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Add fasterq dump #165

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252 changes: 252 additions & 0 deletions src/sra_tools/sra_tools_fasterq_dump/config.vsh.yaml
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name: sra_tools_fasterq_dump
namespace: sra_tools
description:
The fasterq-dump tool extracts data in FASTQ- or FASTA-format from SRA-accessions.
argument_groups:
- name: Inputs
arguments:
- name: --accession
description: |
SRA-accession to download. Does not require to use SRA tool's prefetch
command first to download file. Mutually exclude
type: string
required: false
- name: --prefetch_directory
type: file
required: false
direction: input
description: |
Directory generated by SRA tool 'prefetch'. Mutually exclusive with --accession.
- name: "Output"

- name: "Options"
arguments:
- name: --details
alternatives: ["-x"]
type: bolean_true
description: |
Print details
- name: --progress
alternatives: [-p]
type: boolean_true
description: |
Show progress
- name: --split_spot
alternatives: ["-s"]
type: boolean_true
description: |
Split spots into reads
- name: --split_files
alternatives: ["-s"]
type: boolean_true
description: |
Write reads into different files
- name: --split_3
alternatives: ["-3"]
type: boolean_true
description: |
Writes single reads in special file.
- name: "--concatenate_reads"
type: boolean_true
description: |
Writes whole spots into one file
- name: --skip_technical
type: boolean_true
description: |
Skip technical reads.
- name: --include_technical
type: boolean_true
description: |
Include technical reads.
- name: --minimal_read_length
type: integer
min: 1
description: |
Filter by sequence length.
required: false
- name: --bases
alternatives: [-B]
type: string
description: |
Filter by bases
required: false
- name: --table
type: string
description: |
Name of consensus-table to use for pacbio reads.
required: false
- name: --fasta
type: boolean_true
description: |
Produce fasta output
- name: --fasta_unsorted
type: boolean_true
description: |
Produce unsorted FASTA output
- name: --fasta_reference_table
type: boolean_true
description: |
Produce FASTA output from REFERENCE table.
- name: --fasta_concat_all
type: boolean_true
description: |
Concatenate all rows and produce FASTA output
- name: --internal_ref
type: boolean_true
description: |
Extracts only internal references into the output file.
Internal references are non-standard scaffoldings the submitter
included in the submission and the bases of them are stored in the accession.
- name: --external_ref
type: boolean_true
description: |
Extracts only external references into the output file.
External references are canonical RefSeq accessions that are used in the accession.
- name: --ref_name
type: string
multiple: true
required: false
description: |
This command extracts only the named reference. If a reference is not found, the option is ignored.
If none of the requested references is found, an empty file is produced. Each reference used by an
accession can be named in 2 ways: the canonical name like 'NC_001133.9' or the user-supplied name
like 'I' or 'chr1'. The user can use the '--ref_report' option to inspect the names used.
- name: --seq_defline
type: string
required: false
example: "@$ac.$si $sn length=$rl"
description: |
Supply a defline for the the sequence sections of FASTQ or FASTA.
The format is a text that may contain these variables:
$ac ... the accession
$sn ... the spot-name
$sg ... the spot-group
$si ... the spot-id ( the number of the spot )
$ri ... the read-id ( the number of a read within a spot )
$rl ... the read-length
The accession, spot-id, read-id, and read-length are always available - but the spot-group and/or spot-name
might be missing or empty. If a variable is missing or empty it does not produce an error - it will be
omitted from the defline.

Defaults for FASTQ:
if not splitting: @$ac.$si $sn length=$rl
if splitting: @$ac.$si/$ri $sn length=$rl
Defaults for FASTA:
if not splitting >$ac.$si $sn length=$rl
if splitting: >$ac.$si/$ri $sn length=$rl

- name: --qual_defline
type: string
required: false
example: "@$ac.$si $sn length=$rl"
description: |
Supply a defline for the the quality sections of FASTQ.
The format is a text that may contain these variables:
$ac ... the accession
$sn ... the spot-name
$sg ... the spot-group
$si ... the spot-id ( the number of the spot )
$ri ... the read-id ( the number of a read within a spot )
$rl ... the read-length
The accession, spot-id, read-id, and read-length are always available - but the spot-group and/or spot-name
might be missing or empty. If a variable is missing or empty it does not produce an error - it will be
omitted from the defline.

