pseudogen | automatically generate pseudo-code from source code

I have two files

I have a dataset that shows the human chromosomes with their length (which is here named "value") and their respective genes. Furthermore the genes are divided in 4 groups (gtype) which are RNA, prot-coding, pseudogene and rest. I want to plot the individual chromosomes on the y axis and on the x axis I want to have the density of the chromosomes (which would be "the number of genes per chromosome" divided by the length of the chromosome)with a geom_point,bar or col, then make a facet_wrap based on the gtype of the genes. So 4 plots with one plot only counting RNA genes divided by the value, one plot ony counting the prot-coding genes divided by value.

The plot just divides the total number of all genes by the individual values (it is however normal that chrM would be the biggest)

However I constantly fail at the x axis and I don't know how to get a plot that makes sense. What I have tried so far is a mix of sum(), count(), nrow() and group_by(). Often the x axis is just the total numbers of rows divided by the "value" or the results don't make sense.

Code/Program:

• One of the most used files in Bioinformatics is the fasta file format.
• Fasta files are simple: They contain a "Header" record that starts with a ">", followed by the "Sequence" record, which is everything after the header but before the next record separator (i.e., ">").

I have a large dataset (29 columns by 19000 rows) and I want to be able to compare values on each line and print a descriptive output.

Specifically, I want to query the value in column A (@WTcall) which is effectively a pass/fail statement. If the data fails I want to print the 'fail statement' and move on to the next line, but if the data passes I want to continue describing the data.

The next questions are to determine which classification the data in columns X (@positive) and Y (@negative) fall into:

(Ex:

If column X and column Y >= 0.6 then print "ABC"

If column X and column Y < 0.6 then print "CBA"

If column X >= 0.6 but column Y is < 0.6 print "DEF"

If column X < 0.6 but column Y is >= 0.6 print "FED"

else print "missing data". )

I have included the code that I wrote below as well as a subset of sample data.

The tests I ran before posting are commented out in the code. Briefly, if I comment out the list of 'if and elsif statements', print "@WTcall\t@positive\t@negative\n" and pipe it through a head command - my variables appear to be pulling out the correct information.

The trouble arises in the actual comparisons as every line gets classified with the "Methylated\tMethylated\n" description. It's not clear to me why this is. I know I have entries where the @WTcall column should match $BadPosition (the pass/fail check). Further, if I comment out the 'if statements' again, print "@WTcall\n$BadPosition" and pipe it through sort and uniq - I only get one value for "No_WT_Concensus" and so there should be no typo there or problems matching these values.

I'm sure the issue is obvious and staring me right in the face, so I really appreciate any help.

Thank you.

Code:

I have a data table in tsv format, the content of the file looks like the following.

First post here so I hope I can explain myself at the best.

I need to cross-reference two dataframes by finding if one specific chromosome location given in one of the two dataframes occurs in the range provided by the other one, and as result I would like to have a new column with the gene present in that range.

"genes"is the dataframe with the coordinates (start/end) to be considered as the range