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Between species alignment #3

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Between species alignment #3

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siebrenf Sep 28, 2021
ea4b9d3
gene_selection tests
siebrenf Oct 6, 2021
130192e
new GPRs
siebrenf Oct 6, 2021
907f91c
gene selection
siebrenf Oct 6, 2021
2aed319
gpr better /w numeric timepoints
siebrenf Oct 7, 2021
e68a2ed
divided new funtion over modules
siebrenf Oct 8, 2021
048056c
new code merged with main.ipynb
siebrenf Oct 11, 2021
9f51eb7
rdy for between species
siebrenf Oct 12, 2021
36a8755
between species looks good!
siebrenf Oct 13, 2021
084666d
moved main.py
siebrenf Oct 13, 2021
09f29d6
moved files
siebrenf Oct 14, 2021
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Binary file added alignments/DR_white_mpf.pdf
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Binary file added alignments/DR_white_mpf_MultiAlignment.pdf
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Binary file added alignments/XT_owensA1_mpf.pdf
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Binary file added alignments/XT_owensA1_mpf_MultiAlignment.pdf
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Binary file added alignments/XT_owensA1_stages.pdf
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Binary file added alignments/cross_species_DR_white_mpf_to_XT_owensA1.pdf
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Binary file added alignments/cross_species_DR_white_mpf_to_XT_owensA1_MultiAlignment.pdf
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522 changes: 522 additions & 0 deletions alignments/cross_species_white_mpf_to_owensA1_mpf_alignment.tsv
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54 changes: 54 additions & 0 deletions alignments/owensA1_mpf_to_owensA1_mpf_alignment.tsv
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Original file line number Diff line number Diff line change
@@ -0,0 +1,54 @@
annotated_time inferred_time samples
240 240.0 ['GSM1606183']
270 264.0 ['GSM1606184']
300 300.0 ['GSM1606185']
330 333.0 ['GSM1606186']
360 357.0 ['GSM1606187']
390 381.0 ['GSM1606188']
420 420.0 ['GSM1606189']
450 444.0 ['GSM1606190']
480 468.0 ['GSM1606191']
510 498.0 ['GSM1606192']
540 531.0 ['GSM1606193']
570 561.0 ['GSM1606194']
600 597.0 ['GSM1606195']
630 630.0 ['GSM1606196']
660 672.0 ['GSM1606197']
690 672.0 ['GSM1606198']
720 732.0 ['GSM1606199']
750 759.0 ['GSM1606200']
780 783.0 ['GSM1606201']
810 792.0 ['GSM1606202']
840 840.0 ['GSM1606203']
870 873.0 ['GSM1606204']
900 915.0 ['GSM1606205']
930 945.0 ['GSM1606206']
960 957.0 ['GSM1606207']
990 981.0 ['GSM1606208']
1020 1044.0 ['GSM1606209']
1050 1059.0 ['GSM1606210']
1080 1080.0 ['GSM1606211']
1110 1086.0 ['GSM1606212']
1140 1131.0 ['GSM1606213']
1170 1182.0 ['GSM1606214']
1200 1236.0 ['GSM1606215']
1230 1242.0 ['GSM1606216']
1260 1242.0 ['GSM1606217']
1290 1242.0 ['GSM1606218']
1320 1350.0 ['GSM1606219']
1350 1350.0 ['GSM1606220']
