAAN
+TTAGUJ
+TTAGUJ
+TTAGUJ
+TEUUCJ
+TEUUCJ
+TEUUCJ
+SNR128
+SNR128
+SNR128
+SNR190
+SNR190
+SNR190
+TAAGCJ
+TAAGCJ
+TAAGCJ
+TDGUCJ1
+TDGUCJ1
+TDGUCJ1
+SNR37
+SNR37
+SNR37
+TRACGJ
+TRACGJ
+TRACGJ
+SNR60
+SNR60
+SNR60
+TYGUAJ1
+TYGUAJ1
+TYGUAJ1
+TYGUAJ1
+TRUCUJ1
+TRUCUJ1
+TRUCUJ1
+TDGUCJ2
+TDGUCJ2
+TDGUCJ2
+TDGUCJ3
+TDGUCJ3
+TDGUCJ3
+TRUCUJ2
+TRUCUJ2
+TRUCUJ2
+TVAACJ
+TVAACJ
+TVAACJ
+TMCAUJ1
+TMCAUJ1
+TMCAUJ1
+TGGCCJ1
+TGGCCJ1
+TGGCCJ1
+TKCUUJ
+TKCUUJ
+TKCUUJ
+TWCCAJ
+TWCCAJ
+TWCCAJ
+TWCCAJ
+TMCAUJ2
+TMCAUJ2
+TMCAUJ2
+TLUAAJ
+TLUAAJ
+TLUAAJ
+TMCAUJ3
+TMCAUJ3
+TMCAUJ3
+TSAGAJ
+TSAGAJ
+TSAGAJ
+TGGCCJ2
+TGGCCJ2
+TGGCCJ2
+TRCCUJ
+TRCCUJ
+TRCCUJ
+TDGUCJ4
+TDGUCJ4
+TDGUCJ4
+TYGUAJ2
+TYGUAJ2
+TYGUAJ2
+TYGUAJ2
+TLUAGJ
+TLUAGJ
+TLUAGJ
+TLUAGJ
+SNR3
+SNR3
+SNR3
+SNR64
+SNR64
+SNR64
+TTCGUK
+TTCGUK
+TTCGUK
+TNGUUK
+TNGUUK
+TNGUUK
+TLUAAK
+TLUAAK
+TLUAAK
+TEUUCK
+TEUUCK
+TEUUCK
+TRUCUK
+TRUCUK
+TRUCUK
+TKCUUK
+TKCUUK
+TKCUUK
+TAAGCK1
+TAAGCK1
+TAAGCK1
+SNR38
+SNR38
+SNR38
+TWCCAK
+TWCCAK
+TWCCAK
+TWCCAK
+TVAACK1
+TVAACK1
+TVAACK1
+THGUGK
+THGUGK
+THGUGK
+SNR69
+SNR69
+SNR69
+TVAACK2
+TVAACK2
+TVAACK2
+SNR87
+SNR87
+SNR87
+TLCAAK
+TLCAAK
+TLCAAK
+TLCAAK
+TRACGK
+TRACGK
+TRACGK
+TDGUCK
+TDGUCK
+TDGUCK
+TAAGCK2
+TAAGCK2
+TAAGCK2
+SNR42
+SNR42
+SNR42
+TKUUUK
+TKUUUK
+TKUUUK
+TKUUUK
+SNR80
+SNR80
+SNR80
+SNR67
+SNR67
+SNR67
+SNR53
+SNR53
+SNR53
+TGGCCE
+TGGCCE
+TGGCCE
+TSAGAE
+TSAGAE
+TSAGAE
+TMCAUE
+TMCAUE
+TMCAUE
+RPR1
+RPR1
+RPR1
+TQUUGE2
+TQUUGE2
+TQUUGE2
+TKCUUE1
+TKCUUE1
+TKCUUE1
+TRUCUE
+TRUCUE
+TRUCUE
+SNR14
+SNR14
+SNR14
+TEUUCE1
+TEUUCE1
+TEUUCE1
+THGUGE1
+THGUGE1
+THGUGE1
+TQUUGE1
+TQUUGE1
+TQUUGE1
+TSUGAE
+TSUGAE
+TSUGAE
+TAUGCE
+TAUGCE
+TAUGCE
+SRG1
+SRG1
+SRG1
+TEUUCE2
+TEUUCE2
+TEUUCE2
+SNR4
+SNR4
+SNR4
+SNR52
+SNR52
+SNR52
+THGUGE2
+THGUGE2
+THGUGE2
+TKCUUE2
+TKCUUE2
+TKCUUE2
+TVAACE1
+TVAACE1
+TVAACE1
+SCR1
+SCR1
+SCR1
+TIAAUE1
+TIAAUE1
+TIAAUE1
+TVAACE2
+TVAACE2
+TVAACE2
+TEUUCE3
+TEUUCE3
+TEUUCE3
+TRACGE
+TRACGE
+TRACGE
+TIAAUE2
+TIAAUE2
+TIAAUE2
+THGUGH
+THGUGH
+THGUGH
+TVAACH
+TVAACH
+TVAACH
+TTAGUH
+TTAGUH
+TTAGUH
+TSAGAH
+TSAGAH
+TSAGAH
+TQUUGH
+TQUUGH
+TQUUGH
+TAAGCH
+TAAGCH
+TAAGCH
