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3.6 years ago
mdmurphy18
•
0
I am very new to python. I am trying to upload numericalized genotypic files into python to run some simulations. I am trying to read my genotype file of 279 inbred lines with 49335 SNPs, but I am only getting 16000 SNPs, not all of them. Can anybody give me some tips on how to fully read my genotypic file into python? Anything helps!
Here is what my genotype file as a text file looks like.
"ss96500460" "ss196420262" "ss196420260" "ss196501209" "ss196501212" "ss196419561" "ss196503512" "ss196503516" "ss196500466" "ss196522002" "ss196522004" "ss196417490" "ss196418517" "ss196521998" "ss196500468" "ss196500470" "ss196500472" "ss196500474" "ss196500476" "ss196500478" "ss196500480" "ss196500484" "ss196500482" "ss196500486" "ss196500488" "ss196500492" "ss196500494" "ss196500496" "ss196500498" "ss196500500" "ss196500504" "ss196500506" "ss196500508" "ss196500510" "ss196500512" "ss196500514" "ss196500516"
"3316" 2 2 2 2 2 2 2 2 2 0 0 2 2 2 2 2 2 0 2 2 2 2 2 2 0 2 2 2 0 1 2 2 0 2 2 2 0 2 2 2 2 0 2 2 2 2 2 0 2 2 1 2 2 0 2 2 1 2 1 2 2 2 2 2 0 2 1 0 2 2 1 2 0 0 2 1 1 2 2 2 2 2 2 2 0 0 2 2 0 2 0 2 2 0 0 0 0 0 2 0 2 2 0 0 2 2 1 0 0 2 2 1 0 0 1 0 0 1 2 2 1 2 0 2 2 0 0 0 0 2 2 0 2 2 2 1 1 2 1 1 0 0 2 2 0 0 0 0 1 0 2 2 0 2 2 1 2 2 2 2 0 0 0 0 0 0 2 0 2 1 0 0 0 0 0 2 2 2 0 0 2 0 2 2 0 1 2 2 2 2 2 0 2 0 0 2 2 2 2 0 0 2 0 0 2 2 1 0 2 0 2 1 2 0 2 0 2 0 2 2 0 2 2 0 2 1 2 2 2 0 2 2 0 2 2 2 0 2 0 2 1 0 0 1 0 0 0 2 2 2 2 2 2 0 2 1 1 2 0 1 1 2 2 0 2 0 0 0 0 2 0 0 2 1 0 0 2 0 0 0 2 2 2 2 2 0 2 2 2 2 2 0 2 2 0 2 0 2 2 2 0 0 0 0 2 2 2 1 1 0 0 0 0 0 0 0 2 2 0 0 0 0 2 0 0 2 2 0 2 2 0 2 0 2 2 2 2 0 0 2 2 2 0 2 0 2 2 2 2 2 1 0 2 0 2 2 2 2 2 1 0 2 2 0 0 2 2 0 2 2 2 0 2 2 0 0 0 0 2 2 2 2 2 0 0 0 0 2 0 2 2 2 0 0 2 2 0 2 2 2 1 2 2 0 0 2 2 1 2 2 2 2 0 2 0 2 2 1 1 1 1 2 2 0 0 2 0 2 0 2 0 2 1 2 2 0 0 0 1 0 0 0 1 0 0 1 2 2 2 2 2 0 1 2 0 2 0 2 0 2 0 2 2 2 0 1 1 2 2 1 2 2 0 0 2 2 0 0 2 2 2 1 2 2 2 2 0 1 2 2 0 2 0 0 0 1 0 2 0 0 2 1 0 0 2 0 2 2 2
Here is a function that I have been trying to use
genotype = np.loadtxt("Zm55K_geno_4_py.txt")
I ultimately want this as an array, preferably with snps as the columns and inbred lines as the rows (observations).
Cross-posted https://stackoverflow.com/questions/64050460/how-to-read-a-full-genotype-file-into-python-as-an-array
Please post input details and desired output and the code you've used too.
Wooops! That may actually be more helpful. Updated!
Please do not cross post into more forum at the same time. This is considered a bad practice.
What's the input format? TSV? Are you expecting an output with SNPs as header and observations (?) as rows? If so, maybe would be better to load into a Dataframe with Pandas' module read_csv