Sponsored Content
Top Forums Shell Programming and Scripting Parse file for fields and specific text Post 302949174 by cmccabe on Tuesday 7th of July 2015 05:30:39 PM
Old 07-07-2015
Yes the
Code:
gtf/gff

was created

Code:
wget ftp://ftp.sanger.ac.uk/pub/gencode/r...otation.gtf.gz
gunzip --stdout gencode.v21.annotation.gtf.gz \
    | gtf2bed - \
    | grep "exon" \
    > gencode.exons.bed
bedmap --echo --echo-map Regions.bed gencode.exons.bed

produced output close, but not desired and I thought maybe if I parsed the input it may help. That is if I had a exon file with only 5 rows that may be better.

I'm not sure but maybe:

Code:
 awk -f FNR > 1{for(i=1;i<=NF;i++) {n=split($i,a, "[.:>_]") print a[1]+0,a[2]+0,a[3]+0,substr(a[gene_name],length(a[exon_number])), a[n]} } OFS='\t' gencode.exons.txt > parse.txt

Thank you Smilie.
 

10 More Discussions You Might Find Interesting

1. UNIX for Dummies Questions & Answers

How to parse the specific data from the file

Hi, I need to parse this data FastEthernet0/9,|FastEthernet0/10,|FastEthernet0/11,FastEthernet0/13|, FastEthernet0/12,FastEthernet0/24 . and get only the value like e.g 0/24,0/11. how to do this in shell script. Thanks in Advance. (2 Replies)
Discussion started by: MuthuAlagappan
2 Replies

2. Shell Programming and Scripting

How to read and parse the content of csv file containing # as delimeter into fields using Bash?

#!/bin/bash i=0 cat 1.csv | while read fileline do echo "$fileline" IFS="#" flds=( $fileline ) nrofflds=${#flds} echo "noof fields$nrofflds" fld=0 while do echo "noof counter$fld" echo "$nrofflds" #fld1="${flds}" trying to store the content of line to fields but i... (4 Replies)
Discussion started by: barani75
4 Replies

3. Shell Programming and Scripting

Assigning a specific format to a specific column in a text file using awk and printf

Hi, I have the following text file: 8 T1mapping_flip02 ok 128 108 30 1 665000-000008-000001.dcm 9 T1mapping_flip05 ok 128 108 30 1 665000-000009-000001.dcm 10 T1mapping_flip10 ok 128 108 30 1 665000-000010-000001.dcm 11 T1mapping_flip15 ok 128 108 30... (2 Replies)
Discussion started by: goodbenito
2 Replies

4. Shell Programming and Scripting

Perl: Parse Hex file into fields

Hi, I want to split/parse certain bits of the hex data into another field. Example: Input data is Word1: 4f72abfd Output: Parse bits (5 to 0) into field word1data1=0x00cd=205 decimal Parse bits (7 to 6) into field word1data2=0x000c=12 decimal etc. Word2: efff3d02 Parse bits (13 to... (1 Reply)
Discussion started by: morrbie
1 Replies

5. Shell Programming and Scripting

Capture specific fields in file

Dear Friends, I have a file a.txt 1|3478.12|487|4578.04|4505.5478|rhfj|rehtire|rhj I want to get the field numbers which have decimal values output: Fields: 2,4,5 Plz help (6 Replies)
Discussion started by: i150371485
6 Replies

6. Shell Programming and Scripting

Extract specific line in an html file starting and ending with specific pattern to a text file

Hi This is my first post and I'm just a beginner. So please be nice to me. I have a couple of html files where a pattern beginning with "http://www.site.com" and ending with "/resource.dat" is present on every 241st line. How do I extract this to a new text file? I have tried sed -n 241,241p... (13 Replies)
Discussion started by: dejavo
13 Replies