+RUF5_1
+RUF5_1
+RUF5_1
+RUF5_2
+RUF5_2
+RUF5_2
+TFGAAH1
+TFGAAH1
+TFGAAH1
+TFGAAH1
+TFGAAH2
+TFGAAH2
+TFGAAH2
+TFGAAH2
+SNR32
+SNR32
+SNR32
+TPUGGH
+TPUGGH
+TPUGGH
+TPUGGH
+SNR71
+SNR71
+SNR71
+TTUGUH
+TTUGUH
+TTUGUH
+TVCACH
+TVCACH
+TVCACH
+YIL175W
+YIL175W
+YIL175W
+YIL174W
+YIL174W
+YIL174W
+YIL171W
+YIL171W
+YIL171W
+YIL170W
+YIL170W
+YIL170W
+YIL168W
+YIL168W
+YIL168W
+YIL167W
+YIL167W
+YIL167W
+SNR68
+SNR68
+SNR68
+TTAGUI1
+TTAGUI1
+TTAGUI1
+TIAAUI1
+TIAAUI1
+TIAAUI1
+TECUCI
+TECUCI
+TECUCI
+YIL080W
+YIL080W
+YIL080W
+YIL080W
+TIAAUI2
+TIAAUI2
+TIAAUI2
+TSUGAI
+TSUGAI
+TSUGAI
+TKCUUI
+TKCUUI
+TKCUUI
+TDGUCI1
+TDGUCI1
+TDGUCI1
+TTAGUI2
+TTAGUI2
+TTAGUI2
+TDGUCI2
+TDGUCI2
+TDGUCI2
+TEUUCI
+TEUUCI
+TEUUCI
+ICR1
+ICR1
+ICR1
+PWR1
+PWR1
+PWR1
+YIR043C
+YIR043C
+YIR043C
+YIR044C
+YIR044C
+YIR044C
+YCL075W
+YCL075W
+YCL075W
+YCL074W
+YCL074W
+YCL074W
+TEUUCC
+TEUUCC
+TEUUCC
+TLCAAC
+TLCAAC
+TLCAAC
+TLCAAC
+SNR43
+SNR43
+SNR43
+TPAGGC
+TPAGGC
+TPAGGC
+TNGUUC
+TNGUUC
+TNGUUC
+SNR33
+SNR33
+SNR33
+TGGCCC
+TGGCCC
+TGGCCC
+TMCAUC
+TMCAUC
+TMCAUC
+TKCUUC
+TKCUUC
+TKCUUC
+TQUUGC
+TQUUGC
+TQUUGC
+SNR65
+SNR65
+SNR65
+SNR189
+SNR189
+SNR189
+TSCGAC
+TSCGAC
+TSCGAC
+TSCGAC
+TTAGUC
+TTAGUC
+TTAGUC
+RUF21
+RUF21
+RUF21
+TPUGGF
+TPUGGF
+TPUGGF
+TPUGGF
+RUF20
+RUF20
+RUF20
+TNGUUF
+TNGUUF
+TNGUUF
+TFGAAF
+TFGAAF
+TFGAAF
+TFGAAF
+TGGCCF1
+TGGCCF1
+TGGCCF1
+TYGUAF1
+TYGUAF1
+TYGUAF1
+TYGUAF1
+TGGCCF2
+TGGCCF2
+TGGCCF2
+TSGCUF
+TSGCUF
+TSGCUF
+TSGCUF
+RUF22
+RUF22
+RUF22
+TAAGCF
+TAAGCF
+TAAGCF
+TYGUAF2
+TYGUAF2
+TYGUAF2
+TYGUAF2
+RUF23
+RUF23
+RUF23
+TKCUUF
+TKCUUF
+TKCUUF
+HRA1
+HRA1
+HRA1
+TPUGGA
+TPUGGA
+TPUGGA
+TPUGGA
+SNR18
+SNR18
+SNR18
+TAUGCA
+TAUGCA
+TAUGCA
+TLCAAA
+TLCAAA
+TLCAAA
+TLCAAA
+TSAGAA
+TSAGAA
+TSAGAA
+YAR061W
+YAR061W
+YAR061W
+YAR062W
+YAR062W
+YAR062W
+TPUGGQ
+TPUGGQ
+TPUGGQ
+15S_RRNA
+15S_RRNA
+15S_RRNA
+TWUCAQ
+TWUCAQ
+TWUCAQ
+TEUUCQ
+TEUUCQ
+TEUUCQ
+TSUGAQ2
+TSUGAQ2
+TSUGAQ2
+21S_RRNA
+21S_RRNA
+21S_RRNA
+21S_RRNA
+TTUGUQ1
+TTUGUQ1
+TTUGUQ1
+TCGCAQ
+TCGCAQ
+TCGCAQ
+THGUGQ
+THGUGQ
+THGUGQ
+TLUAAQ
+TLUAAQ
+TLUAAQ
+TQUUGQ
+TQUUGQ
+TQUUGQ
+TKUUUQ
+TKUUUQ
+TKUUUQ
+TRUCUQ1
+TRUCUQ1
+TRUCUQ1
