The synolog_info.py is designed to parse through the species cache and/or the results of a Synolog analysis for specific features. As such, there are different types of options one can implement
Although some of the arguments are shared between the different options, no two options share the exact same set of flags
Options for geneBelow are a couple of examples depicting the different pieces of information obtainable across the different modes
# get information regarding a specific gene % synolog_info.py gene --path ./path/to/synolog/output_files/ \ --id org_id \ --gene_id gene_id \ --cache ./path/to/species/cache/
Here is an example from Turtles test case from the Synolog manuscript
# get the information for CD207 from the red-eared slider % synolog_info.py gene --path ./turtle_synolog_analysis/ \ --id Tscr.def.def \ --gene_id CD207 \ --cache ./species_cache/ Reading annotations.. Reading hit files.. Reading ortholog information.. Reading tree cluster information.. Ortholog and Synteny Information for Tscr.def.def CD207 Location: NC_048302.1: 138075670 - 138085319 / Gene index: 962 Isoforms found for CD207: XM_034772556.1, XP_034628447.1 Top <= 5 hits for hits files Comparison: Agig.def.pnc --> Tscr.def.def Isform: XP_034628447.1 qseqid sseqid pident length mismatchgapopen qstart qend sstart send evalue bitscore g18758.t1 XP_034628447.1 84.831 178 25 1 58 233 130 307 2.58e-107 312.0 g157.t1 XP_034628447.1 28.378 148 86 4 147 287 122 256 8.57e-08 53.9 g111.t1 XP_034628447.1 33.333 99 58 5 91 184 209 304 1.24e-07 51.6 g113.t1 XP_034628447.1 34.783 69 38 2 30 98 175 236 6.10e-06 44.3 g867.t1 XP_034628447.1 37.500 48 30 0 109 156 165 212 1.99e-05 44.3 Comparison: Cmyd.def.def --> Tscr.def.def Isform: XP_034628447.1 qseqid sseqid pident length mismatchgapopen qstart qend sstart send evalue bitscore XP_037754370.1 XP_034628447.1 60.251 239 56 3 36 272 106 307 1.54e-90 271.0 XP_007053807.2 XP_034628447.1 37.324 142 81 4 193 327 160 300 4.83e-19 87.0 XP_007061946.2 XP_034628447.1 31.788 151 95 4 359 504 154 301 1.59e-12 71.2 XP_007061946.2 XP_034628447.1 28.082 146 91 4 810 950 164 300 3.76e-08 57.8 XP_007061946.2 XP_034628447.1 26.126 222 124 9 603 811 109 303 2.68e-06 52.0 Comparison: Gfla.def.def --> Tscr.def.def Isform: XP_034628447.1 qseqid sseqid pident length mismatchgapopen qstart qend sstart send evalue bitscore XP_050799400.1 XP_034628447.1 62.712 236 35 4 53 286 123 307 6.68e-90 270.0 XP_050780810.1 XP_034628447.1 37.500 128 72 3 84 205 176 301 6.44e-24 97.1 XP_050778994.1 XP_034628447.1 44.444 63 32 1 1 60 65 127 2.22e-10 60.5 XP_050775509.1 XP_034628447.1 32.759 116 73 3 69 180 133 247 2.24e-10 59.3 XP_050777474.1 XP_034628447.1 28.261 138 70 7 23 154 185 299 3.96e-05 45.8 Comparison: Mter.def.def --> Tscr.def.def Isform: XP_034628447.1 qseqid sseqid pident length mismatchgapopen qstart qend sstart send evalue bitscore XP_053886306.1 XP_034628447.1 74.312 218 21 2 53 268 123 307 2.27e-108 316.0 XP_053861594.1 XP_034628447.1 33.065 124 82 1 1463 1585 1 124 2.09e-16 83.6 XP_053861594.1 XP_034628447.1 33.065 124 82 1 52 174 1 124 2.09e-16 83.6 XP_053861853.1 XP_034628447.1 29.143 175 106 7 37 205 137 299 1.16e-09 57.8 XP_053861753.1 XP_034628447.1 27.536 138 71 7 45 176 185 299 2.65e-04 43.5 Comparison: