Modules and scripts of general use for the Computational Genomics Lab
To install this module, run the following commands:
perl Makefile.pl
make
make test
make install
This package depends on the following Perl modules, make sure they are installed on your system:
perl -MCPAN -e'install Term::ANSIColor Inline Inline::C Inline::Files Inline::Filters'
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Global.pm
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Largeseqs.pm
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Unalias.pm
Using a gene list to filter records from another file in FASTA or tabular format.
Usage
PROGRAM: grepID - version 1.0
USAGE:
grepID [options] ids.file genes.file > filtered_genes.file
DESCRIPTION:
Using a gene list to filter records from another files, including
files in fasta format or tabular (via CGL::Largeseqs.pm). Now also
featuring record extraction from quality files in fasta format.
COMMAND-LINE OPTIONS:
-c, --column <col_num[, ..., [colnum]]>
-I, --column-FILTER <col_num[, ..., [colnum]]>
-D, --column-DATA <col_num[, ..., [colnum]]>
First <col_num> it is assumed to be a sequence ID.
-S, --slurp-mode
Read all fields from each ids.file lines and set
as gene IDs.
-X, --expand-filenames
Take a pattern such as "file[N].ext:range" and
produce a set of files in which "[N]" has been replaced
by all the elements of the range.
-N, --negate-filter
Select those sequences/records that are not in the
ids.file (so that, the program returns the complement matches).
-j, --join
-J, --full-join
-p, --add-prefix
-s, --add-suffix
-a, --forcebase
-f, --forcebase-FILTER
-d, --forcebase-DATA
"forcebase" defines unique IDs, input IDs in the form
"ID_00000.00.xxx" are converted to "ID_00000".
By default, trimming on the last suffix after a dot,
so a generic ID is produced, from "ID_00000.00.xxx"
we got "ID_00000.00".
-A, --as-is-ids
Leave IDs "as is", do not change the IDs,
"ID_00000.00.xxx" is kept as "ID_00000.00.xxx".
-F, --fasta-file
-T, --tabular-file
-Q, --quality-file
The following command-line options are set by default
when using "CGL::Global.pm":
-h, --help Shows this help.
--version Shows version for current script.
-v, --verbose Execution messages are sent to STDERR.
-V, --color-verbose Messages are text-coloured to highlight
different kinds of messages.
--debug All execution messages are sent to STDERR,
including dumps of the internal data structures.
Converting a sequence input stream in FASTA format to tabular.
Usage
PROGRAM: fa2tbl - version 1.0
USAGE:
fa2tbl [ options ] < prot_seq.fasta > prot_seq.tbl
DESCRIPTION:
Converting a sequence input stream in fasta format to tabular.
It is quite fast as it uses C functions from CGL::Largeseqs.pm (via
Inline perl module).
COMMAND-LINE OPTIONS:
-Z, --gzip-output
Compress output on the fly and send to stdout.
-T, --use-tabs
Using tab char instead of whitespace to separate output fields.
The following command-line options are set by default
when using "CGL::Global.pm":
-h, --help Shows this help.
--version Shows version for current script.
-v, --verbose Execution messages are sent to STDERR.
-V, --color-verbose Messages are text-coloured to highlight
different kinds of messages.
--debug All execution messages are sent to STDERR,
including dumps of the internal data structures.
Converting a sequence input stream in tabular format to FASTA.
Usage
PROGRAM: tbl2fa - version 1.0
USAGE:
tbl2fa [ options ] < prot_seq.tbl > prot_seq.fasta
DESCRIPTION:
Converting a sequence input stream in tabular format to fasta.
It is quite fast as it uses C functions from CGL::Largeseqs.pm (via
Inline perl module).
COMMAND-LINE OPTIONS:
-Z, --gzip-output
Compress output on the fly and send to stdout.
The following command-line options are set by default
when using "CGL::Global.pm":
-h, --help Shows this help.
--version Shows version for current script.
-v, --verbose Execution messages are sent to STDERR.
-V, --color-verbose Messages are text-coloured to highlight
different kinds of messages.
--debug All execution messages are sent to STDERR,
including dumps of the internal data structures.
Calculates the overall coverage for all queries and targets from BLAST output, accounting for overlaps among HSPs within each single query and target sequence.
Usage
PROGRAM: coverage_blastshorttbl
DESCRIPTION
Computes different coverage statistics for each Query and each Target of a
BLAST run.
