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Full Discussion: Extraction of sequences from files
Top Forums Shell Programming and Scripting Extraction of sequences from files Post 302952276 by Don Cragun on Monday 17th of August 2015 01:59:51 AM
Old 08-17-2015
Quote:
Originally Posted by harpreetmanku04
it is showing cannot open file1

---------- Post updated at 12:23 AM ---------- Previous update was at 12:18 AM ----------

Code:
csm@csm-HP-Z420:~/Desktop/sequences/sequences to extract for fold$ awk 'FNR==NR {T[$1];next} $1 in T {P=NR+1} NR<=P' only_ids.txt sequences.fasta  >hkm


this creates only empty hkm output file
You started out by telling us you had file1 and file2 and confusingly gave alternative names ids.txt and sequences.fasta. Now you tell us the command above says there is no file1 when it doesn't reference file1???

When sitting in the directory where you ran the above command, please show us the output of the command:
Code:
ls -l file1 file2 ids.txt only_ids.txt sequences.fasta hkm

 

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LEARN ABOUT MINIX

zdiff

ZDIFF(1)                                                      General Commands Manual                                                     ZDIFF(1)

NAME

       zcmp, zdiff - compare compressed files

SYNOPSIS

       zcmp [ cmp_options ] file1 [ file2 ]
       zdiff [ diff_options ] file1 [ file2 ]

DESCRIPTION

       Zcmp  and  zdiff are used to invoke the cmp or the diff program on files compressed via gzip.  All options specified are passed directly to
       cmp or diff.  If only file1 is specified, it is compared to the uncompressed contents of file1.gz.  If two files are specified, their  con-
       tents  (uncompressed  if  necessary)  are  fed to cmp or diff.  The input files are not modified.  The exit status from cmp or diff is pre-
       served.

SEE ALSO

       cmp(1), diff(1), zmore(1), zgrep(1), znew(1), zforce(1), gzip(1), gzexe(1)

BUGS

       Messages from the cmp or diff programs may refer to file names such as "-" instead of to the file names specified.

                                                                                                                                          ZDIFF(1)
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