Extend the degradation rates and production rates data from Neymotin to all genes, not just regulatory transcription factors

[kdahlquist]

@kdahlquist needs to provide an update to the degradation rates and production rates for all genes in the Neymotin data, not just the regulatory transcription factors.

[kdahlquist]

I found the file with the extended list of degradation rates from Neymotin et al. 2014. I did a QA visual inspection of the data and found the following:

• There is a total of 5380 records.
• 72 records are noncoding RNA as follows:
• systematic_name standard_name
  YNCI0012 ICR1
  YNCM0032C RNA170
  YNCE0007C RPR1
  YNCF0003C RUF20
  YNCA0003W snR18
  YNCM0026C snR24
  YNCK0009W snR38
  YNCG0014C snR39
  YNCG0014C snR39B
  YNCN0001W snR40
  YNCP0015C snR41
  YNCP0015C snR47
  YNCG0026W snR48
  YNCO0007W snR50
  YNCP0013C snR51
  YNCE0020C snR52
  YNCE0003W snR53
  YNCL0042C snR55
  YNCB0003W snR56
  YNCO0003C snR58
  YNCP0003W snR59
  YNCJ0009C snR60
  YNCL0041C snR61
  YNCO0015C snR62
  YNCK0001W snR64
  YNCN0014W snR66
  YNCE0002W snR67
  YNCK0013W snR69
  YNCH0014W snR71
  YNCM0017W snR72
  YNCM0015W snR74
  YNCM0014W snR75
  YNCM0013W snR76
  YNCM0012W snR77
  YNCM0011W snR78
  YNCL0005C snR79
  YNCE0001C snR80
  YNCO0006W snR81
  YNCM0002C snR85
  YNCE0017W SRG1
  YNCD0012W tD(GUC)D
  YNCK0005C tE(UUC)K
  YNCB0002W tF(GAA)B
  YNCF0008C tG(GCC)F2
  YNCP0009W tG(GCC)P1
  YNCG0011W tH(GUG)G2
  YNCG0033W tI(AAU)G
  YNCP0020W tI(AAU)P1
  YNCE0009C tK(CUU)E1
  YNCG0004W tK(UUU)G1
  YNCL0047W tK(UUU)L
  YNCO0016W tK(UUU)O
  YNCD0031C tL(CAA)D
  YNCN0007W tL(CAA)N
  YNCD0008W tL(UAA)D
  YNCL0049C tL(UAA)L
  YNCL0032C tL(UAG)L1
  YNCP0019W tN(GUU)P
  YNCH0013C SUF8
  YNCO0031W tP(UGG)O3
  YNCJ0008W tR(ACG)J
  YNCD0019C tS(AGA)D2
  YNCD0028W tS(AGA)D3
  YNCG0025C tS(AGA)G
  YNCG0046W tT(UGU)G2
  YNCG0018C tV(AAC)G1
  YNCG0002C tV(AAC)G3
  YNCD0022C tV(CAC)D
  YNCH0016C tV(CAC)H
  YNCG0009C tW(CCA)G1
  YNCK0010W tW(CCA)K
  YNCP0001C tW(CCA)P
• They did not have the correct systematic name, so I looked them up at SGD. SUF8 also did not have the correct standard name, so I fixed that, too.
• Changed standard name of DUR1,2 to DUR12; ARG5,6 to ARG56, and ADE5,7 to ADE57 as per the updated standard names for these genes.
• Changed standard name of IMP2' to IMP21
• TOA1 was duplicated in the original data from Neymotin. Values were the same, so deleted one record. Total records are now 5379
• Updated the standard names of many more genes (forgot to record how many, on the order of hundreds) who had been assigned standard names since 2014.

New version of the degradation rates table is found here: https://lmu.box.com/s/yllyj5ds2ndfq6vtf93gh9kcm28egr6f

[kdahlquist]

Production rates table has been updated. We are using 2X degradation rate as the production rate initial guesses, so took the revised degradation rate table with corrected IDs and computed the new production rates. The file can be found here: https://lmu.box.com/s/yllyj5ds2ndfq6vtf93gh9kcm28egr6f

@ntran18, would you please update the Expression database with these two tables? We do not need to keep the old versions of the data, this is a replacement.

[ntran18]

I modified the scripts to update production rates and degradation rates for expression easily. In term of logic, I didn't change anything. I make the code more organize and add command line arguments so we can easily update different tables. I also add a line of code to clear table each time we load a new production rates and degradation rates.

The next step is for @ceciliazaragoza, @MilkaZek, and @Amelie1253 to update it locally with my updated documentation to verify that the code is working for everyone and the documentation is clear for everyone.

PR