How to split the header line into its components

Question

[Inayat]

I have txt file containing several of these header lines

>lcl|NC_001133.9_cds_NP_009332.1_1 [gene=PAU8] [locus_tag=YAL068C] [db_xref=SGD:S000002142,GeneID:851229] [protein=seripauperin PAU8] [protein_id=NP_009332.1] [location=complement(1807..2169)] [gbkey=CDS]

I want to read specific values 1807 and 2169 mentioned in "location". I have tried to use split() and strip command in python but it doesn't work as expected. Can you please suggest the way how to do this? Any kind of help will be appreciated.

Thank you

Answer 1

[5heikki]

awk 'BEGIN{FS="\\[location="}{print $2}' input.txt | awk 'BEGIN{FS="("}{print $2}' | awk 'BEGIN{FS=")"}{print $1}'

Answer 2

[cpad0112]

$awk -v OFS="\t" -F "=|\(|\..|\)" '/^>/ {print $11,$12}' test.fa                                                                                                                        
1807    2169

$ awk -v OFS="\t" -F "complement|\(|\..|\)" ' /^>/ {print $6,$7}' test.fa

input:

$ cat test.fa                                                                                                                                                                        
>lcl|NC_001133.9_cds_NP_009332.1_1 [gene=PAU8] [locus_tag=YAL068C] [db_xref=SGD:S000002142,GeneID:851229] [protein=seripauperin PAU8] [protein_id=NP_009332.1] [location=complement(1807..2169)] [gbkey=CDS]

[cpad0112]

$ grep -Po '(?<=complement\().*(?=\)\])' test.fa | sed 's/\../\t/'                   
1807    2169

Answer 3

[ATpoint]

echo ">lcl|NC_001133.9_cds_NP_009332.1_1 [gene=PAU8] [locus_tag=YAL068C] [db_xref=SGD:S000002142,GeneID:851229] [protein=seripauperin PAU8] [protein_id=NP_009332.1] [location=complement(1807..2169)] [gbkey=CDS]" \
| awk -F "location=" '{print $2}' | \
| cut -d "(" -f2 | cut -d ")" -f1 \
| awk -F "." 'OFS="\t" {print $1, $3}'