Apologies, this is my first post. I thought it would be easier to explain with an ammended file but I've learnt this confuses things. My file 2 looks like this.
If I
this prints out the "MSTRG###"; string that I want to match to (I don't want to match the string from gene_id.
Last edited by Don Cragun; 05-10-2017 at 11:59 PM..
Reason: Add ICODE tags.
I am trying to match a pattern exactly in a shell script. I have tried two methods
awk '/\<mpath${CURR_MP}\>/{print $1 $2}' multipath
perl -ne '/\bmpath${CURR_MP}\b/ and print' /var/tmp/multipath
Both these methods require that I use the escape character. I am guessing that is why... (8 Replies)
Hi folks,
I have a text file that I need to parse, and I cant figure it out. The source is a report breaking down softwares from various companies with some basic info about them (see source snippet below). Ultimately what I want is an excel sheet with only Adobe and Microsoft software name and... (5 Replies)
Hi All,
Does anyone know how to print 1H1A....... in peal script
print line ^1H1A....... if next line equal 5R0RECEIPT....
Thank for help:D
Cat st.txt
1H1A-IN-11-5410-0009420|1010047766|dsds|1|N|IN|IN|000000|1||N|<<<line match
5R0RECEIPT|
5R0RECEIPT|... (2 Replies)
Hi all,
I'm trying to do some work on the authorized_keys file to do a check if there's any information after the hash key.. At the end of the hash key's in the file, there can be an = or ==
Is there a way to check if anything exists after these equals and if so print it out or else print... (2 Replies)
Hello,
I need an awk command to print only the lines that match regex on xth field from file.
For example if I use this command
awk -F"|" ' $22 == "20130117090000.*" 'It wont work, I think, because single quotes wont allow the usage of the metacharacter star * . On the other hand I dont know... (2 Replies)
Hi,
I have the logs :
cat logsx.txt
744906,{"reportingGroups":,"version":"2.0"}
678874,{"reportingGroups":,"version":"2.0"}
193571,{"reportingGroups":,"version":"2.0"}
811537,{"reportingGroups":,"version":"2.0"}
772024,{"reportingGroups":,"version":"2.0"}... (5 Replies)
I need to fetch particular string from log file based on grep condition match.
Actual requirement is need to print the next word from the same line based on grep string condtion match.
File :Java.lanag.xyz......File copied completed : abc.txt
Ouput :abc.txt
I have used below... (5 Replies)
Hello,
one step in a shell script i am writing, involves Grep command to search a regular expression in a line an only print the string after the match
an example line is below
/logs/GRAS/LGT/applogs/lgt-2016-08-24/2016-08-24.8.log.zip:2016-08-24 19:12:48,602 ERROR... (9 Replies)
Hi,
I have some data like below:
John 254
Chris 254
Matt 123
Abe 123
Raj 487
Moh 487
How can i print it using awk to have:
254 John,Chris
123 Matt,Abe
487 Raj,Moh
Thanks. (4 Replies)
Dear team,
Need support to built awk script for below requirement
Input file
LOTC cluster state:
-------------------
Node safNode=SC_2_1 joined cluster |
Node safNode=SC_2_2 joined cluster |
Node safNode=PL_2_3 fail cluster |
AMF cluster state:
------------------... (16 Replies)
Discussion started by: shanul karim
16 Replies
LEARN ABOUT DEBIAN
bp_unflatten_seq
BP_UNFLATTEN_SEQ(1p) User Contributed Perl Documentation BP_UNFLATTEN_SEQ(1p)NAME
unflatten_seq - unflatten a genbank or genbank-style feature file into a nested SeqFeature hierarchy
SYNOPSIS
unflatten_seq.PLS -e 3 -gff ~/cvs/bioperl-live/t/data/AE003644_Adh-genomic.gb
unflatten_seq.PLS --detail ~/cvs/bioperl-live/t/data/AE003644_Adh-genomic.gb
unflatten_seq.PLS -i foo.embl --from embl --to chadoxml -o out.chado.xml
unflatten_seq.PLS --notypemap --detail --to asciitree -ethresh 2 AE003644_Adh-genomic.gb
DESCRIPTION
This script will unflatten a genbank or genbank-style file of SeqFeatures into a nested hierarchy.
See Bio::SeqFeature::Tools::Unflattener
In a GenBank/EMBL representation, features are 'flat' - for example, there is no link between an mRNA and a CDS, other than implicit links
(eg via tags or via splice site coordinates) which may be hard to code for.
This is most easily illustrated with the default output format, asciitree
An unflattened genbank feature set may look like this (AB077698)
Seq: AB077698
databank_entry 1..2701[+]
gene
mRNA
CDS hCHCR-G 80..1144[+]
exon 80..1144[+]
five_prime_UTR 1..79[+]
located_sequence_feature 137..196[+]
located_sequence_feature 239..292[+]
located_sequence_feature 617..676[+]
located_sequence_feature 725..778[+]
three_prime_UTR 1145..2659[+]
polyA_site 1606..1606[+]
polyA_site 2660..2660[+]
Or like this (portion of AE003734)
gene
mRNA CG3320-RA
CDS CG3320-PA 53126..54971[-]
exon 52204..53323[-]
exon 53404..53631[-]
exon 53688..53735[-]
exon 53798..53918[-]
exon 54949..55287[-]
mRNA CG3320-RB
CDS CG3320-PB 53383..54971[-]
exon 52204..53631[-]
exon 53688..53735[-]
exon 53798..53918[-]
exon 54949..55287[-]
The unflattening will also 'normalize' the containment hierarchy (in the sense of standardising it - e.g. making sure there is always a
transcript record, even if genbank just specifies CDS and gene)
By default, the GenBank types will be mapped to SO types
See Bio::SeqFeature::Tools::TypeMapper
COMMAND LINE ARGUMENTS
-i|input FILE
input file (can also be specified as last argument)
-from FORMAT
input format (defaults to genbank)
probably doesnt make so much sense to use this for non-flat formats; ie other than embl/genbank
-to FORMAT
output format (defaults to asciitree)
should really be a format that is nested SeqFeature aware; I think this is only asciitree, chadoxml and gff3
-gff
with export to GFF3 format (pre-3 GFFs make no sense with unflattened sequences, as they have no set way of representing feature
graphs)
-o|output FILE
outfile defaults to STDOUT
-detail
show extra detail on features (asciitree mode only)
-e|ethresh INT
sets the error threshold on unflattening
by default this script will throw a wobbly if it encounters weird stuff in the genbank file - raise the error threshold to signal these
to be ignored (and reported on STDERR)
-nomagic
suppress use_magic in unflattening (see Bio::SeqFeature::Tools::Unflattener
-notypemap
suppress type mapping (see Bio::SeqFeature::Tools::TypeMapper
TODO
Bio::SeqFeature::Tools::Unflattener allows fine-grained control over the unflattening process - need to add more options to allow this
control at the command line
FEEDBACK
Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the
Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via
email or the web:
https://redmine.open-bio.org/projects/bioperl/
AUTHOR
Chris Mungall E<lt>cjm-at-bioperl.orgE<gt>
perl v5.14.2 2012-03-02 BP_UNFLATTEN_SEQ(1p)