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Add two missing species

This commit is contained in:
Samuel Ortion 2025-01-12 16:09:58 +01:00
parent fdf0b282b3
commit 5bc8f82d48
Signed by: sortion
GPG Key ID: 9B02406F8C4FB765
2 changed files with 4 additions and 0 deletions
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2
workflow/families_and_TAGs/concat.csv
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@ -3,8 +3,10 @@ Arabidopsis lyrata,32667,26320,6348,5012,494,1571,1834,3868,4739,14
Glycine max,55897,50258,5640,8421,437,2626,2922,6692,7890,32 Glycine max,55897,50258,5640,8421,437,2626,2922,6692,7890,32
Gossypium raimondii,38208,32975,5234,5519,333,1964,2163,5202,6155,23 Gossypium raimondii,38208,32975,5234,5519,333,1964,2163,5202,6155,23
Malus domestica Golden,40624,34948,5677,6912,858,2340,2707,5643,6988,15 Malus domestica Golden,40624,34948,5677,6912,858,2340,2707,5643,6988,15
Medicago truncatula,50444,39818,10627,5965,639,3264,3864,8195,10712,19
Musa acuminata,35012,28752,6261,4698,624,949,1069,2345,2745,21 Musa acuminata,35012,28752,6261,4698,624,949,1069,2345,2745,21
Oryza sativa,35775,23377,12399,4605,787,1440,1835,3544,4906,19 Oryza sativa,35775,23377,12399,4605,787,1440,1835,3544,4906,19
Phaseolus vulgaris,28134,22763,5372,4126,686,1743,1888,4702,5383,21
Prunus persica,26873,20222,6652,3653,292,1758,1949,4962,5928,22 Prunus persica,26873,20222,6652,3653,292,1758,1949,4962,5928,22
Solanum tuberosum,39021,31477,7545,4465,1044,2558,2891,6488,7903,16 Solanum tuberosum,39021,31477,7545,4465,1044,2558,2891,6488,7903,16
Theobroma cacao,29188,21051,8138,3614,606,1593,1836,4041,5069,22 Theobroma cacao,29188,21051,8138,3614,606,1593,1836,4041,5069,22

1 Species Genes Duplicates Singletons Families LargestFamily TAG0 TAG1 TAG0 Genes TAG1 Genes Largest TAG0
3 Glycine max 55897 50258 5640 8421 437 2626 2922 6692 7890 32
4 Gossypium raimondii 38208 32975 5234 5519 333 1964 2163 5202 6155 23
5 Malus domestica Golden 40624 34948 5677 6912 858 2340 2707 5643 6988 15
6 Medicago truncatula 50444 39818 10627 5965 639 3264 3864 8195 10712 19
7 Musa acuminata 35012 28752 6261 4698 624 949 1069 2345 2745 21
8 Oryza sativa 35775 23377 12399 4605 787 1440 1835 3544 4906 19
9 Phaseolus vulgaris 28134 22763 5372 4126 686 1743 1888 4702 5383 21
10 Prunus persica 26873 20222 6652 3653 292 1758 1949 4962 5928 22
11 Solanum tuberosum 39021 31477 7545 4465 1044 2558 2891 6488 7903 16
12 Theobroma cacao 29188 21051 8138 3614 606 1593 1836 4041 5069 22

