I am trying to get the unique values of a column from a tab. The values are repeated and the file has 1,000+ lines, I just want to have the names of the values, not all, and the ones that are repeated. I'm working on my code, but when I do "RUN" it generates the separate and random letters of the values (see example in 'Output' below). I hope someone can help me find my mistake. Please and thank you very much!
Code:
# Open file
file = open('SGD_features.tab')
# Demonstrate the use of a data structure to represent all unique feature types (column 2).
# Iterate for just one iteration
for line in file:
# Get rid of new lines at the end.
line = line.strip()
# File is tab-delimited.
elems = line.split("\t")
features = elems[1]
unique_list = str(set(features))
print(unique_list)
Output:
{'O', 'F', 'R'}
{'S', 'C', 'D'}
{'O', 'F', 'R'}
{'S', 'C', 'D'}
{'S', 'A', 'R'}
{'e', 'l', 'o', 'm', 'r', 't'}
{'e', 'l', 'i', 'p', 'a', 'o', 'm', 'r', '_', 't', 'c'}
{'X', 'e', 'l', 'm', '_', 't', 'n'}
{'X', 'e', 'b', 'l', 'i', 'p', 'a', 'o', 'm', 'r', '_', 't', 'c', 'n'}
{'O', 'F', 'R'}
{'S', 'C', 'D'}
{'O', 'F', 'R'}
{'S', 'C', 'D'}
And so on...
DESIRED OUTPUT:
ORF
CDS
ARS
telomere
telomeric_repeat
X_element
X_element_combinatorial_repeat
EX. FILE
S000036595 noncoding_exon snR18 1 142367 142468 W 2011-02-03 2000-05-19|2007-05-08
S000000002 ORF Verified YAL002W VPS8 CORVET complex membrane-binding subunit VPS8|VPL8|VPT8|FUN15 chromosome 1 L000003013 1 143707 147531 W 2011-02-03 2004-01-14|1996-07-31 Membrane-binding component of the CORVET complex; involved in endosomal vesicle tethering and fusion in the endosome to vacuole protein targeting pathway; interacts with Vps21p; contains RING finger motif
S000031737 CDS YAL002W 1 143707 147531 W 2011-02-03 2004-01-14|1996-07-31
S000121255 ARS ARS108 ARSI-147 chromosome 1 1 147398 147717 2014-11-18 2014-11-18|2007-03-07 Autonomously Replicating Sequence
S000000001 ORF Verified YAL001C TFC3 transcription factor TFIIIC subunit TFC3|tau 138|TSV115|FUN24 chromosome 1 L000000641|L000002287 1 151166 147594 C -1 2011-02-03 1996-07-31 Subunit of RNA polymerase III transcription initiation factor complex; part of the TauB domain of TFIIIC that binds DNA at the BoxB promoter sites of tRNA and similar genes; cooperates with Tfc6p in DNA binding; largest of six subunits of the RNA polymerase III transcription initiation factor complex (TFIIIC)
S000030735 CDS YAL001C 1 151006 147594 C 2011-02-03 1996-07-31
S000030734 CDS YAL001C 1 151166 151097 C 2011-02-03 1996-07-31
S000030736 intron YAL001C 1 151096 151007 C 2011-02-03 1996-07-31
If order doesn't matter, you could do it by creating a set from the items in column 2 of the lines in the file:
with open('SGD_features.tab') as file:
unique_features = set(line.split('\t')[1] for line in file)
for feature in unique_features:
print(feature)