Tscr.def.def --> Agig.def.pnc Isform: XP_034628447.1 qseqid sseqid pident length mismatchgapopen qstart qend sstart send evalue bitscore XP_034628447.1 g18758.t1 84.831 178 25 1 130 307 58 233 7.18e-107 310.0 XP_034628447.1 g18752.t1 65.929 226 27 3 130 307 58 281 1.25e-95 283.0 XP_034628447.1 g18759.t1 62.882 229 34 3 130 307 58 286 2.80e-89 268.0 XP_034628447.1 g18761.t1 60.088 228 41 2 130 307 45 272 8.21e-85 256.0 XP_034628447.1 g18757.t1 70.455 176 46 2 136 307 125 298 4.04e-84 255.0 Comparison: Tscr.def.def --> Cmyd.def.def Isform: XP_034628447.1 qseqid sseqid pident length mismatchgapopen qstart qend sstart send evalue bitscore XP_034628447.1 XP_037754370.1 64.414 222 40 3 123 307 53 272 6.30e-89 268.0 XP_034628447.1 XP_043400921.1 65.403 211 36 2 134 307 59 269 5.59e-87 263.0 XP_034628447.1 XP_043400917.1 60.593 236 40 3 123 307 53 286 7.90e-87 263.0 XP_034628447.1 XP_043400920.1 62.613 222 42 3 123 307 12 229 1.95e-86 260.0 XP_034628447.1 XP_037754381.1 63.514 222 38 4 123 307 54 269 1.14e-85 259.0 Comparison: Tscr.def.def --> Gfla.def.def Isform: XP_034628447.1 qseqid sseqid pident length mismatchgapopen qstart qend sstart send evalue bitscore XP_034628447.1 XP_050799400.1 65.502 229 28 2 130 307 58 286 1.68e-94 282.0 XP_034628447.1 XP_050799399.1 61.135 229 38 2 130 307 58 286 2.06e-86 261.0 XP_034628447.1 XP_050799397.1 61.572 229 37 2 130 307 58 286 2.92e-86 261.0 XP_034628447.1 XP_050799406.1 60.526 228 40 2 130 307 58 285 1.38e-85 259.0 XP_034628447.1 XP_050799391.1 60.000 225 39 2 130 303 58 282 1.45e-84 256.0 Comparison: Tscr.def.def --> Mter.def.def Isform: XP_034628447.1 qseqid sseqid pident length mismatchgapopen qstart qend sstart send evalue bitscore XP_034628447.1 XP_053886306.1 75.355 211 19 1 130 307 58 268 3.72e-107 313.0 XP_034628447.1 XP_053886636.1 73.529 170 41 1 142 307 70 239 1.10e-85 258.0 XP_034628447.1 XP_053886635.1 64.286 196 40 2 142 307 70 265 1.46e-80 246.0 XP_034628447.1 XP_053886637.1 62.136 206 48 2 132 307 25 230 1.65e-80 244.0 XP_034628447.1 XP_053885618.1 65.000 120 9 1 132 218 21 140 2.81e-40 139.0 Homolog information for Tscr.def.def CD207 Found 4 out of 4 comparisons Gfla.def.def: LOC127046423 Agig.def.pnc: g18754 Cmyd.def.def: LOC119566158 Mter.def.def: LOC128838464 Tscr.def.def CD207 was found to have 0 tandem duplicates and 0 retrocopies and is a member of orthogroup 1714 containing 28 members 1714 gene 28 5 Agig.def.pnc g18751 E 16 HiC_scaffold_5 145172770 145188088 1714 gene 28 5 Agig.def.pnc g18752 D 0 HiC_scaffold_5 145225747 145239522 1714 gene 28 5 Agig.def.pnc g18753 D 0 HiC_scaffold_5 145257595 145283386 1714 gene 28 5 Agig.def.pnc g18754 D 0 HiC_scaffold_5 145299377 145309687 1714 gene 28 5 Agig.def.pnc g18755 D 0 HiC_scaffold_5 145349780 145359097 1714 gene 28 5 Agig.def.pnc g18756 D 0 HiC_scaffold_5 145386114 145421675 1714 gene 28 5 Agig.def.pnc g18757 D 0 HiC_scaffold_5 145487865 145503537 1714 gene 28 5 Agig.def.pnc g18758 D 0 HiC_scaffold_5 145541215 145554966 1714 gene 28 5 Agig.def.pnc g18759 D 0 HiC_scaffold_5 145573016 145597104 1714 gene 28 5 Agig.def.pnc g18760 D 0 HiC_scaffold_5 145613079 145630529 1714 gene 28 5 Agig.def.pnc g18761 D 0 HiC_scaffold_5 145708511 145722273 1714 gene 28 5 Agig.def.pnc g18762 D 0 HiC_scaffold_5 