Redirecting stdout inside a loop Post: 302912736

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Top Forums UNIX for Dummies Questions & Answers Redirecting stdout inside a loop Post 302912736 by Corona688 on Monday 11th of August 2014 03:20:29 PM

08-11-2014

Registered User

Quote:

Originally Posted by hmortens

The stout.miRNA.bash.$date_formatted is where /Processed reads/ and /Trimmed reads/ comes from.

No it is not... They only get put there because your program writes them there in the first place. So that's no more use to me than it is to you -- less, actually, because you have some idea where it's being extracted from and I don't.

Quote:

It was buried in my previous posting. The first few lines of the file for the first sample are:

Code:

**testing** /illumina/runs/Runs/140513_H207_0249_AD2B9LACXX/Unaligned_Lane1/Project_DefaultProject/Sample_GRC270_DEHP2_67C/GRC270_DEHP2_67C_CGATGT_L001_R1_001.fastq.gz
/illumina/runs/Runs/140513_H207_0249_AD2B9LACXX/Unaligned_Lane1/Project_DefaultProject/Sample_GRC270_DEHP2_67C
GRC270_DEHP2_67C
cutadapt version 1.2.1
Command line parameters: -a AGATCGGAAGAGCACACGTCT -o /illumina/runs/Runs/140513_H207_0249_AD2B9LACXX/Unaligned_Lane1/Project_DefaultProject/Sample_GRC270_DEHP2_67C/GRC270_DEHP2_67C_cutadapt_AdapterRemoved.fastq.gz /illumina/runs/Runs/140513_H207_0249_AD2B9LACXX/Unaligned_Lane1/Project_DefaultProject/Sample_GRC270_DEHP2_67C/GRC270_DEHP2_67C_CGATGT_L001_R1_001.fastq.gz
Maximum error rate: 10.00%
   No. of adapters: 1
   Processed reads:      2139267
   Processed bases:    109102617 bp (109.1 Mbp)
     Trimmed reads:      2075206 (97.0%)
     Trimmed bases:     53680380 bp (53.7 Mbp) (49.20% of total)
   Too short reads:            0 (0.0% of processed reads)
    Too long reads:            0 (0.0% of processed reads)
        Total time:    155.78 s
     Time per read:      0.07 ms

=== Adapter 1 ===

Adapter 'AGATCGGAAGAGCACACGTCT', length 21, was trimmed 2075206 times.

No. of allowed errors:
0-9 bp: 0; 10-19 bp: 1; 20-21 bp: 2

Lengths of removed sequences
length	count	expected	max. errors
3	13563	33426.0	0
4	13593	8356.5	0
5	19992	2089.1	0
6	143974	522.3	0
7	48435	130.6	0
8	22001	32.6	0

Okay, so you have two seperate kinds of files -- the summaries and the samples. They come in matched pairs which you want to process together, extracting all of one and some of the other.

"$LOCATION"/Sample_* matches all sample files (not folders).

"$LOCATION"/*_fastqc matches all folders containing summaries, corresponding to the samples above.

What exactly do these paths / filenames have in common? You can't use * to match one and * to match the other when you want pairs, since they both expand to complete lists. Do you find the sample in Sample_abcde, and the summary in abcde_fastqc ?

Corona688

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LEARN ABOUT DEBIAN

ssake

SSAKE(1)						      General Commands Manual							  SSAKE(1)

NAME

       ssake - assembling millions of very short DNA sequences

SYNOPSIS

       Progressive assembly of millions of short DNA sequences by k-mer search through a prefix tree and 3' extension.

OPTIONS

       -f     Fasta file containing all the [paired (-p 1) / unpaired (-p 0)] reads (required) paired reads must now be separated by ":"

       -s     Fasta file containing sequences to use as seeds exclusively (specify only if different from read set, optional)

       -m     Minimum number of overlapping bases with the seed/contig during overhang consensus build up (default -m 16)

       -o     Minimum number of reads needed to call a base during an extension (default -o 3)

       -r     Minimum base ratio used to accept a overhang consensus base (default -r 0.7)

       -t     Trim up to -t base(s) on the contig end when all possibilities have been exhausted for an extension (default -t 0)>

       -p     Paired-end reads used? (-p 1=yes, -p 0=no, default -p 0)

       -v     Runs in verbose mode (-v 1=yes, -v 0=no, default -v 0, optional)

       -b     Base name for your output files (optional)

       ============ Options below only considered with -p 1 ============

       -d     Mean distance expected/observed between paired-end reads (default -d 200, optional)

       -e     Error (%) allowed on mean distance   e.g. -e 0.75  == distance +/- 75% (default -e 0.75, optional)

       -k     Minimum number of links (read pairs) to compute scaffold (default -k 2, optional)

       -a     Maximum link ratio between two best contig pairs *higher values lead to least accurate scaffolding* (default -a 0.70, optional)

       -z     Minimum contig size to track paired-end reads (default -z 50, optional)

       -g     Fasta file containing unpaired sequence reads (optional)

SEE ALSO

       /usr/share/doc/ssake/SSAKE.readme between

AUTHORS

       This  manual page was written by Andreas Tille <tille@debian.org> for the Debian system (but may be used by others).  Permission is granted
       to copy, distribute and/or modify this document under the terms of the GNU General Public License, Version 2 any later version published by
       the Free Software Foundation.

       On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common-licenses/GPL.

								   January 2008 							  SSAKE(1)