Pipeline throws an error when SAMcollapse.py does not return a tRNA group in group comparison analysis

[SBaindoor]

Hi,

This issue occurs only in group comparison analysis.
I have 3 files for control and 3 files for treatment which I’m running a group comparison analysis on. The SAMcollapse.py file (called in BAM_COLLAPSE module) does not return any matches for one of the files(counterGroup in the results for this file is 0), this results in the values being set to NA in Combined_case_tRNAs-almost-mapped_RPM.depth and throws an error in the DATA_TRANSFORMATIONS module when calculating mean(of the column with NA). Is it possible to handle the absence tRNAgroups in a file without throwing an error?

Thank you

[SBaindoor]

.command.err content:

Traceback (most recent call last):
File "/mnt/raid1/tsRNAsearch/bin/MeanCalculator.py", line 24, in
data = map(float, data)
ValueError: could not convert string to float: NA
Traceback (most recent call last):
File "/mnt/raid1/tsRNAsearch/bin/MeanCalculator.py", line 24, in
data = map(float, data)
ValueError: could not convert string to float: NA
Traceback (most recent call last):
File "/mnt/raid1/tsRNAsearch/bin/Mean-to-RelativeDifference.py", line 23, in
feature, mean1, mean2, std1, std2 = items[0], float(items[2]), float(items[6]), float(items[3]), float(items[7])
IndexError: list index out of range

Combined_T_tRNAs-almost-mapped_RPM.depth file contents, the last column(NA) is from the file that did not have any tRNA groups returned by SAMcollapse.py

[GiantSpaceRobot]

Hi there. I've just made a fix, please download the newest version of the pipeline (or just replace MeanCalculator.py) and try again. NA values are now replaced with zero prior to continuing with the pipeline. Let me know if this fixes the issue, thanks.

[SBaindoor]

Hi,

Thank you for replying so soon.

I updated the MeanCalculator.py and got an error in the FISHERS_METHOD part of the pipeline.

The .command.err contents are :
Warning message:
replacing previous import ‘vctrs::data_frame’ by ‘tibble::data_frame’ when loading ‘dplyr’

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

filter, lag

The following objects are masked from ‘package:base’:

intersect, setdiff, setequal, union

Error in if (mean1 >= 1 || mean2 >= 1) { :
missing value where TRUE/FALSE needed
In addition: Warning message:
In if (mapply.df == "Error") { :
the condition has length > 1 and only the first element will be used
Execution halted

[SBaindoor]

I noticed that in SAMcollapse.py there was a macthing MT gene but it was not returned because in line 61 of the file
if all(tRNAgroup in x for x in database_matches) == True
condition was failing as it was trying to compare MT_TK to chrMT.tRNA18-MT_TK and chrMT.tRNA17-MT_TA (database_matches, for reference only) so I changed the code to only compare the MT_ part.
I changed line 54 and 56 to
tRNAgroup = (v[0].split("\t")[2].split("-")[1].split("_")[0])+"_"
This helped by returning a matched tRNAgroup.

[SBaindoor]

Hi,

Thank you for replying so soon.

I updated the MeanCalculator.py and got an error in the FISHERS_METHOD part of the pipeline.

The .command.err contents are : Warning message: replacing previous import ‘vctrs::data_frame’ by ‘tibble::data_frame’ when loading ‘dplyr’

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

filter, lag

The following objects are masked from ‘package:base’:

intersect, setdiff, setequal, union

Error in if (mean1 >= 1 || mean2 >= 1) { : missing value where TRUE/FALSE needed In addition: Warning message: In if (mapply.df == "Error") { : the condition has length > 1 and only the first element will be used Execution halted

Hi,

Please let me know if you need more information regarding the issue.

Thank you

[GiantSpaceRobot]

Looks like the same problem as before. I'll have to make a fix that corrects the NA values earlier in the pipeline.
Unfortunately I won't be able to fix this in the next few days as I can only update this pipeline in my spare time. I'll get to it as soon as I can though, thanks!

[SBaindoor]

Thank you for replying, no problem at all