145745341 145748403 1714 gene 28 5 Agig.def.pnc g18763 D 0 HiC_scaffold_5 145769598 145776955 1714 gene 28 5 Agig.def.pnc g18764 D 0 HiC_scaffold_5 145798162 145812518 1714 gene 28 5 Agig.def.pnc g18765 D 0 HiC_scaffold_5 145845279 145860997 1714 gene 28 5 Agig.def.pnc g18766 D 0 HiC_scaffold_5 145874303 145886286 1714 gene 28 5 Agig.def.pnc g18768 D 0 HiC_scaffold_5 145919776 145931586 1714 gene 28 5 Cmyd.def.def LOC119566158 LOC119566158 B 3 NC_057852.1 139853273 139869673 1714 gene 28 5 Cmyd.def.def LOC114022419 LOC114022419 D 0 NC_057852.1 139904366 139921595 1714 gene 28 5 Cmyd.def.def LOC119566160 LOC119566160 D 0 NC_057852.1 139938181 139956158 1714 gene 28 5 Cmyd.def.def LOC119566159 LOC119566159 D 0 NC_057852.1 139979797 139995874 1714 gene 28 5 Gfla.def.def LOC127046423 LOC127046423 C 2 NC_066619.1 285987351 286155074 1714 gene 28 5 Gfla.def.def LOC127046421 LOC127046421 D 0 NC_066619.1 286091323 286371703 1714 gene 28 5 Gfla.def.def LOC127046424 LOC127046424 D 0 NC_066619.1 286183319 286317440 1714 gene 28 5 Mter.def.def LOC128838464 LOC128838464 C 2 NC_071509.1 2378989 2395629 1714 gene 28 5 Mter.def.def LOC128837941 LOC128837941 D 0 NC_071509.1 2410491 2425373 1714 gene 28 5 Mter.def.def CD207 CD207 D 0 NC_071509.1 2488109 2509489 1714 gene 28 5 Tscr.def.def CD207 CD207 C 0 NC_048302.1 138075670 138085319 Conserved Synteny Cluster membership per species Comparison: Tscr.def.def --> Agig.def.pnc 373 613 100 forward Agig.def.pnc HiC_scaffold_5 15 1147 975865 148554578 Tscr.def.def NC_048302.1 15 996 1703261 140332721 373 gene Agig.def.pnc Tscr.def.def g18754 HiC_scaffold_5 1082 145299377 145309687 CD207 CD207 NC_048302.1 962 138075670 138085319 373 gene Agig.def.pnc Tscr.def.def g18757 HiC_scaffold_5 1085 145487865 145503537 CD207 CD207 NC_048302.1 962 138075670 138085319 373 gene Agig.def.pnc Tscr.def.def g18758 HiC_scaffold_5 1086 145541215 145554966 CD207 CD207 NC_048302.1 962 138075670 138085319 373 gene Agig.def.pnc Tscr.def.def g18761 HiC_scaffold_5 1089 145708511 145722273 CD207 CD207 NC_048302.1 962 138075670 138085319 373 gene Agig.def.pnc Tscr.def.def g18766 HiC_scaffold_5 1094 145874303 145886286 CD207 CD207 NC_048302.1 962 138075670 138085319 373 gene Agig.def.pnc Tscr.def.def g18751 HiC_scaffold_5 1079 145172770 145188088 CD207 CD207 NC_048302.1 962 138075670 138085319 373 gene Agig.def.pnc Tscr.def.def g18752 HiC_scaffold_5 1080 145225747 145239522 CD207 CD207 NC_048302.1 962 138075670 138085319 373 gene Agig.def.pnc Tscr.def.def g18753 HiC_scaffold_5 1081 145257595 145283386 CD207 CD207 NC_048302.1 962 138075670 138085319 373 gene Agig.def.pnc Tscr.def.def g18755 HiC_scaffold_5 1083 145349780 145359097 CD207 CD207 NC_048302.1 962 138075670 138085319 373 gene Agig.def.pnc Tscr.def.def g18756 HiC_scaffold_5 1084 145386114 145421675 CD207 CD207 NC_048302.1 962 138075670 138085319 373 gene Agig.def.pnc Tscr.def.def g18759 HiC_scaffold_5 1087 145573016 145597104 CD207 CD207 NC_048302.1 962 138075670 138085319 373 gene Agig.def.pnc Tscr.def.def g18760 HiC_scaffold_5 1088 145613079 145630529 CD207 CD207 NC_048302.1 962 138075670 138085319 373 gene Agig.def.pnc Tscr.def.def g18762 HiC_scaffold_5 1090 145745341 145748403 CD207 CD207 NC_048302.1 962 138075670 138085319 373 gene Agig.def.pnc