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Multiple results as input to grep or awk

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# 1  
Old 11-20-2013
Multiple results as input to grep or awk
Hi:
This is my first post in this forum. apologies if I am asking question that has been asked here multiple times.


I wrote a python script that prints list of identifiers. I have another file notoriously big and with no particular format.

I plan to search the identifiers in this file and print line that contains that pattern and next line.

Code:
$ python get_IDs.py | sort
TCONS_00142932
TCONS_00142933
TCONS_00142934
TCONS_00142935

I want to search these 4 patterns in another file MYBIGFILE.pep and print line that has this TCONS_00142932 and following line.


I am currently doing one by one...

Code:
$ cat transcripts.fasta.transdecoder.pep | grep -A1 'TCONS_00142932'
>cds.TCONS_00142932
MIINWNQVSVLWKCLLKQSASYQDRRQSWRRASMKETNRRKSLHPIHQGITELSRSISVD

How can I automate this using either awk or grep through piping..


something like:

Code:
$ python get_IDs.py | sort | grep -A1 'PAT$1'...

>cds.TCONS_00142932
MIINWNQVSVLWKCLLKQSASYQDRRQSWRRASMKETNRRKSLHPIHQGITELSRSISVD
>cds.TCONS_00142933
KYRSNNWNQVSVLQSASYQDRRQSWRRASMKETNRRKSLHPIHQGITELSRSISVD
>cds.TCONS_00142934
MTSVTRSEIIDEKGPVMSKTHDHQLESSLSPVEVFAKTSASLEMNQGVSEERIHLGSSPK
....

Thanks.
Adrian
Moderator's Comments:
Mod Comment Please use code tags
Last edited by jim mcnamara; 11-20-2013 at 07:14 PM..
# 2  
Old 11-20-2013
If you shorten your previous grep to
Code:
grep -A1 'TCONS_00142932' transcripts.fasta.transdecoder.pep

you have freed the stdin, and can use it for the other input:
Code:
python get_IDs.py | sort | grep -A1 -f - transcripts.fasta.transdecoder.pep

P.S. please wrap your code in [code] tags!
# 3  
Old 11-20-2013
Hi,
You can try:
Code:
grep -A1 -f <(python get_IDs.py | sort | grep -v '^$') bigfile.pep

Regards.
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