I have some large tab separated data sets that have long commented sections, followed by the table header, formatted like this:
##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description="Average mapping quality for each allele present in the genotype">
##FORMAT=<ID=SS,Number=1,Type=Integer,Description="Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown">
##FORMAT=<ID=SSC,Number=1,Type=Integer,Description="Somatic Score">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR
chr1 2985885 . c G . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/0:0/0:202:36,166,0,0:0,202,0,0:255:225:0:36:60:60:0:. 0/1:0/1:321:29,108,37,147:0,137,184,0:228:225:228:36,36:60:60,60:2:225
chr1 3312963 . C T . . . GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC 0/1:0/1:80:36,1,43,0:0,37,0,43:80:195:80:36,31:60:60,60:1:. 0/0:0/0:143:138,5,0,0:0,143,0,0:255:195:255:36:60:60:3:57
Everything that starts with ##
is a comment that needs to be stripped out, but I need to keep the header that starts with #CHROM
. Is there any way to do this? The only options I am seeing for Pandas read_table
allow only a single character for the comment string, and I do not see options for regular expressions.
The code I am using is this:
SS_txt_df = pd.read_table(SS_txt_file,sep='t',comment='#')
This removes all lines that start with #
, including the header I want to keep
EDIT: For clarification, the header region starting with ##
is of variable length. In bash this would simply be grep -Ev '^##'
.
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