1380 1359.0 ['GSM1606221']
1410 1359.0 ['GSM1606222']
1440 1437.0 ['GSM1606223']
1500 1572.0 ['GSM1606224']
1560 1572.0 ['GSM1606225']
1620 1572.0 ['GSM1606226']
1680 1680.0 ['GSM1606227']
1740 1680.0 ['GSM1606228']
1800 1908.0 ['GSM1606229']
1860 1908.0 ['GSM1606230']
1920 1908.0 ['GSM1606231']
1980 1956.0 ['GSM1606232']
2040 2052.0 ['GSM1606233']
2100 2112.0 ['GSM1606234']
2160 2112.0 ['GSM1606235']
5 changes: 5 additions & 0 deletions alignments/owensA1_mpf_to_owensA2_mpf_alignment.tsv
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Original file line number Diff line number Diff line change
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annotated_time inferred_time samples
690 666.0 ['GSM1606265']
1290 1227.0 ['GSM1606266']
1800 1968.0 ['GSM1606267']
1980 1974.0 ['GSM1606268']
42 changes: 42 additions & 0 deletions alignments/owensA1_mpf_to_owensB1_mpf_alignment.tsv
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Original file line number Diff line number Diff line change
@@ -0,0 +1,42 @@
annotated_time inferred_time samples
240 240.0 ['GSM1606327']
270 258.0 ['GSM1606328']
300 294.0 ['GSM1606329']
330 324.0 ['GSM1606330']
360 351.0 ['GSM1606331']
390 378.0 ['GSM1606332']
420 399.0 ['GSM1606333']
450 432.0 ['GSM1606334']
480 468.0 ['GSM1606335']
510 504.0 ['GSM1606336']
540 534.0 ['GSM1606337']
570 561.0 ['GSM1606338']
600 588.0 ['GSM1606339']
630 591.0 ['GSM1606340']
660 645.0 ['GSM1606341']
690 678.0 ['GSM1606342']
720 726.0 ['GSM1606343']
750 747.0 ['GSM1606344']
780 747.0 ['GSM1606345']
810 753.0 ['GSM1606346']
840 819.0 ['GSM1606347']
870 843.0 ['GSM1606348']
900 897.0 ['GSM1606349']
930 936.0 ['GSM1606350']
960 954.0 ['GSM1606351']
990 954.0 ['GSM1606352']
1020 996.0 ['GSM1606353']
1050 996.0 ['GSM1606354']
1080 1044.0 ['GSM1606355']
1110 1116.0 ['GSM1606356']
1140 1143.0 ['GSM1606357']
1170 1176.0 ['GSM1606358']
1200 1176.0 ['GSM1606359']
1230 1200.0 ['GSM1606360']
1260 1200.0 ['GSM1606361']
1290 1275.0 ['GSM1606362']
1320 1338.0 ['GSM1606363']
1350 1488.0 ['GSM1606364']
1380 1488.0 ['GSM1606365']
1410 1488.0 ['GSM1606366']
1440 1566.0 ['GSM1606367']
13 changes: 13 additions & 0 deletions alignments/owensA1_mpf_to_tanA_mpf_alignment.tsv
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Original file line number Diff line number Diff line change
@@ -0,0 +1,13 @@
annotated_time inferred_time samples
300 351.0 ['GSM919922']
390 444.0 ['GSM919923']
480 567.0 ['GSM919924', 'GSM919925']
870 873.0 ['GSM919926']
900 918.0 ['GSM919927']
930 984.0 ['GSM919928', 'GSM919929']
960 1170.0 ['GSM919930']
1050 1197.0 ['GSM919931']
1140 1386.0 ['GSM919932']
1620 1536.0 ['GSM919933']
1800 1794.0 ['GSM919934']
1980 2106.0 ['GSM919935']
14 changes: 14 additions & 0 deletions alignments/owensA1_mpf_to_tanB_mpf_alignment.tsv
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Original file line number Diff line number Diff line change
@@ -0,0 +1,14 @@
annotated_time inferred_time samples
240 249.0 ['GSM919943']
300 327.0 ['GSM919944']
