awk to output the percentage of a field compared to length
The awk below using the sample input would output the following: Basically, it averages the text in $5 that matches if $7 < 30 .
Code:
awk '{if(len==0){last=$5;total=$7;len=1;getline}if($5!=last){printf("%s\t%f\n", last, total/len);last=$5;total=$7;len=1}else{total+=$7;len+=1}}END{printf("%s\t%f\n", last, total/len)}' Input.txt > output.txt
My question is I can not seem to add the correct syntax that will also output the total # of lines in $6 that represent $5 and the % of 7 < 30 I know my words may not be all that helpful so hopefully the desired output will help. Thank you .
Desired output
Code:
ID Average Reads % of Baits
AGRN:exon.1 4.5714285 3.16742 (221 (# of lines in $6 / the # 0f lines < 30 in $7)
the boild is only to show the math and does not need rto be included.
Last edited by cmccabe; 09-30-2015 at 05:57 PM..
Reason: fixed formatting; [mod] extra code tags, added details
Is there a command that sets a variable length?
I have a input of a variable length field but my output for that field needs to be set to 32 char.
Is there such a command?
I am on a sun box running ksh
Thanks (2 Replies)
Dear All,
1.txt (tab in between each value in a line)
a b c
a b c
a c d
you can see below, why with ~ i can output with tab, but = cannot?
# awk -F'\t' '$2 ~ /b/' 1
a b c
a b c
# awk -F'\t' '$2 = "b"' 1
a b c
a b c
a b d
... (1 Reply)
Hello Everyone,
I am stuck with one issue while working on abstract flat file which i have to use as input and load data to table.
Input Data-
------ ------------------------ ---- -----------------
WFI001 Xxxxxx Control Work Item A Number of Records
------ ------------------------... (5 Replies)
In awk, how do I print all fields with a specified output field separator?
I have tried the following, which does not print the output FS:
echo a b c d | awk 'BEGIN{OFS = ";"}{print $0}' (3 Replies)
Hi all,
I have a requirement to replace a field with a character as per the length of the field.
Suppose i have a file where second field is of 20 character length. I want to replace second field with 20 stars (*). like ********************
As the field is not a fixed one, i want to do the... (2 Replies)
Need an awk script to calculate the percentage of value field and replace
I have a input file called file.txt with the following content:
john|622.5674603562933|8|br:1;cn:3;fr:1;jp:1;us:2
andy|0.0|12|**:3;br:1;ca:2;de:2;dz:1;fr:2;nl:1
in fourth filed of input file, calulate percentage of each... (1 Reply)
I have a input file called file.txt with the following content:
john|622.5674603562933|8|br:1;cn:3;fr:1;jp:1;us:2
andy|0.0|12|**:3;br:1;ca:2;de:2;dz:1;fr:2;nl:1
in fourth filed of input file, calulate percentage of each sub filed seperated by ; semicolon and replace value with percentage .
i... (11 Replies)
I have several questions about using awk. I'm hoping someone could lend me a hand. (I'm also hoping that my questions make sense.)
I have a file that contains pipe separated data. Each line has similar data but the number of fields and the field position on each line is variable. ... (3 Replies)
The awk below produces the current output, which will add +1 to $3. However, I am trying to add the length of the matching characters between $5 and $6 to $3. I have tried using sub as a variable to store the length but am not able to do so correctly. I added comments to each line and the... (4 Replies)
Discussion started by: cmccabe
4 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)
09-30-2015
.