7. Shell Programming and Scripting

Parse text file using specific tags

awk -F "" '/<href=>|<href=>|<top>|<top>/ {print $3, OFS=\t}' source.txt > output.txt I'm not quite sure how to parse the attached file, but what I am trying to do is in a output file have the link (href=), name (after the <), and count (<top>) in 3 separate columns. My attempt is the above... (2 Replies)
Discussion started by: cmccabe
2 Replies

8. Shell Programming and Scripting

awk script to parse case with information in two fields of file

The below awk parser works for most data inputs, but I am having trouble with the last one. The problem is in the below rules steps 1 and 2 come from $2 (NC_000013.10:g.20763686_20763687delinsA) and steps 3 and 4 come from $1 (NM_004004.5:c.34_35delGGinsT). Parse Rules: The header is... (0 Replies)
Discussion started by: cmccabe
0 Replies

9. Shell Programming and Scripting

Replacing entire fields with specific text at end or beginning of field

Greetings. I've got a csv file with data along these lines: Spumoni's Pizza Place, Placemats n Things, Just Lamps Counterfeit Dollars by Vinnie, Just Shades, Dollar StoreI want to replace the entire comma-delimited field if it matches something ending in "Place" or beginning with "Dollar",... (2 Replies)
Discussion started by: palmfrond
2 Replies

10. UNIX for Advanced & Expert Users

Script to parse and compare information in two fields of file

Hello, I am working parsing a large input file1(field CFA) I have to compare the the file1 field(CFA byte 88-96) with the content of the file2(It contains only one field) and and insert rows equal in another file. Here is my code and sample input file: ... (7 Replies)
Discussion started by: GERMANOS
7 Replies
PAGESIZES(5F)															     PAGESIZES(5F)

NAME
pagesizes - HylaFAX page size definitions DESCRIPTION
The pagesizes database defines the page dimensions and guaranteed reproducible areas (GRA) for well-known page sizes. The GRA is the por- tion of the page that is guaranteed to be imaged during facsimile transmission. This region is typically less than the full page dimen- sions because of paper roller contacts and other mechanical aspects of the printing process in a facsimile machine. All HylaFAX programs that require page size information read the information from this database using a page size name. Documents should be prepared such that the full page dimensions are employed with the imaged area contained within the GRA. The system-wide default page size to use in preparing documents for transmission is given by the ``default'' entry in the database. (NB: the default entry should be placed last so that inverse matches find the real page size name and not the default entry.) The page size database is an ASCII file with the following format. Each entry consists of whitespace-separated fields: name abbrev width height gra-width gra-height top-margin left-margin Fields have the following interpretation: name the full name for the page size; e.g. ISO A4; abbrev an abbreviated version of the full name for use in compact listings such as the receive queue listing printed by faxstat(1); width the full width of the page; height the full height of the page; gra-width the width of the GRA; gra-height the height of the GRA; top-margin the margin between the top of the full page and the top of the GRA; left-margin the margin between the left side of the full page the left side of the GRA. The first two fields must be separated from the subsequent fields by a tab character (possibly followed by more whitespace); this is done to easily permit blank characters to be included in names. Otherwise fields can be separated by any amount of any kind of whitespace. Numbers are all base 10 and in basic measurement units (BMU); defined as 1/1200 x 25.4 millimeters for paper output with a scale factor of one. All fields must be present on a single line; otherwise the entry is ignored. Comments are introduced by the ``#'' character and con- tinue to the end the line. Page size database lookups are either by name or by page dimensions. Lookups by name are done by sequentially scanning the entries in the database for the first entry that has a matching abbreviation or substring of the page size name field. The string comparisons ignore case so, for example, ``a4'' would match a full name of ``ISO A4''. Lookups by dimension scan the entire database and return the page with the closest dimensions using a straightforward distance metric. If the difference in dimensions of the closest match is greater than 1/2 inch on each side, then no page entry is returned for a lookup by dimension. SEE ALSO
hylafax-client(1), faxmail(1), faxstat(1), sendfax(1), sgi2fax(1), textfmt(1). December 5, 1994 PAGESIZES(5F)
All times are GMT -4. The time now is 09:35 AM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy