sed to remove all lines in file that are not .vcf.gz extention

I am trying to use sed to remove all lines in a file that are nor vcf.gz . The sed below runs but returns all the files with vcf.gz in them, rather then just the ones that end in only that extention. Thank you :).

file

/output/Home/Auto_user_S5-00580-5-Medexome_66_030/plugin_out/variantCaller_out.40/IonXpress_007/TSVC_variants_IonXpress_007.vcf.gz
/output/Home/Auto_user_S5-00580-5-Medexome_66_030/plugin_out/variantCaller_out.40/IonXpress_007/TSVC_variants_IonXpress_007.vcf.gz.tbi
/output/Home/Auto_user_S5-00580-5-Medexome_66_030/plugin_out/variantCaller_out.40/IonXpress_007/TSVC_variants_IonXpress_007.genome.vcf.gz
/output/Home/Auto_user_S5-00580-5-Medexome_66_030/plugin_out/variantCaller_out.40/IonXpress_007/TSVC_variants_IonXpress_007.genome.vcf.gz.tbi
/output/Home/Auto_user_S5-00580-5-Medexome_66_030/plugin_out/variantCaller_out.40/IonXpress_008/TSVC_variants_IonXpress_008.vcf.gz
/output/Home/Auto_user_S5-00580-5-Medexome_66_030/plugin_out/variantCaller_out.40/IonXpress_008/TSVC_variants_IonXpress_008.vcf.gz.tbi
/output/Home/Auto_user_S5-00580-5-Medexome_66_030/plugin_out/variantCaller_out.40/IonXpress_008/TSVC_variants_IonXpress_008.genome.vcf.gz
/output/Home/Auto_user_S5-00580-5-Medexome_66_030/plugin_out/variantCaller_out.40/IonXpress_008/TSVC_variants_IonXpress_008.genome.vcf.gz.tbi

desired output

/output/Home/Auto_user_S5-00580-5-Medexome_66_030/plugin_out/variantCaller_out.40/IonXpress_007/TSVC_variants_IonXpress_007.vcf.gz
/output/Home/Auto_user_S5-00580-5-Medexome_66_030/plugin_out/variantCaller_out.40/IonXpress_008/TSVC_variants_IonXpress_008.vcf.gz

sed

sed -i '/.vcf.gz/!d' file

sed  '/.vcf.gz$/!d' file
/output/Home/Auto_user_S5-00580-5-Medexome_66_030/plugin_out/variantCaller_out.40/IonXpress_007/TSVC_variants_IonXpress_007.vcf.gz
/output/Home/Auto_user_S5-00580-5-Medexome_66_030/plugin_out/variantCaller_out.40/IonXpress_007/TSVC_variants_IonXpress_007.genome.vcf.gz
/output/Home/Auto_user_S5-00580-5-Medexome_66_030/plugin_out/variantCaller_out.40/IonXpress_008/TSVC_variants_IonXpress_008.vcf.gz
/output/Home/Auto_user_S5-00580-5-Medexome_66_030/plugin_out/variantCaller_out.40/IonXpress_008/TSVC_variants_IonXpress_008.genome.vcf.gz

Again your spec is incorrect, here in the desired output derived from your input.

Hello cmccabe,

The desired output you have shown doesn't look like it needs only those records which have vcf.gz at end, if this is the case then 2 more records are left in your shown output line number 3 and 7. If in case you want to get output as I mentioned then you could try following with sed .

sed -n '/.vcf.gz$/p'   Input_file

Also sed -i option writes output into it's Input_file itself so please beware of using it.

Thanks,
R. Singh

I suppose a sideways thought on this would be "How are you creating the list?"

If it is a find then you could add a bit that says -name "*.cvf.gz" as in:-

find /output/Home -name "*.cvf.gz"

I hope that this helps, or at least doesn't get in the way.

Robin

I can not seem to remove the .genome.vcf.gz from the output. Thank you :).

file

/output/Home/Auto_user_S5-00580-5-Medexome_66_030/plugin_out/variantCaller_out.40/IonXpress_007/TSVC_variants_IonXpress_007.vcf.gz
IonXpress_007
/output/Home/Auto_user_S5-00580-5-Medexome_66_030/plugin_out/variantCaller_out.40/IonXpress_007/TSVC_variants_IonXpress_007.vcf.gz.tbi
IonXpress_007
/output/Home/Auto_user_S5-00580-5-Medexome_66_030/plugin_out/variantCaller_out.40/IonXpress_007/TSVC_variants_IonXpress_007.genome.vcf.gz
/output/Home/Auto_user_S5-00580-5-Medexome_66_030/plugin_out/variantCaller_out.40/IonXpress_008/TSVC_variants_IonXpress_008.vcf.gz
IonXpress_007
/output/Home/Auto_user_S5-00580-5-Medexome_66_030/plugin_out/variantCaller_out.40/IonXpress_008/TSVC_variants_IonXpress_008.vcf.gz.tbi
IonXpress_007
/output/Home/Auto_user_S5-00580-5-Medexome_66_030/plugin_out/variantCaller_out.40/IonXpress_008/TSVC_variants_IonXpress_008.genome.vcf.gz

output

/output/Home/Auto_user_S5-00580-5-Medexome_66_030/plugin_out/variantCaller_out.40/IonXpress_007/TSVC_variants_IonXpress_007.vcf.gz
/output/Home/Auto_user_S5-00580-5-Medexome_66_030/plugin_out/variantCaller_out.40/IonXpress_007/TSVC_variants_IonXpress_007.genome.vcf.gz
/output/Home/Auto_user_S5-00580-5-Medexome_66_030/plugin_out/variantCaller_out.40/IonXpress_008/TSVC_variants_IonXpress_008.vcf.gz
/output/Home/Auto_user_S5-00580-5-Medexome_66_030/plugin_out/variantCaller_out.40/IonXpress_008/TSVC_variants_IonXpress_008.genome.vcf.gz

desired output

/output/Home/Auto_user_S5-00580-5-Medexome_66_030/plugin_out/variantCaller_out.40/IonXpress_007/TSVC_variants_IonXpress_007.vcf.gz
/output/Home/Auto_user_S5-00580-5-Medexome_66_030/plugin_out/variantCaller_out.40/IonXpress_008/TSVC_variants_IonXpress_008.vcf.gz

Hello cmccabe,

If there is always a file which is ending with any digit and then have .vcf.gz eg--> _007.vcf.gz or _008.vcf.gz .
Then following may help in same.

sed -n '/[0-9].vcf.gz$/p'   Input_file

OR

awk '($0 ~ /[0-9].vcf.gz$/)'   Input_file

Thanks,
R. Singh

Please read your post#1 carefully. WHERE did you specify THAT?
Everyone who answered ran in a false direction first!

sed  '/.vcf.gz$/!d;/genome/d' file
/output/Home/Auto_user_S5-00580-5-Medexome_66_030/plugin_out/variantCaller_out.40/IonXpress_007/TSVC_variants_IonXpress_007.vcf.gz
/output/Home/Auto_user_S5-00580-5-Medexome_66_030/plugin_out/variantCaller_out.40/IonXpress_008/TSVC_variants_IonXpress_008.vcf.gz

Yes, either that or, if you want to filter out specifically the files *genome.vcf.gz , then:

sed '/vcf.gz$/!d;/genome.vcf.gz$/d' /path/to/input

I hope this helps.

bakunin

Thank you all :). I apologize for not being more clear in my post and will ensure that I am in the future, thanks again.