Defaults for FASTQ:
if not splitting: +$ac.$si $sn length=$rl
if splitting: +$ac.$si/$ri $sn length=$rl
- name: --only_unaligned
alternatives: [-U]
type: boolean_true
description: |
Process only unaligned reads.
- name: "--only_aligned"
alternatives: [-a]
type: boolean_true
description: |
Process only aligned reads.
- name: "--log-level"
alternatives: "-L"
type: string
choices: [fatal, sys, int, err, warn, info, debug]
example: warn
required: false




















# Unused arguments:
# -F|--format format (special, fastq, default=fastq)
-o|--outfile output-file
-O|--outdir output-dir
-b|--bufsize size of file-buffer dflt=1MB
-c|--curcache size of cursor-cache dflt=10MB
-m|--mem memory limit for sorting dflt=100MB
-t|--temp where to put temp. files dflt=curr dir
-e|--threads how many thread dflt=6
-p|--progress show progress
-x|--details print details
-s|--split-spot split spots into reads
-S|--split-files write reads into different files
-3|--split-3 writes single reads in special file
--concatenate-reads writes whole spots into one file
-Z|--stdout print output to stdout
-f|--force force to overwrite existing file(s)
--skip-technical skip technical reads
--include-technical include technical reads
-M|--min-read-len filter by sequence-len
--table which seq-table to use in case of pacbio
-B|--bases filter by bases
-A|--append append to output-file
--fasta produce FASTA output
--fasta-unsorted produce FASTA output, unsorted
--fasta-ref-tbl produce FASTA output from REFERENCE tbl
--fasta-concat-all concatenate all rows and produce FASTA
--internal-ref extract only internal REFERENCEs
--external-ref extract only external REFERENCEs
--ref-name extract only these REFERENCEs
--ref-report enumerate references
--use-name print name instead of seq-id
--seq-defline custom defline for sequence: $ac=accession,
$sn=spot-name, $sg=spot-group, $si=spot-id,
$ri=read-id, $rl=read-length
--qual-defline custom defline for qualities: same as
seq-defline
-U|--only-unaligned process only unaligned reads
-a|--only-aligned process only aligned reads
--disk-limit explicitly set disk-limit
--disk-limit-tmp explicitly set disk-limit for temp. files
--size-check switch to control: on=perform size-check
(default), off=do not perform size-check,
only=perform size-check only
--ngc <PATH> PATH to ngc file