2
workflow/families_and_TAGs/input.csv
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@ -9,3 +9,5 @@ Vigna radiata,/media/data/sync/Documents/course/master/M2/S1/comparative_genomic
Vigna angularis,/media/data/sync/Documents/course/master/M2/S1/comparative_genomics/data/Vigna_angularis.Vigan1.1.pep.all.fa.gz,/media/data/sync/Documents/course/master/M2/S1/comparative_genomics/data/Vigna_angularis.Vigan1.1.60.gff3.gz,/media/data/sync/Documents/course/master/M2/S1/comparative_genomics/data/Vigna_angularis_Blastp_longIsoforme Vigna angularis,/media/data/sync/Documents/course/master/M2/S1/comparative_genomics/data/Vigna_angularis.Vigan1.1.pep.all.fa.gz,/media/data/sync/Documents/course/master/M2/S1/comparative_genomics/data/Vigna_angularis.Vigan1.1.60.gff3.gz,/media/data/sync/Documents/course/master/M2/S1/comparative_genomics/data/Vigna_angularis_Blastp_longIsoforme
Theobroma cacao,/media/data/sync/Documents/course/master/M2/S1/comparative_genomics/data/Theobroma_cacao.Theobroma_cacao_20110822.pep.all.fa.gz,/media/data/sync/Documents/course/master/M2/S1/comparative_genomics/data/Theobroma_cacao.Theobroma_cacao_20110822.60.gff3.gz,/media/data/sync/Documents/course/master/M2/S1/comparative_genomics/data/Theobroma_cacao_Blastp_longIsoforme Theobroma cacao,/media/data/sync/Documents/course/master/M2/S1/comparative_genomics/data/Theobroma_cacao.Theobroma_cacao_20110822.pep.all.fa.gz,/media/data/sync/Documents/course/master/M2/S1/comparative_genomics/data/Theobroma_cacao.Theobroma_cacao_20110822.60.gff3.gz,/media/data/sync/Documents/course/master/M2/S1/comparative_genomics/data/Theobroma_cacao_Blastp_longIsoforme
Arabidopsis lyrata,/media/data/sync/Documents/course/master/M2/S1/comparative_genomics/data/Arabidopsis_lyrata.v.1.0.pep.all.fa.gz,/media/data/sync/Documents/course/master/M2/S1/comparative_genomics/data/Arabidopsis_lyrata.v.1.0.60.gff3.gz,/media/data/sync/Documents/course/master/M2/S1/comparative_genomics/data/Arabidopsis_lyrata_Blastp_longIsoforme Arabidopsis lyrata,/media/data/sync/Documents/course/master/M2/S1/comparative_genomics/data/Arabidopsis_lyrata.v.1.0.pep.all.fa.gz,/media/data/sync/Documents/course/master/M2/S1/comparative_genomics/data/Arabidopsis_lyrata.v.1.0.60.gff3.gz,/media/data/sync/Documents/course/master/M2/S1/comparative_genomics/data/Arabidopsis_lyrata_Blastp_longIsoforme
Medicago truncatula,/media/data/sync/Documents/course/master/M2/S1/comparative_genomics/data/Medicago_truncatula.MedtrA17_4.0.pep.all.fa.gz,/media/data/sync/Documents/course/master/M2/S1/comparative_genomics/data/Medicago_truncatula.MedtrA17_4.0.40.gff3.gz,/media/data/sync/Documents/course/master/M2/S1/comparative_genomics/data/Medicago_truncatula_Blastp_longIsoforme
Phaseolus vulgaris,/media/data/sync/Documents/course/master/M2/S1/comparative_genomics/data/Phaseolus_vulgaris.PhaVulg1_0.pep.all.fa.gz,/media/data/sync/Documents/course/master/M2/S1/comparative_genomics/data/Phaseolus_vulgaris.PhaVulg1_0.60.chr.gff3.gz,/media/data/sync/Documents/course/master/M2/S1/comparative_genomics/data/Phaseolus_vulgaris_Blastp_longIsoforme

1 Glycine max /media/data/sync/Documents/course/master/M2/S1/comparative_genomics/data/Glycine_max.Glycine_max_v2.1.pep.all.fa.gz /media/data/sync/Documents/course/master/M2/S1/comparative_genomics/data/Glycine_max.Glycine_max_v2.1.60.chr.gff3.gz /media/data/sync/Documents/course/master/M2/S1/comparative_genomics/data/Glycine_max_Blastp_longIsoforme
9 Vigna angularis /media/data/sync/Documents/course/master/M2/S1/comparative_genomics/data/Vigna_angularis.Vigan1.1.pep.all.fa.gz /media/data/sync/Documents/course/master/M2/S1/comparative_genomics/data/Vigna_angularis.Vigan1.1.60.gff3.gz /media/data/sync/Documents/course/master/M2/S1/comparative_genomics/data/Vigna_angularis_Blastp_longIsoforme
10 Theobroma cacao /media/data/sync/Documents/course/master/M2/S1/comparative_genomics/data/Theobroma_cacao.Theobroma_cacao_20110822.pep.all.fa.gz /media/data/sync/Documents/course/master/M2/S1/comparative_genomics/data/Theobroma_cacao.Theobroma_cacao_20110822.60.gff3.gz /media/data/sync/Documents/course/master/M2/S1/comparative_genomics/data/Theobroma_cacao_Blastp_longIsoforme
11 Arabidopsis lyrata /media/data/sync/Documents/course/master/M2/S1/comparative_genomics/data/Arabidopsis_lyrata.v.1.0.pep.all.fa.gz /media/data/sync/Documents/course/master/M2/S1/comparative_genomics/data/Arabidopsis_lyrata.v.1.0.60.gff3.gz /media/data/sync/Documents/course/master/M2/S1/comparative_genomics/data/Arabidopsis_lyrata_Blastp_longIsoforme
12 Medicago truncatula /media/data/sync/Documents/course/master/M2/S1/comparative_genomics/data/Medicago_truncatula.MedtrA17_4.0.pep.all.fa.gz /media/data/sync/Documents/course/master/M2/S1/comparative_genomics/data/Medicago_truncatula.MedtrA17_4.0.40.gff3.gz /media/data/sync/Documents/course/master/M2/S1/comparative_genomics/data/Medicago_truncatula_Blastp_longIsoforme
13 Phaseolus vulgaris /media/data/sync/Documents/course/master/M2/S1/comparative_genomics/data/Phaseolus_vulgaris.PhaVulg1_0.pep.all.fa.gz /media/data/sync/Documents/course/master/M2/S1/comparative_genomics/data/Phaseolus_vulgaris.PhaVulg1_0.60.chr.gff3.gz /media/data/sync/Documents/course/master/M2/S1/comparative_genomics/data/Phaseolus_vulgaris_Blastp_longIsoforme