+TGUCCQ
+TGUCCQ
+TGUCCQ
+TDGUCQ
+TDGUCQ
+TDGUCQ
+TSGCUQ1
+TSGCUQ1
+TSGCUQ1
+TRACGQ2
+TRACGQ2
+TRACGQ2
+TAUGCQ
+TAUGCQ
+TAUGCQ
+TIGAUQ
+TIGAUQ
+TIGAUQ
+TYGUAQ
+TYGUAQ
+TYGUAQ
+TNGUUQ
+TNGUUQ
+TNGUUQ
+TMCAUQ1
+TMCAUQ1
+TMCAUQ1
+TFGAAQ
+TFGAAQ
+TFGAAQ
+TTXXXQ2
+TTXXXQ2
+TTXXXQ2
+TVUACQ
+TVUACQ
+TVUACQ
+TMCAUQ2
+TMCAUQ2
+TMCAUQ2
+RPM1
+RPM1
+RPM1
Binary file trips_create_annotation/test-data/test_org.sqlite has changed
--- a/trips_create_annotation/trips_create_annotation.xml	Wed Apr 13 10:58:41 2022 +0000
+++ b/trips_create_annotation/trips_create_annotation.xml	Sun Apr 17 08:45:11 2022 +0000
@@ -1,10 +1,10 @@
-<tool id="trips_create_annotation" name="Create TRIPS-Viz annotation" version="1.1">
+<tool id="trips_create_annotation" name="Create TRIPS-Viz annotation" version="1.0">
     <description>Covert GFF3/GTF and transcriptome FASTA to custom annotation sqlite</description>
     <requirements>
         <requirement type="package" version="0.19.0">pysam</requirement>
         <requirement type="package" version="2.0.0">sqlitedict</requirement>
         <requirement type="package" version="3.37.1">sqlite</requirement>
-        <requirement type="package" version="3.0.2">python-intervaltree</requirement>
+        <requirement type="package" version="3.0.2">intervaltree</requirement>
 
     </requirements>
     <command><![CDATA[
@@ -23,13 +23,13 @@
     </outputs>
     <tests>
         <test>
-        <param name="input1" value="test_organism" ftype="text"/>
+        <param name="input1" value="test_org" ftype="text"/>
         <param name="input2" value="test.gtf" ftype="gff"/>
         <param name="input3" value="test.fasta" ftype="fasta"/>
         <param name="input4" value="0" ftype="integer"/>
-        <param name="input5" value="YAL012W" ftype="text"/>
+        <param name="input5" value="YDL248W" ftype="text"/>
         <param name="input6" value="YDL248W" ftype="text"/>
-        <output name="output1" file="test_organism.sqlite" ftype="sqlite" lines_diff="4" />
+        <output name="output1" file="test_org.sqlite" ftype="sqlite" lines_diff="4" />
         </test>
     </tests>
     <help>