i trying search file chromosomes want, such chr1.
i parsed file columns want in function get_columns(). when print parsed filed in function works fine. however, when try search word using returned file, seems though giving me first line. assigned variable search_file function , when print out first line of parsed file. how can search chromosome throughout whole file parsed in first function?
#! /usr/bin/python input_file = open( "code_work/genfile.txt", "ru" ) def get_columns (myfile): arow in myfile: no_new = arow.lstrip("\n") split = no_new.split('\t') sec_split = split[8].split(';') new_file = split[0] + "\t" + split[3] + "\t" + split[4] + "\t" + split[6] + "\t" + sec_split[0] + "\t" + sec_split[1] + "\t" + sec_split[2] return new_file search_file = get_columns(input_file) import re original = raw_input('enter word:') print re.findall(r"\b" + re.escape(original) + "[\w]*", search_file) input_file.close()
you have return statement inside for loop. means function returns after first line.
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