390 420.0 ['GSM919945']
480 516.0 ['GSM919946']
720 651.0 ['GSM919947', 'GSM919948']
900 882.0 ['GSM919949']
930 936.0 ['GSM919950']
960 1092.0 ['GSM919951']
1050 1143.0 ['GSM919952']
1140 1287.0 ['GSM919953', 'GSM919954']
1620 1578.0 ['GSM919955']
1800 1968.0 ['GSM919956']
1980 2100.0 ['GSM919957']
107 changes: 107 additions & 0 deletions alignments/white_mpf_to_levin_mpf_alignment.tsv
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Original file line number Diff line number Diff line change
@@ -0,0 +1,107 @@
annotated_time inferred_time samples
40.0 63.0 ['GSM1483736']
80.0 72.0 ['GSM1483737']
120.0 153.0 ['GSM1483738']
160.0 157.5 ['GSM1483739']
200.0 166.5 ['GSM1483740']
240.0 203.94 ['GSM1483741']
280.0 203.94 ['GSM1483742']
320.0 265.32 ['GSM1483743']
360.0 276.36 ['GSM1483744']
400.0 303.96 ['GSM1483745']
440.0 315.0 ['GSM1483746']
480.0 342.0 ['GSM1483747']
520.0 360.0 ['GSM1483748']
560.0 432.0 ['GSM1483749']
600.0 480.0 ['GSM1483750']
640.0 493.98 ['GSM1483751']
680.0 521.94 ['GSM1483752']
720.0 549.9 ['GSM1483753']
760.0 563.88 ['GSM1483754']
800.0 591.84 ['GSM1483755']
840.0 653.82 ['GSM1483756']
880.0 687.84 ['GSM1483757']
920.0 823.92 ['GSM1483758']
960.0 857.94 ['GSM1483759']
1000.0 891.96 ['GSM1483760']
1040.0 960.0 ['GSM1483761']
1080.0 978.0 ['GSM1483762']
1120.0 1050.0 ['GSM1483763']
1160.0 1050.0 ['GSM1483764']
1200.0 1086.0 ['GSM1483765']
1240.0 1170.0 ['GSM1483766']
1280.0 1200.0 ['GSM1483767']
1320.0 1200.0 ['GSM1483768']
1360.0 1260.0 ['GSM1483769']
1400.0 1320.0 ['GSM1483770']
1440.0 1320.0 ['GSM1483771']
1480.0 1320.0 ['GSM1483772']
1520.0 1350.0 ['GSM1483773']
1560.0 1380.0 ['GSM1483774']
1600.0 1440.0 ['GSM1483775']
1640.0 1476.0 ['GSM1483776']
1680.0 1476.0 ['GSM1483777']
1720.0 1512.0 ['GSM1483778']
1760.0 1584.0 ['GSM1483779']
1800.0 1584.0 ['GSM1483780']
1840.0 1620.0 ['GSM1483781']
1880.0 1692.0 ['GSM1483782']
1920.0 1728.0 ['GSM1483783']
1960.0 1800.0 ['GSM1483784']
2000.0 1800.0 ['GSM1483785']
2040.0 1836.0 ['GSM1483786']
2080.0 1836.0 ['GSM1483787']
2120.0 1836.0 ['GSM1483788']
2160.0 1836.0 ['GSM1483789']
2200.0 1872.0 ['GSM1483790']
2240.0 1872.0 ['GSM1483791']
2280.0 1872.0 ['GSM1483792']
2320.0 1908.0 ['GSM1483793']
2360.0 1908.0 ['GSM1483794']
2400.0 1980.0 ['GSM1483795']
2440.0 1980.0 ['GSM1483796']
2480.0 1980.0 ['GSM1483797']
2520.0 1980.0 ['GSM1483798']
2560.0 2016.0 ['GSM1483799']
2600.0 2016.0 ['GSM1483800']
2640.0 2016.0 ['GSM1483801']
2680.0 2232.0 ['GSM1483802']
2720.0 2232.0 ['GSM1483803']
2760.0 2304.0 ['GSM1483804']
2800.0 2304.0 ['GSM1483805']
2840.0 2376.0 ['GSM1483806']
2880.0 2376.0 ['GSM1483807']
2920.0 2376.0 ['GSM1483808']
2960.0 2376.0 ['GSM1483809']
3000.0 2376.0 ['GSM1483810']
3040.0 2376.0 ['GSM1483811']
3080.0 2592.0 ['GSM1483812']
3120.0 2592.0 ['GSM1483813']
3160.0 2592.0 ['GSM1483814']
3200.0 2592.0 ['GSM1483815']
3240.0 2592.0 ['GSM1483816']
3280.0 2592.0 ['GSM1483817']
3320.0 2592.0 ['GSM1483818']
3360.0 2592.0 ['GSM1483819']
3400.0 2808.0 ['GSM1483820']
3440.0 2808.0 ['GSM1483821']