USAGE
coverageblasttbl [options] blast.output6.tbl > coverage.tbl
OPTIONS
-prog [ BLASTN | BLASTP | BLASTX | TBLASTX | TBLASTN ]
-Qaa
-Taa
-debug
Input requirements
Run BLAST with the following option:
-outfmt '6 qseqid qlen sseqid slen qstart qend sstart send length score
evalue bitscore pident nident mismatch positive gapopen gaps ppos qframe
sframe qseq sseq'
Output table
1. Query(Q)/Target(T)
2. Query/Target Id
3. Query/Target length
4. Total Forward(+) alignment length
5. Total Forward(+) alignment coverage
6. Total Reverse(-) alignment length
7. Total Reverse(-) alignment coverage
8. Total NoStrand(.) alignment length
9. Total NoStrand(.) alignment coverage
10. Total All(+,-,.) alignment length
11. Total All(+,-,.) alignment coverage
12. BestHit alignment length
13. BestHit alignment coverage
14. BestHit information (id, length, score, e-value)
Translating cDNA sequences into open reading frames
Usage
PROGRAM: cdna2orfs - version 1.0
USAGE:
cdna2orfs [ options ] < prot_seq.tbl > prot_seq.fasta
DESCRIPTION:
Translating an input stream of cDNA sequences in fasta format to
all the possible open reading frames, output is also in fasta format.
The program assumes the sequence to be in forward strand.
It is quite fast as it uses C functions from largeseqs.pm (via
Inline perl module).
COMMAND-LINE OPTIONS:
-N, --do-not-translate
Return de ORF sequences at nucleotide level instead of the
translated ORFs, which is the default option.
-B, --both-strands
Check forward and reverse, by default only looking at forward.
Useful when not sure if proper orientation was given for
the RNA/cDNA sequence.
-l, --largest-only
-m, --min-length <integer>
By default all the possible open reading frames are calculated.
When 'l' switch is provided, then returns only the largest of all
the ORFs obtained when the input sequence is translated
in all three phases from the initial nucleotide.
The 'm' switch allows to define a length cut-off, where <integer>
refers to the minimum amino acid length that an ORF should have to
be outputed.
If both options are provided, 'l' and 'm', for each cDNA sequence,
the largest ORF is printed out only when it is larger than
the length cutoff.
-u, --unique-orf
If more than one ORF has the same length, the one with the
smaller phase is printed when filtering by length.
-d, --full-orf-desc
Append the location, strand and phase information to the
sequence description.
-Z, --gzip-output
Compress output on the fly and send to stdout.
The following command-line options are set by default
when using "CGL::Global.pm":
-h, --help Shows this help.
--version Shows version for current script.
-v, --verbose Execution messages are sent to STDERR.
-V, --color-verbose Messages are text-coloured to highlight
different kinds of messages.
--debug All execution messages are sent to STDERR,
including dumps of the internal data structures.
Converting a sequence input stream in tabular format to shuffled tabular.
Usage
PROGRAM: tblshuffle - version 1.0
USAGE:
tblshuffle [ options ] < prot_seq.tbl > prot_seq_shuffled.tbl
DESCRIPTION:
Converting a sequence input stream in tabular format to another
tabular file with all sequences shuffled.
It is quite fast as it uses C functions from largeseqs.pm (via
Inline perl module).
COMMAND-LINE OPTIONS:
-Z, --gzip-output
Compress output on the fly and send to stdout.
The following command-line options are set by default
when using "CGL::Global.pm":
-h, --help Shows this help.
--version Shows version for current script.
-v, --verbose Execution messages are sent to STDERR.
-V, --color-verbose Messages are text-coloured to highlight
different kinds of messages.
--debug All execution messages are sent to STDERR,
including dumps of the internal data structures.
Cleaning fasta sequences from non-standard symbols (like '*'), also providing reverse, complement, and reverse-complement options.
Usage
PROGRAM: fa2fa - version 1.0
USAGE:
fa2fa [ options ] < prot_seq.tbl > prot_seq.fasta
DESCRIPTION:
Fixing fasta files: standard sequence IDs, removing weird chars,
and so on.
It is quite fast as it uses C functions from largeseqs.pm (via
Inline perl module).
COMMAND-LINE OPTIONS:
-R, --reverse-seq
Returns the reverse sequence of each input sequence.
-C, --complement-seq
Returns the complement sequence for each input sequence.
-RC, --reverse-complement
Returning the reverse-complement for all the input seqs.
-Z, --gzip-output
Compress output on the fly and send to stdout.
-p, --fix-id-prefix <regexp>
-s, --fix-id-suffix <regexp>
Fixing IDs by removing a prefix or a suffix from the ID string.
