Skip to content

Latest commit

 

History

History
206 lines (143 loc) · 6.21 KB

README.md

File metadata and controls

206 lines (143 loc) · 6.21 KB
Raw

Get FAST{A,Q} info

Some useful summary tools for FASTA and FASTQ formatted files.

These tools gives a brief summary of number of sequences, min, max, and average sequence lengths, for FASTA or FASTQ formatted files.

For installation, see file INSTALL.

get_fasta_info

Description:

Program written in C. Distributed under the MIT license.

Will report number of sequences, min/max/average sequence lengths, and file name read, as tab-delimited output. In addition, if option -g is used, the program will also report min/max/average proportion of missing data (symbols NX?-). Prints to both STDOUT and STDERR. Can read compressed (gzip) input files.

Note: If empty sequences are present, their length (0) will still be used when calculating the average sequence length in the file.

Options:

  • -h print brief usage information
  • -g report missing data
  • -n do not print the output header
  • -p print real path for input file

Examples:

$ src/get_fasta_info data/fasta.*
Nseqs	Min.len	Max.len	Avg.len	File
3	1	3	2	fasta.fasta
Nseqs	Min.len	Max.len	Avg.len	File
3	1	3	2	fasta.fasta.gz

$ src/get_fasta_info -n data/fasta.*
3	1	3	2	fasta.fasta
3	1	3	2	fasta.fasta.gz

$ src/get_fasta_info -n -p data/fasta.*
3	1	3	2	/full/path/to/fasta.fasta
3	1	3	2	/full/path/to/fasta.fasta.gz

$ src/get_fasta_info data/fasta.* 2>/dev/null
3	1	3	2	fasta.fasta
3	1	3	2	fasta.fasta.gz

$ src/get_fasta_info -g data/gaps.fna
Nseqs	Min.len	Max.len	Avg.len	Min.gap	Max.gap	Avg.gap	File
3	10	10	10	0.00	1.00	0.47	gaps.fna
Which files are not aligned (all of the same length)?
$ src/get_fasta_info -n data/*.fas | \
    awk '$2 != $3 {print $NF}'
Which files have 9 sequences, and are aligned (all of the same length)?
$ src/get_fasta_info -n data/*.fas | \
    awk '$1 == 9 && $2 == $3 {print $NF}'
Which files have zero-length sequences?
$ src/get_fasta_info -n data/*.fas | \
    awk '!$2 {print $NF}'
Which files have at least one sequence with all missing data
$ src/get_fasta_info -g -n data/*.f?? | \
    awk '$6 == 1.00 {print $NF}'
Remove the files found in the previous example (note the addition of -p)
$ rm -v $(src/get_fasta_info -g -n -p data/*.f?? | \
    awk '$6 == 1.00 {print $NF}')

get_fastq_info

Description:

Program written in C. Distributed under the MIT license.

Will report number of sequences, min/max/average sequence lengths, and average read quality, as tab-delimited output. Prints to both STDOUT and STDERR. Can read compressed (gzip) input files.

Note: If empty sequences are present, their length (0) will still be used when calculating the average sequence length in the file.

Options:

  • -h print brief usage information
  • -n do not print the output header
  • -q report average read quality
  • -p print real path for input file

Examples:

$ src/get_fastq_info data/fastq.*
Nseqs	Min.len	Max.len	Avg.len	File
4	150	150	150	fastq.fastq
Nseqs	Min.len	Max.len	Avg.len	File
1000	78	150	150	fastq.fq.gz

$ src/get_fastq_info -q data/fastq.*
Nseqs	Min.len	Max.len	Avg.len	Avg.qual	File
4	150	150	150	36	fastq.fastq
Nseqs	Min.len	Max.len	Avg.len	Avg.qual	File
1000	78	150	150	35	fastq.fq.gz

$ src/get_fastq_info -n -q data/fastq.*
4	150	150	150	36	fastq.fastq
1000	78	150	150	35	fastq.fq.gz

get_fasta_info.pl

Description:

Perl-script with the same basic functionality as the (faster) C-program, but can also read bzip format (if bzip2 is installed) in addition to .gz, .zip, and .Z. It does not, however, handle compressed tar archives (.tar.gz, etc).

Options:

  • -h print brief Usage information
  • -n do not print the output header

Examples:

$ scripts/get_fasta_info.pl data/*.fas
Nseqs	Min.len	Max.len	Avg.len	File
9	643	649	647	dat/1.fas
Nseqs	Min.len	Max.len	Avg.len	File
14	216	339	290	dat/2.fas

$ scripts/get_fasta_info.pl -n data/*.fas
9	643	649	647	dat/1.fas
14	216	339	290	dat/2.fas

$ scripts/get_fasta_info.pl data/*.fas 2>/dev/null | \
    sort -k4 | awk '{print $NF,$1}'
dat/2.fas 14
dat/1.fas 9

Note: The get_fasta_info.pl is based on modified code from the internet. I will acknowledge the original author (as soon as I locate him/her!). If you recognize the code, please send me a note!

get_fasta_details.pl

Description:

Perl-script to read FASTA-formatted file and report a tab-separated list of sequence length, sequence number (in file), file name, FASTA header.

Distributed under the MIT license.

Can sort in ascending/descending order on sequence length.

Options:

  • -s, --sort Sort the output on sequence length, shortest first
  • -r, --revsort Sort the output on sequence length, longest first
  • -h, --help Display help text

Examples:

$ scripts/get_fasta_details.pl data/*.fas
649	0	dat/1.fas	gi|256009056|gb|ACU54623.1| ...
643	1	dat/1.fas	gi|586972334|gb|EWT07678.1| ...
645	2	dat/1.fas	gi|908398554|ref|WP_049755449.1| ...
...
318	0	dat/2.fas	gi|949018528|gb|KRO28616.1| ...
283	1	dat/2.fas	gi|949023402|gb|KRO32148.1| ...
315	2	dat/2.fas	gi|949028303|gb|KRO35658.1| ...
...

Tip on decompression

For the tools that can read compressed input files, de-compression of large files will take a proportionally large amount of the total compute (real) time. One way to try to minimize this is to use an auxiliary compression tool that can do decompression in parallel. Here is an example using pigz (https://zlib.net/pigz/) on a 1.2G input file.

Note that we use process substitution (<()) to allow the output from pigz to be used as input to the program. This will also mean that the name of the file descriptor ("63" in the example below) is printed in the output, and not the original file name. Time saved is dependent on the system.

$ TIMEFORMAT=%0lR && time get_fasta_info file.fas.gz
Nseqs	Min.len	Max.len	Avg.len	File
33173436	35	150	150	file.fas.gz
0m40s

$ TIMEFORMAT=%0lR && time get_fasta_info <(pigz -d -c file.fas.gz)
Nseqs	Min.len	Max.len	Avg.len	File
33173436	35	150	150	63
0m23s