3480.0 2808.0 ['GSM1483822']
3520.0 2808.0 ['GSM1483823']
3560.0 2808.0 ['GSM1483824']
3600.0 2808.0 ['GSM1483825']
3640.0 2808.0 ['GSM1483826']
3680.0 2808.0 ['GSM1483827']
3720.0 2808.0 ['GSM1483828']
3760.0 2808.0 ['GSM1483829']
3800.0 2880.0 ['GSM1483830']
3840.0 3024.0 ['GSM1483831']
3880.0 3024.0 ['GSM1483832']
3920.0 3168.0 ['GSM1483833']
3960.0 3168.0 ['GSM1483834']
4000.0 3168.0 ['GSM1483835']
4040.0 3312.0 ['GSM1483836']
4080.0 3312.0 ['GSM1483837']
4120.0 3312.0 ['GSM1483838']
4160.0 3312.0 ['GSM1483839']
4200.0 3312.0 ['GSM1483840']
4240.0 3312.0 ['GSM1483841']
12 changes: 12 additions & 0 deletions alignments/white_mpf_to_marletaz_mpf_alignment.tsv
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Original file line number Diff line number Diff line change
@@ -0,0 +1,12 @@
annotated_time inferred_time samples
120.0 90.0 ['GSM2837572']
360.0 281.88 ['GSM2837576']
480.0 384.0 ['GSM2837578']
720.0 535.92 ['GSM2837568']
960.0 755.88 ['GSM2837569']
1200.0 1200.0 ['GSM2837570']
1560.0 1350.0 ['GSM2837571']
1800.0 1620.0 ['GSM2837573']
2160.0 1800.0 ['GSM2837574']
2880.0 2736.0 ['GSM2837575']
4320.0 3888.0 ['GSM2837577']
19 changes: 19 additions & 0 deletions alignments/white_mpf_to_white_mpf_alignment.tsv
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Original file line number Diff line number Diff line change
@@ -0,0 +1,19 @@
annotated_time inferred_time samples
0.0 0.0 ['1-cell-1', '1-cell-2', '1-cell-3', '1-cell-4', '1-cell-5']
45.0 45.0 ['2-cell-1', '2-cell-2', '2-cell-3', '2-cell-4', '2-cell-5']
135.0 135.0 ['128-cell-1', '128-cell-2', '128-cell-3', '128-cell-4', '128-cell-5']
180.0 171.0 ['1k-cell-1', '1k-cell-2', '1k-cell-3', '1k-cell-4', '1k-cell-5']
259.8 259.8 ['Dome-1', 'Dome-2', 'Dome-3', 'Dome-4', 'Dome-5']
315.0 319.5 ['50pc-epiboly-1', '50pc-epiboly-2', '50pc-epiboly-3', '50pc-epiboly-4', '50pc-epiboly-5']
360.0 355.5 ['Shield-1', 'Shield-2', 'Shield-3', 'Shield-4', 'Shield-5']
480.0 468.0 ['75pc-epiboly-1', '75pc-epiboly-2', '75pc-epiboly-3', '75pc-epiboly-4', '75pc-epiboly-5']
619.8 653.82 ['1-4-somites-1', '1-4-somites-2', '1-4-somites-3', '1-4-somites-4', '1-4-somites-5']
960.0 960.0 ['14-19-somites-1', '14-19-somites-2', '14-19-somites-3', '14-19-somites-4', '14-19-somites-5']
1140.0 1122.0 ['20-25-somites-1', '20-25-somites-2', '20-25-somites-3', '20-25-somites-4', '20-25-somites-5']
1440.0 1440.0 ['Prim-5-1', 'Prim-5-2', 'Prim-5-3', 'Prim-5-4', 'Prim-5-5']
1800.0 1764.0 ['Prim-15-1', 'Prim-15-2', 'Prim-15-3', 'Prim-15-4', 'Prim-15-5']
2160.0 2160.0 ['Prim-25-1', 'Prim-25-2', 'Prim-25-3', 'Prim-25-4', 'Prim-25-5']
2880.0 2808.0 ['Long-pec-1', 'Long-pec-2', 'Long-pec-3', 'Long-pec-4', 'Long-pec-5']
4320.0 4464.0 ['Protruding-mouth-1', 'Protruding-mouth-2', 'Protruding-mouth-3', 'Protruding-mouth-4', 'Protruding-mouth-5']
5760.0 5760.0 ['Day-4-1', 'Day-4-2', 'Day-4-3', 'Day-4-4', 'Day-4-5']
7200.0 7200.0 ['Day-5-1', 'Day-5-2', 'Day-5-3', 'Day-5-4', 'Day-5-5']
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