I am working on a linux system using python3 with a file in .psl format common to genetics. This is a tab separated file that contains some cells with comma separated values. An small example file with some of the features of a .psl is below.
input.psl
1 2 3 x read1 8,9, 2001,2002,
1 2 3 mt read2 8,9,10 3001,3002,3003
1 2 3 9 read3 8,9,10,11 4001,4002,4003,4004
1 2 3 9 read4 8,9,10,11 4001,4002,4003,4004
I need to filter this file to extract only regions of interest. Here, I extract only rows with a value of 9 in the fourth column.
import csv
def read_psl_transcripts():
psl_transcripts = []
with open("input.psl") as input_psl:
csv_reader = csv.reader(input_psl, delimiter='\t')
for line in input_psl:
#Extract only rows matching chromosome of interest
if '9' == line[3]:
psl_transcripts.append(line)
return psl_transcripts
I then need to be able to print or write these selected lines in a tab delimited format matching the format of the input file with no additional quotes or commas added. I cant seem to get this part right and additional brackets, quotes and commas are always added. Below is an attempt using print().
outF = open("output.psl", "w")
for line in read_psl_transcripts():
print(str(line).strip('"\''), sep='\t')
Any help is much appreciated. Below is the desired output.
1 2 3 9 read3 8,9,10,11 4001,4002,4003,4004
1 2 3 9 read4 8,9,10,11 4001,4002,4003,4004
You might be able to solve you problem with a simple awk statement.
awk '$4 == 9' input.pls > output.pls
But with python you could solve it like this:
write_pls = open("output.pls", "w")
with open("input.pls") as file:
for line in file:
splitted_line = line.split()
if splitted_line[3] == '9':
out_line = '\t'.join(splitted_line)
write_pls.write(out_line + "\n")
write_pls.close()