Tscr.def.def g18763 HiC_scaffold_5 1091 145769598 145776955 CD207 CD207 NC_048302.1 962 138075670 138085319 373 gene Agig.def.pnc Tscr.def.def g18764 HiC_scaffold_5 1092 145798162 145812518 CD207 CD207 NC_048302.1 962 138075670 138085319 373 gene Agig.def.pnc Tscr.def.def g18765 HiC_scaffold_5 1093 145845279 145860997 CD207 CD207 NC_048302.1 962 138075670 138085319 373 gene Agig.def.pnc Tscr.def.def g18768 HiC_scaffold_5 1096 145919776 145931586 CD207 CD207 NC_048302.1 962 138075670 138085319 Comparison: Tscr.def.def --> Gfla.def.def 69 712 100 forward Gfla.def.def NC_066619.1 1035 2188 137494885 288959762 Tscr.def.def NC_048302.1 15 996 1703261 140332721 69 gene Gfla.def.def Tscr.def.def LOC127046423 LOC127046423 NC_066619.1 2133 285987351 286155074 CD207 CD207 NC_048302.1 962 138075670 138085319 69 gene Gfla.def.def Tscr.def.def LOC127046421 LOC127046421 NC_066619.1 2135 286091323 286371703 CD207 CD207 NC_048302.1 962 138075670 138085319 69 gene Gfla.def.def Tscr.def.def LOC127046424 LOC127046424 NC_066619.1 2137 286183319 286317440 CD207 CD207 NC_048302.1 962 138075670 138085319 Comparison: Tscr.def.def --> Mter.def.def 219 543 100 inverse Mter.def.def NC_071509.1 1 698 9828 98279334 Tscr.def.def NC_048302.1 346 988 49004633 139473122 219 gene Mter.def.def Tscr.def.def LOC128838464 LOC128838464 NC_071509.1 47 2378989 2395629 CD207 CD207 NC_048302.1 962 138075670 138085319 219 gene Mter.def.def Tscr.def.def LOC128837941 LOC128837941 NC_071509.1 49 2410491 2425373 CD207 CD207 NC_048302.1 962 138075670 138085319 219 gene Mter.def.def Tscr.def.def CD207 CD207 NC_071509.1 50 2488109 2509489 CD207 CD207 NC_048302.1 962 138075670 138085319 Comparison: Tscr.def.def --> Cmyd.def.def 268 719 100 forward Tscr.def.def NC_048302.1 1 996 89525 140332721 Cmyd.def.def NC_057852.1 100 1450 4046356 142302462 268 gene Tscr.def.def Cmyd.def.def CD207 CD207 NC_048302.1 962 138075670 138085319 LOC119566158 LOC119566158 NC_057852.1 1394 139853273 139869673 268 gene Tscr.def.def Cmyd.def.def CD207 CD207 NC_048302.1 962 138075670 138085319 LOC114022419 LOC114022419 NC_057852.1 1396 139904366 139921595 268 gene Tscr.def.def Cmyd.def.def CD207 CD207 NC_048302.1 962 138075670 138085319 LOC119566159 LOC119566159 NC_057852.1 1401 139979797 139995874 268 gene Tscr.def.def Cmyd.def.def CD207 CD207 NC_048302.1 962 138075670 138085319 LOC119566160 LOC119566160 NC_057852.1 1399 139938181 139956158 Tree Cluster Membership Entry CD207 Tree Cluster ID: 504 #TreeClusterID NumElements OrgCount Org Chrom GeneType GeneID GeneName Index StartBP EndBP SyntenyClusterIDs 504 300 4 Tscr.def.def NC_048302.1 gene CD207 CD207 962 138075670 138085319 Agig.def.pnc (g18754), Gfla.def.def (LOC127046423), Mter.def.def (CD207) synolog_info.py is done.
# get information regarding a specific org % synolog_info.py org --path ./path/to/synolog/output_files/ \ --id org_id
# get all orthogroups where org_a and org_b have a local expansion % synolog_info.py orthogroup --path ./path/to/synolog/output_files/ \ --expansions org_a,org_b
# get all orthogroups only org_a, org_b, and org_c are present % synolog_info.py orthogroup --path ./path/to/synolog/output_files/ \ --orgs org_a,org_b,org_c \ --restrict
Core |
Species Cache |
Execution control |
Utility programs |