Que nous débutions ou que nous soyons des bioinformaticiens chevronnés, il y a toujours un moment où nous sommes bloqués.
Quelles sont les options et arguments de mon outils ? Comment lui indiquer ma donnée d'entrée ? Comment extraire l'information X de mon fichier ? Il existe plusieurs moyens d'obtenir des réponses à (presque) toutes vos questions !
man est la commande qu'il vous faut. Elle veut litteralement dire manuel donc vous permettra d'afficher toute l'aide dont vous avez besoin pour la grande majorité des commandes inclus par défaut dans le langage bash.
Pour l'utiliser : man commande_mystere
Essayons. whoami est une commande possédant l'un des plus petits manuels. Mais que fait-elle ?
In [6]:
# Afficher l'aide de whoami
man whoami
WHOAMI(1) User Commands WHOAMI(1)
NAME
whoami - print effective userid
SYNOPSIS
whoami [OPTION]...
DESCRIPTION
Print the user name associated with the current effective user ID.
Same as id -un.
--help display this help and exit
--version
output version information and exit
AUTHOR
Written by Richard Mlynarik.
REPORTING BUGS
GNU coreutils online help: <https://www.gnu.org/software/coreutils/>
Report whoami translation bugs to <https://translationpro‐
ject.org/team/>
COPYRIGHT
Copyright © 2018 Free Software Foundation, Inc. License GPLv3+: GNU
GPL version 3 or later <https://gnu.org/licenses/gpl.html>.
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.
SEE ALSO
Full documentation at: <https://www.gnu.org/software/coreutils/whoami>
or available locally via: info '(coreutils) whoami invocation'
GNU coreutils 8.30 September 2019 WHOAMI(1)
On retrouve donc d'abord le nom de la commande et un résumé de ce qu'elle fait.
Puis le "synopsis" vous expliquant comment l'écrire.
La description vous liste l'ensemble des options existantes, leur but et leur utilisation.
Ici la commande whoami permet donc d'afficher votre nom d'utilisateur courant sans besoin de mettre d'argument.
Vous pouvez essayer cette commande et vérifier que man ne vous a pas menti :
In [7]:
# Utilisation de la commande whoami
whoami
pfrancois
Pour un outil autre¶
Vous avez trouvé un outil qui, théoriquement, fait ce dont vous avez besoin. Vous voulez en savoir plus !
Si nous affirmons que cette option est à 100% standardisée, nous trouverons un contre-exemple. Disons donc que vous ne risquez pas de trop vous tromper en utilisant l'option --help (ou sa forme courte -h)
Testons avec le fameux "fastqc" vu précédemment afin d'enfin lever le voile sur ce que fait cet outil.
Faites un module load de fastqc/0.11.9
In [9]:
# Import de l'outil fastqc en version 0.11.9
module load fastqc/0.11.9
Affichez son aide
In [13]:
# Version courte
fastqc -h
FastQC - A high throughput sequence QC analysis tool
SYNOPSIS
fastqc seqfile1 seqfile2 .. seqfileN
fastqc [-o output dir] [--(no)extract] [-f fastq|bam|sam]
[-c contaminant file] seqfile1 .. seqfileN
DESCRIPTION
FastQC reads a set of sequence files and produces from each one a quality
control report consisting of a number of different modules, each one of
which will help to identify a different potential type of problem in your
data.
If no files to process are specified on the command line then the program
will start as an interactive graphical application. If files are provided
on the command line then the program will run with no user interaction
required. In this mode it is suitable for inclusion into a standardised
analysis pipeline.
The options for the program as as follows:
-h --help Print this help file and exit
-v --version Print the version of the program and exit
-o --outdir Create all output files in the specified output directory.
Please note that this directory must exist as the program
will not create it. If this option is not set then the
output file for each sequence file is created in the same
directory as the sequence file which was processed.
--casava Files come from raw casava output. Files in the same sample
group (differing only by the group number) will be analysed
as a set rather than individually. Sequences with the filter
flag set in the header will be excluded from the analysis.
Files must have the same names given to them by casava
(including being gzipped and ending with .gz) otherwise they
won't be grouped together correctly.
--nano Files come from nanopore sequences and are in fast5 format. In
this mode you can pass in directories to process and the program
will take in all fast5 files within those directories and produce
a single output file from the sequences found in all files.
--nofilter If running with --casava then don't remove read flagged by
casava as poor quality when performing the QC analysis.
--extract If set then the zipped output file will be uncompressed in
the same directory after it has been created. By default
this option will be set if fastqc is run in non-interactive
mode.
-j --java Provides the full path to the java binary you want to use to
launch fastqc. If not supplied then java is assumed to be in
your path.
--noextract Do not uncompress the output file after creating it. You
should set this option if you do not wish to uncompress
the output when running in non-interactive mode.
--nogroup Disable grouping of bases for reads >50bp. All reports will
show data for every base in the read. WARNING: Using this
option will cause fastqc to crash and burn if you use it on
really long reads, and your plots may end up a ridiculous size.
You have been warned!
--min_length Sets an artificial lower limit on the length of the sequence
to be shown in the report. As long as you set this to a value
greater or equal to your longest read length then this will be
the sequence length used to create your read groups. This can
be useful for making directly comaparable statistics from
datasets with somewhat variable read lengths.
-f --format Bypasses the normal sequence file format detection and
forces the program to use the specified format. Valid
formats are bam,sam,bam_mapped,sam_mapped and fastq
-t --threads Specifies the number of files which can be processed
simultaneously. Each thread will be allocated 250MB of
memory so you shouldn't run more threads than your
available memory will cope with, and not more than
6 threads on a 32 bit machine
-c Specifies a non-default file which contains the list of
--contaminants contaminants to screen overrepresented sequences against.
