Question: Getting the targets from a dat file
0
gravatar for ailtonpcf
13 days ago by
ailtonpcf0
Federal University of Uberlandia, Patos de Minas, Brazil
ailtonpcf0 wrote:

I used miranda and RNAhybrid to find miRNAs in a miRNA-seq. My database was the 3'UTR from Homo sapiens hosted in the UTRDB. In the end I have a csv file with the ID of thousands of targets. So, how I can get the genes targets from a dat file usind the csv file as input? Summarizing, I want to provide the 'ID' and get back the 'DE'.

ID   3HSAA000001; SV 1; linear; mRNA; STD; HUM; 216 BP.
XX
AC   CA000001;
XX
DT   01-JUL-2009 (Rel. 1, Created)
DT   01-JUL-2009 (Rel. 1, Last updated, Version 1)
XX
DE   3'UTR in Homo sapiens alpha-1-B glycoprotein (A1BG), mRNA.
XX
DR   ASPicDB; b7e045ed97;
DR   UTRaspic; BA000001;
DR   GeneID; 1;
XX
OS   Homo sapiens (human)
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC   Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC   Homo.
XX
UT   3'UTR; Complete; 1 exon(s)
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..216
FT                   /organism="Homo sapiens"
FT                   /mol_type="mRNA"
FT                   /db_xref="taxon:9606"
FT                   /db_xref="RefSeq:NM_130786"
FT   3'UTR           1..216
FT                   /source="ASPicDB::b7e045ed97:1551..1766"
FT                   /gene="A1BG"
R perl python dat utrdb • 106 views
ADD COMMENTlink modified 12 days ago by finswimmer6.2k • written 13 days ago by ailtonpcf0
0
gravatar for finswimmer
12 days ago by
finswimmer6.2k
Germany
finswimmer6.2k wrote:

Hello ailtonpcf ,

how should your output look like? Here is a way using grep. It will print out the line with ID followed by the line with DE

ids.txt looks like this:

3HSAA000001
3HSAA000002
3HSAA000003

The command to use:

$ grep -E "^ID|^DE" 3UTRaspic.Hum.dat|grep -A1 -f ids.txt
ID   3HSAA000001; SV 1; linear; mRNA; STD; HUM; 216 BP.
DE   3'UTR in Homo sapiens alpha-1-B glycoprotein (A1BG), mRNA.
ID   3HSAA000002; SV 1; linear; mRNA; STD; HUM; 1844 BP.
DE   3'UTR in Homo sapiens alpha-1-B glycoprotein (A1BG), mRNA.
ID   3HSAA000003; SV 1; linear; mRNA; STD; HUM; 172 BP.
DE   3'UTR in Homo sapiens alpha-1-B glycoprotein (A1BG), mRNA

fin swimmer

ADD COMMENTlink written 12 days ago by finswimmer6.2k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1830 users visited in the last hour