<regexp> sets a regular expression which defines what has to be
removed from input sequence IDs.
The following command-line options are set by default
when using "CGL::Global.pm":
-h, --help Shows this help.
--version Shows version for current script.
-v, --verbose Execution messages are sent to STDERR.
-V, --color-verbose Messages are text-coloured to highlight
different kinds of messages.
--debug All execution messages are sent to STDERR,
including dumps of the internal data structures.
From a sequence file in fasta format, compute N50 assembly statistics for different sequence length ranges.
Usage
PROGRAM: N50stats - version 1.0
USAGE:
N50stats [options] seqsfile.fasta
DESCRIPTION:
From a sequence file in fasta format, compute N50 assembly statistics
for different sequence length ranges. This script extends previous
count_fasta program developed by Joseph Fass at the Bioinformatics
Core at UC Davis Genome Center, modified from a script by Brad Sickler.
The point is to get further info from sequences length distribution,
as well as segmenting the N50 calculation by fixed length ranges,
ressembling the output produced by SOAPdenovo on the ScaffStats file.
When several fasta files are provided this program will calculate
all the assembly statistics as if they were coming from a single file.
This can be useful when the assembler produces separate files
for scaffolds, contigs, singletons and/or other, and we do not want
to keep another copy of the sequences in a merged file.
COMMAND-LINE OPTIONS:
-G, --genome-length <int>
Estimated genome size, which is used to calculate NG50. It is
similar to N50 but corrected by expected genome size. It accepts
SI units: 'k' for kilo bases, 'M' for mega bases, and 'G' for
giga bases; for instance "10k" instead of "10000". Just notice
there is no space allowed between the number and the unit symbol.
-B, --bin-size <int>
Bin size for the lengths histogram printed to STDERR when
computing the N50 stats. By default it uses 1000bp, but any
positive integer value can be provided. If bin size is set
to zero, the histogram is not calculated then. It also accepts
SI units as the previous seitch.
-S, --scaffold-label
-C, --contig-label
First one sets the labels of the different output items to include
"Scaffold", while the second sets it to "Contig". By default, the
label is simply set to "Sequence". In case both are simultaneously
provided, none of those command-line switches will be considered
by the program (setting it back to "Sequence").
-T, --title <string>
If defined, write a header showing this title.
-M, --save-histogram <output_file>
Filename where to save the histogram, otherwise by default
it will be sent to the STDERR channel. If bin size is set
to zero, see corresponding switch info, this file will not
be created either.
-L, --save-length-vectors <vectors_file>
Provide a filename where length vectors will be stored for later
analyses and visualization (using R for instance). Output file
has two columns, one with the factor, the second with a length,
repeated as many times as lengths were defined for the factor.
The program will generate a file having as many rows as two times
the number of input sequences.
Normalize gene/protein names according to the HGNC dictionary, or to any specified symbol dictionary. Can also be used for any other symbol mappings by using option
-d. seeman gunaliasorman CGL::Unalias.
Usage
Usage:
gunalias [-h] [-i INPUT] [-o OUTPUT] [-c COLUMN [-c COLUMN] ...] [-s SEPARATOR] [-d DICTIONARY]
Options:
-h, -help
Shows this help.
-v, -verbose
Change verbosity.
-i, -input FILE
Input file to normalize gene names from. If not specified, will
use STDIN.
-o, -output FILE
Output file to write normalized table. If not specified, will
write to STDOUT.
-c, -columns INTEGER
Columns in input or STDIN where the gene names are so that
gunalias can normalize them. Should be bigger than 1. Default is
1. Normalize multiple columns by specifying the option multiple
times, e.g.: `gunalias -c 1 -c 2`
-s, -separator STRING
Separator character (or Perl-compatible regular expression) that
defines columns in input or STDIN. By default "\t".
-d, -dictionary FILE
Dictionary file for CGL::Unalias to use. If not specified,
gunalias will use the default HGNC dictionary of the
CGL::Unalias module.
Changing name of sequence identifiers in fasta file
fa2tbl fasta.fa | gunalias -c 1 -d ids.txt | tbl2fa > fasta.newids.fa
Copyright (C) 2018 Computational Genomics Lab @ UB with contributions from J.F. Abril, S. Castillo-Lara, R. Arenas-Galnares
This program is free software; you can redistribute it and/or modify it under the terms of the the Artistic License (2.0). You may obtain a copy of the full license at:
http://www.perlfoundation.org/artistic_license_2_0
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