So, I am trying to write a script that that will pick up pairs of files with the same name (not the same content) but that are different in one character (one is *R1 the other is *R2)...
Something like: look ate the files, whenever they are the same except in the R1/R2, than run ...
The if that I tried is I think is going into the the file content rather than the name....
Did this make any sense?
Thanks a lot.
This is what I was able to do so far....
Code:
#!/bin/bash
file1_path="~/All_files/"
var1=S*R1.fastq.gz
echo $var1
file2_path="~/All_files/"
var2=S*R2.fastq.gz
echo $var2
if ["${VAR1:0:18}" = "${VAR2:0:18}"] ; then
Moderator's Comments:
Please wrap all code, files, input & output/errors in CODE tags.
It makes it far easier to read and preserves spaces for indenting and/or fixed-width data.
Daily we are getting some datafiles to our unix server location FTPIN.
Incoming File names will be present in the location "/xyz/test/" as below:
"infile_A1_YYYYMMDD",
"infile_A2_YYYYMMDD",
"infile_B1_YYYYMMDD",
"infile_C1_YYYYMMDD"
"infile_C2_YYYYMMDD"
Where A, B and C are the... (3 Replies)
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Hi,
I have a file1 like this:
ABAT
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Discussion started by: anaigini45
1 Replies
LEARN ABOUT DEBIAN
srf2fastq
srf2fastq(1) Staden io_lib srf2fastq(1)NAME
srf2fastq - Converts SRF files to Sanger fastq format
SYNOPSIS
srf2fastq [options] srf_archive ...
DESCRIPTION
srf2fastq extracts sequences and qualities from one or more SRF archives and writes them in Sanger fastq format to stdout.
Note that Illumina also have a fastq format (used in the GERALD directories) which differs slightly in the use of log-odds scores for the
quality values. The format described here is using the traditional Phred style of quality encoding.
OPTIONS -c Outputs calibrated confidence values using the ZTR CNF1 chunk type for a single quality per base. Without this use the original
Illumina _prb.txt files consisting of four quality values per base, stored in the ZTR CNF4 chunks.
-C Masks out sequences tagged as bad quality.
-s root
Generates files on disk with filenames starting root, one file per non-explicit element in the SRF/ZTR region (REGN) chunk. Typi-
cally this results in two files for paired end runs. The filename suffixes come from the names listed in the SRF region chunks.
This option conflicts with the -S parameter.
-S Splits sequences into regions, but sequentially lists each sequence region to stdout instead of splitting to separate files on disk.
This option conflicts with the -s parameter.
-n When using -s the filename suffixes are simply numbered (starting with 1) instead of using the names listed in the SRF region
chunks.
-a Appends region index to the sequence names. Ie generate "name/1" and "name/2" for a paired read.
-e Include any explicit sequence (ZTR region chunk of type 'E') in the sequence output. The explicit sequence is also included in the
quality line too. Currently this is utilised by ABI SOLiD to store the last base of the primer.
-r region list
Reverse complements the sequence and reverses the quality values for all regions in the region list. This is a comma separated list
of integer values enumerating the regions, starting from 1. Note that this option only works when either -s or -S are specified.
EXAMPLES
To extract only the good quality sequences from all srf files in the current directory using calibrated confidence values (if available).
srf2fastq -c -C *.srf > runX.fastq
To extract a paired end run into two separate files with sequences named name/1 and name/2.
srf2fastq -s runX -a -n runX.srf
To extract a paired end run as a single file, alternating forward and reverse sequences, with the second read being reverse complemented.
srf2fastq -S -r 2 runX.srf > runX.fastq
AUTHOR
James Bonfield, Steven Leonard - Wellcome Trust Sanger Institute
December 10 srf2fastq(1)
11-25-2019
