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Match first pattern first then extract second pattern match

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# 1  
Old 12-04-2009
Match first pattern first then extract second pattern match
My input file:
Code:
<accession>Q91G55</accession>
<name>043L_IIV6</name>
<protein>
<recommendedName>
<location>
<position position="294"/>
</location>
<fullName>Uncharacterized protein 043L</fullName>

<accession>P18556</accession>
<name>1106L_ASFB7</name>
<protein>
<recommendedName>
<fullName>Protein MGF 110-6L</fullName>

<accession>O55734</accession>
<name>120L_IIV6</name>
<fullName>Uncharacterized protein 120L</fullName>
.
.

My desired output file (extract accession number first, then extract the fullname belong to its):
Code:
<fullName>Uncharacterized protein 043L</fullName>
<fullName>Protein MGF 110-6L</fullName>
<fullName>Uncharacterized protein 120L</fullName>

This is the code I try, but it is not a good code because it will extract some <fullName> detail about other <accession> Smilie

Code:
grep -A8 '<accession>' file | grep '<fullName>'

The original file, each group start with <accession> and end with <fullName>, but the detail description on it, is different within each group.
Actually at first I won't extract all the <accession> from a long list of list. I only want to extract specific <accession> from a long list of data. From those selected <accession> detail, I want extract all of its <fullName>.
Thanks a lot for any suggestion and advice.
Last edited by patrick87; 12-05-2009 at 08:43 PM.. Reason: more code tags
# 2  
Old 12-04-2009
I don't understand what you need. From the description I'd say that your expected output is not correct.

Maybe you are looking for something like this:
Code:
awk '/^<accession/ {print} /^<fullName/ {print}' infile
<accession>Q91G55</accession>
<fullName>Uncharacterized protein 043L</fullName>
<accession>P18556</accession>
<fullName>Protein MGF 110-6L</fullName>
<accession>O55734</accession>
<fullName>Uncharacterized protein 120L</fullName>

If you only want the output you have shown in your example, use a simple grep to get he lines that contain "fullName".

Exact output example of what you need would help. The descriptions are confusing, sorry.
# 3  
Old 12-04-2009
Why don't you grep only for <fullName>:
Code:
grep '<fullName>' file

# 4  
Old 12-05-2009
Quote:
Originally Posted by zaxxon
I don't understand what you need. From the description I'd say that your expected output is not correct.

Maybe you are looking for something like this:
Code:
awk '/^<accession/ {print} /^<fullName/ {print}' infile
<accession>Q91G55</accession>
<fullName>Uncharacterized protein 043L</fullName>
<accession>P18556</accession>
<fullName>Protein MGF 110-6L</fullName>
<accession>O55734</accession>
<fullName>Uncharacterized protein 120L</fullName>

If you only want the output you have shown in your example, use a simple grep to get he lines that contain "fullName".

Exact output example of what you need would help. The descriptions are confusing, sorry.
Hi zaxxon,
sorry that my question let you all confusing Smilie
Actually I won't select all the <accession> from a long list of list. I only want to extract specific <accession> from a long list of data. From those selected <accession> detail, I want extract all of its <fullName>. Hope that you can understand my problem now Smilie
sorry if my problem give you all confusing Smilie

---------- Post updated at 07:42 PM ---------- Previous update was at 07:41 PM ----------

Hi Franklin52,
sorry that my question let you all confusing
Actually at first I won't extract all the <accession> from a long list of list. I only want to extract specific <accession> from a long list of data. From those selected <accession> detail, I want extract all of its <fullName>. Hope that you can understand my problem now Smilie
sorry if my problem give you all confusing Smilie
# 5  
Old 12-06-2009
Debian
patrick87, your sample input file make us confused. So I have to guess.

I change your input file, in number two session, there is no keyword accession. Please confirm, if this is your desired output.

Code:
$ cat input.txt
<accession>Q91G55</accession>
<name>043L_IIV6</name>
<protein>
<recommendedName>
<location>
<position position="294"/>
</location>
<fullName>Uncharacterized protein 043L</fullName>

<name>1106L_ASFB7</name>
<protein>
<recommendedName>
<fullName>Protein MGF 110-6L</fullName>

<accession>O55734</accession>
<name>120L_IIV6</name>
<fullName>Uncharacterized protein 120L</fullName>

$  awk 'BEGIN {RS=""; FS="\n"} /<accession>/ {for (i=1;i<=NF;i++) {if ($i~/<fullName>/) {print $i}}}' input.txt
<fullName>Uncharacterized protein 043L</fullName>
<fullName>Uncharacterized protein 120L</fullName>

# 6  
Old 12-06-2009
Thanks a lot, rdcwayx.
You are right!
Although the code will take some time when deal with huge data, it still worked perfectly Smilie
Thanks a lot for sharing.
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