The file must contain sets of named contaminants in the
form name[tab]sequence. Lines prefixed with a hash will
be ignored.
-a Specifies a non-default file which contains the list of
--adapters adapter sequences which will be explicity searched against
the library. The file must contain sets of named adapters
in the form name[tab]sequence. Lines prefixed with a hash
will be ignored.
-l Specifies a non-default file which contains a set of criteria
--limits which will be used to determine the warn/error limits for the
various modules. This file can also be used to selectively
remove some modules from the output all together. The format
needs to mirror the default limits.txt file found in the
Configuration folder.
-k --kmers Specifies the length of Kmer to look for in the Kmer content
module. Specified Kmer length must be between 2 and 10. Default
length is 7 if not specified.
-q --quiet Supress all progress messages on stdout and only report errors.
-d --dir Selects a directory to be used for temporary files written when
generating report images. Defaults to system temp directory if
not specified.
BUGS
Any bugs in fastqc should be reported either to simon.andrews@babraham.ac.uk
or in www.bioinformatics.babraham.ac.uk/bugzilla/
In [12]:
# Version longue
fastqc --help
FastQC - A high throughput sequence QC analysis tool
SYNOPSIS
fastqc seqfile1 seqfile2 .. seqfileN
fastqc [-o output dir] [--(no)extract] [-f fastq|bam|sam]
[-c contaminant file] seqfile1 .. seqfileN
DESCRIPTION
FastQC reads a set of sequence files and produces from each one a quality
control report consisting of a number of different modules, each one of
which will help to identify a different potential type of problem in your
data.
If no files to process are specified on the command line then the program
will start as an interactive graphical application. If files are provided
on the command line then the program will run with no user interaction
required. In this mode it is suitable for inclusion into a standardised
analysis pipeline.
The options for the program as as follows:
-h --help Print this help file and exit
-v --version Print the version of the program and exit
-o --outdir Create all output files in the specified output directory.
Please note that this directory must exist as the program
will not create it. If this option is not set then the
output file for each sequence file is created in the same
directory as the sequence file which was processed.
--casava Files come from raw casava output. Files in the same sample
group (differing only by the group number) will be analysed
as a set rather than individually. Sequences with the filter
flag set in the header will be excluded from the analysis.
Files must have the same names given to them by casava
(including being gzipped and ending with .gz) otherwise they
won't be grouped together correctly.
--nano Files come from nanopore sequences and are in fast5 format. In
this mode you can pass in directories to process and the program
will take in all fast5 files within those directories and produce
a single output file from the sequences found in all files.
--nofilter If running with --casava then don't remove read flagged by
casava as poor quality when performing the QC analysis.
--extract If set then the zipped output file will be uncompressed in
the same directory after it has been created. By default
this option will be set if fastqc is run in non-interactive
mode.
-j --java Provides the full path to the java binary you want to use to
launch fastqc. If not supplied then java is assumed to be in
your path.
--noextract Do not uncompress the output file after creating it. You
should set this option if you do not wish to uncompress
the output when running in non-interactive mode.
--nogroup Disable grouping of bases for reads >50bp. All reports will
show data for every base in the read. WARNING: Using this
option will cause fastqc to crash and burn if you use it on
really long reads, and your plots may end up a ridiculous size.
You have been warned!
--min_length Sets an artificial lower limit on the length of the sequence
to be shown in the report. As long as you set this to a value
greater or equal to your longest read length then this will be
the sequence length used to create your read groups. This can
be useful for making directly comaparable statistics from
datasets with somewhat variable read lengths.
-f --format Bypasses the normal sequence file format detection and
forces the program to use the specified format. Valid
formats are bam,sam,bam_mapped,sam_mapped and fastq
-t --threads Specifies the number of files which can be processed
simultaneously. Each thread will be allocated 250MB of
memory so you shouldn't run more threads than your
available memory will cope with, and not more than
6 threads on a 32 bit machine
-c Specifies a non-default file which contains the list of
--contaminants contaminants to screen overrepresented sequences against.
The file must contain sets of named contaminants in the
form name[tab]sequence. Lines prefixed with a hash will
be ignored.
-a Specifies a non-default file which contains the list of
--adapters adapter sequences which will be explicity searched against
the library. The file must contain sets of named adapters
in the form name[tab]sequence. Lines prefixed with a hash
will be ignored.
-l Specifies a non-default file which contains a set of criteria
--limits which will be used to determine the warn/error limits for the
various modules. This file can also be used to selectively
remove some modules from the output all together. The format
needs to mirror the default limits.txt file found in the
Configuration folder.
-k --kmers Specifies the length of Kmer to look for in the Kmer content
module. Specified Kmer length must be between 2 and 10. Default
length is 7 if not specified.
-q --quiet Supress all progress messages on stdout and only report errors.
-d --dir Selects a directory to be used for temporary files written when
generating report images. Defaults to system temp directory if
not specified.
BUGS
Any bugs in fastqc should be reported either to simon.andrews@babraham.ac.uk
or in www.bioinformatics.babraham.ac.uk/bugzilla/
Quand rien n'va plus¶
Cette solution peut paraître simpliste et évidente mais elle est trop souvent oubliée !
Voici votre meilleur allié : https://www.google.fr/
Une semaine de formation ne peut vous enseigner toutes les commandes et méthodes de la bioinformatique. Mais en comprendre la logique et acquérir les bases pour reformuler une question biologique en version informatique seront essentiels.
Quand vos tuteurs ne seront plus là, voici également quelques exemples de cheat sheet listant les commandes les plus courantes du bash.