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hyphaltip / Mtub.summary_mean_table.tab
Last active December 2, 2019 06:44
running Kallisto
GENE Glycerol_5.7 Glycerol_7 Pyruvate_5.7 Pyruvate_7 Pfam GO
MT_RS00005 106.0542 314.5750 173.0920 237.8235 AAA,Bac_DnaA,Bac_DnaA_C,IstB_IS21 GO:0005524,GO:0006270,GO:0006275,GO:0043565
MT_RS00010 128.9815 243.9095 184.8480 208.7100 DNA_pol3_beta,DNA_pol3_beta_2,DNA_pol3_beta_3 GO:0003677,GO:0003887,GO:0006260,GO:0008408,GO:0009360
MT_RS00015 32.2150 42.6219 42.1174 33.6780 AAA_23,SMC_N
MT_RS00020 77.4342 95.4774 81.4021 79.0631 DciA
MT_RS00025 326.5180 309.6865 318.9515 274.1600 DNA_gyraseB,DNA_gyraseB_C,HATPase_c,Toprim GO:0003677,GO:0003918,GO:0005524,GO:0006265
MT_RS00030 263.7685 271.5500 278.9960 244.5060 DNA_gyraseA_C,DNA_topoisoIV GO:0003677,GO:0003916,GO:0003918,GO:0005524,GO:0006265
MT_RS00035 165.9535 200.4295 213.7435 182.7295 DUF3566
MT_RS00050 0.0000 0.0000 0.0000 0.0000
MT_RS00055 108.4240 188.3470 154.3880 211.6495 CwsA
@hyphaltip
hyphaltip / Duplications.csv
Last active May 6, 2019 21:56
Duplications_plot
We can't make this file beautiful and searchable because it's too large.
Orthogroup,Species Tree Node,Gene Tree Node,Support,,Genes 1,Genes 2
OG0000000,N0,n0,0.5555555555555556,,"Friedmanniomyces_endolithicus_CCFEE_5311_proteins_B0A54_07948, Friedmanniomyces_endolithicus_CCFEE_5311_proteins_B0A54_07877, Friedmanniomyces_simplex_CCFEE_5184_proteins_B0A55_16660, Hortaea_thailandica_CCFEE_6315_proteins_B0A50_06622, Rachicladosporium_antarcticum_CCFEE_5527_proteins_B0A48_18704, Friedmanniomyces_simplex_CCFEE_5184_proteins_B0A55_16414, Friedmanniomyces_simplex_CCFEE_5184_proteins_B0A55_12604, Friedmanniomyces_simplex_CCFEE_5184_proteins_B0A55_09235, Rachicladosporium_antarcticum_CCFEE_5527_proteins_B0A48_00096, Rachicladosporium_antarcticum_CCFEE_5527_proteins_B0A48_01272, Rachicladosporium_monterosium_CCFEE_5018_proteins_B0A51_14967, Rachicladosporium_monterosium_CCFEE_5018_proteins_B0A51_12024, Friedmanniomyces_endolithicus_CCFEE_5311_proteins_B0A54_01557, Friedmanniomyces_endolithicus_CCFEE_5311_proteins_B0A54_07758, Friedmanniomyces_endolithicus_CCFEE_5311_proteins_B0A54_16930","F
@hyphaltip
hyphaltip / data.txt
Last active February 22, 2019 20:40
GriffinEvo_question
2 zlm z2m
1 2
0 2 residual
0.1777 5.08123E-002
5.08123E-002 0.4513
1 2 line
0.8389 -6.64123E-002
-6.64123E-002 0.554
@hyphaltip
hyphaltip / ortho2pattern.py
Last active December 17, 2018 05:44
ortho2pattern
#!/usr/bin/env python3
import csv
input = 'Orthogroups.csv'
outfile = 'phyletic_patterns.txt'
# open report file you will write to
patterns = dict()
with open(input) as csvfile:
# columns with gene info by species are tab delimited
reader = csv.reader(csvfile,delimiter="\t")
@hyphaltip