-h|--help Output brief explanation for the program.
-V|--version Display the version of the program then
quit.
-L|--log-level <level> Logging level as number or enum string. One
of (fatal|sys|int|err|warn|info|debug) or
(0-6) Current/default is warn.
-v|--verbose Increase the verbosity of the program
status messages. Use multiple times for more
verbosity. Negates quiet.
-q|--quiet Turn off all status messages for the
program. Negated by verbose.
--option-file <file> Read more options and parameters from the
file.
70 changes: 70 additions & 0 deletions src/sra_tools/sra_tools_fasterq_dump/helpt.txt
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```
docker run -t --rm ncbi/sra-tools fasterq-dump --help
```

Usage:
fasterq-dump <path> [options]
fasterq-dump <accession> [options]

Options:
-F|--format format (special, fastq, default=fastq)
-o|--outfile output-file
-O|--outdir output-dir
-b|--bufsize size of file-buffer dflt=1MB
-c|--curcache size of cursor-cache dflt=10MB
-m|--mem memory limit for sorting dflt=100MB
-t|--temp where to put temp. files dflt=curr dir
-e|--threads how many thread dflt=6
-p|--progress show progress
-x|--details print details
-s|--split-spot split spots into reads
-S|--split-files write reads into different files
-3|--split-3 writes single reads in special file
--concatenate-reads writes whole spots into one file
-Z|--stdout print output to stdout
-f|--force force to overwrite existing file(s)
--skip-technical skip technical reads
--include-technical include technical reads
-M|--min-read-len filter by sequence-len
--table which seq-table to use in case of pacbio
-B|--bases filter by bases
-A|--append append to output-file
--fasta produce FASTA output
--fasta-unsorted produce FASTA output, unsorted
--fasta-ref-tbl produce FASTA output from REFERENCE tbl
--fasta-concat-all concatenate all rows and produce FASTA
--internal-ref extract only internal REFERENCEs
--external-ref extract only external REFERENCEs
--ref-name extract only these REFERENCEs
--ref-report enumerate references
--use-name print name instead of seq-id
--seq-defline custom defline for sequence: $ac=accession,
$sn=spot-name, $sg=spot-group, $si=spot-id,
$ri=read-id, $rl=read-length
--qual-defline custom defline for qualities: same as
seq-defline
-U|--only-unaligned process only unaligned reads
-a|--only-aligned process only aligned reads
--disk-limit explicitly set disk-limit
--disk-limit-tmp explicitly set disk-limit for temp. files
--size-check switch to control: on=perform size-check
(default), off=do not perform size-check,
only=perform size-check only
--ngc <PATH> PATH to ngc file

-h|--help Output brief explanation for the program.
-V|--version Display the version of the program then
quit.
-L|--log-level <level> Logging level as number or enum string. One
of (fatal|sys|int|err|warn|info|debug) or
(0-6) Current/default is warn.
-v|--verbose Increase the verbosity of the program
status messages. Use multiple times for more
verbosity. Negates quiet.
-q|--quiet Turn off all status messages for the
program. Negated by verbose.
--option-file <file> Read more options and parameters from the
file.
for more information visit:
https://github.com/ncbi/sra-tools/wiki/HowTo:-fasterq-dump
https://github.com/ncbi/sra-tools/wiki/08.-prefetch-and-fasterq-dump
68 changes: 68 additions & 0 deletions src/sra_tools/sra_tools_fasterq_dump/script.sh
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#!/usr/bin/env bash

unset_if_false=(
par_details
par_progress
par_split_spot
par_split_files
par_split_3
par_concatenate_reads
skip_technical
include_technical
exclude_technical
par_fasta
par_fasta_unsorted
par_fasta_reference_table
par_fasta_concat_all
par_internal_ref
par_external_ref
par_only_unaligned
par_only_aligned
)

for par in ${unset_if_false[@]}; do
test_val="${!par}"
[[ "$test_val" == "false" ]] && unset $par
done

if [ -z "$par_accession" ] && [ -z "$par_prefetch_directory" ]; then
echo "Either 'accesssion' or 'prefetch_directory' must be specified."
exit 1
fi

if [ ! -z "$par_accession" ] && [ ! -z "$par_prefetch_directory" ]; then
echo "'accesssion' or 'prefetch_directory' are mutually exclusive arguments."
exit 1
fi
input=${par_accession-$par_prefetch_directory}



fasterq-dump \
${par_details:+--details} \
${par_progress:+--progress} \
${par_split_spot:+--split-spot} \
${par_split_files:+--split-files} \
${par_concatenate_reads:+--concatenate-reads} \
${par_split_3:+--split-3} \
${par_skip_technical:+--skip-technical} \
${par_include_technical:+--include-technical} \
${par_exclude_technical:+--exclude-technical} \
${par_minimal_read_length:+--min-read-len $par_minimal_read_length} \
${par_table:+--table $par_table} \
${par_bases:+--bases $par_bases} \
${par_fasta+--fasta} \
${par_fasta_unsorted+--fasta-unsorted} \
${par_fasta_reference_table+--fasta-ref-tbl} \
${par_fasta_concat_all+--fasta-concat-all} \
${par_internal_ref+--internal-ref} \
${par_external_ref+--external-ref} \
${par_seq_defline:+--seq-defline ${par_seq_defline@Q}} \
${par_qual_defline:+--qual-defline ${par_seq_defline@Q}} \
${par_only_unaligned+--only-unaligned} \
${par_only_aligned+--only-aligned} \
${par_log_level+--log-level $par_log_level} \
${meta_memory_mb:+--memory "${meta_memory_mb}M"} \
--force \
"$input"

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