hyphaltip / tabulate.py
Created December 7, 2017 04:52
tabulate_gene_tree
def tabulate_names(tree):
cladenames={}
for idx, clade in enumerate(tree.find_clades()):
if clade.name:
clade.name = '%d_%s' % (idx, clade.name)
else:
clade.name = str(idx)
cladenames[clade.name] = clade
return cladenames
@hyphaltip
hyphaltip / input.fasta
Last active November 28, 2017 03:21
biopython fasta parser
>tr|E3Q6S8|E3Q6S8_COLGM RNAse P Rpr2/Rpp21/SNM1 subunit domain-containing protein OS=Colletotrichum graminicola (strain M1.001 / M2 / FGSC 10212) GN=GLRG_02386 PE=4 SV=1
MAKPKSESLPNRHAYTRVSYLHQAAAYLATVQSPTSDSTTNSSQPGHAPHAVDHERCLET
NETVARRFVSDIRAVSLKAQIRPSPSLKQMMCKYCDSLLVEGKTCSTTVENASKGGKKPW
ADVMVTKCKTCGNVKRFPVSAPRQKRRPFREQKAVEGQDTTPAVSEMSTGAD
@hyphaltip
hyphaltip / example_long_phobius.out
Created November 17, 2017 01:05
phobius_long
ID CU098_000001
FT DOMAIN 1 361 NON CYTOPLASMIC.
//
ID CU098_000002
FT DOMAIN 1 689 NON CYTOPLASMIC.
//
ID CU098_000003
FT DOMAIN 1 23 CYTOPLASMIC.
FT TRANSMEM 24 45
FT DOMAIN 46 64 NON CYTOPLASMIC.
@hyphaltip
hyphaltip / Proteins.Pfam.domtbl.txt
Last active March 30, 2017 15:36
R.stolonifer MAT(+) locus genes
# --- full sequence --- -------------- this domain ------------- hmm coord ali coord env coord
# target name accession tlen query name accession qlen E-value score bias # of c-Evalue i-Evalue score bias from to from to from to acc description of target
#------------------- ---------- ----- -------------------- ---------- ----- --------- ------ ----- --- --- --------- --------- ------ ----- ----- ----- ----- ----- ----- ----- ---- ---------------------
Pyr_redox_2 PF07992.12 292 G232|G232.mRNA.5875.1 - 463 5.7e-65 219.3 1.6 1 1 2.9e-68 7.9e-65 218.8 1.6 1 292 7 328 7 328 0.92 Pyridine nucleotide-disulphide oxidoreductase
Pyr_redox_dim PF02852.20 110 G232|G232.mRNA.5875.1 - 463 1.3e-30 105.8 0.4 1 1 9.5e-34 2.6e-30 104.8 0.4 1 109 351 461 351 462 0.98 Pyridine nucleotide-disulphid
@hyphaltip
hyphaltip / keybase.md
Last active February 15, 2017 21:19
keybase.md

Keybase proof

I hereby claim:

  • I am hyphaltip on github.
  • I am jstajich (https://keybase.io/jstajich) on keybase.
  • I have a public key ASC8-VwcAtZtsxNJYK_KCTCyAt6_D_OGci0hEmYNVpgMSAo

To claim this, I am signing this object:

@hyphaltip
hyphaltip / Bifiguratus_TEF1_hits.FASTA.out
Created January 17, 2017 22:13
Bifiguratus EF1
# fasta36 -E 1e-10 Sacch_TEF1.fa ../pep/Bifiguratus_adelaidae_AZ0501.all.maker.proteins.aa.fasta
FASTA searches a protein or DNA sequence data bank
version 36.3.7a Jan, 2015(preload9)
Please cite:
W.R. Pearson & D.J. Lipman PNAS (1988) 85:2444-2448
Query: Sacch_TEF1.fa
1>>>TEF1 YPR080W SGDID:S000006284 - 459 aa
Library: ../pep/Bifiguratus_adelaidae_AZ0501.all.maker.proteins.aa.fasta
3229420 residues in 6120 sequences