SpliceFamAlignMulti

Program Version 2020

computes multiple spliced alignment of all CDS and genes of a gene family, computes CDS orthology groups, and predicts new CDS by homology

Authors: Safa Jammali, Abigail Djossou et al. Université de Sherbrooke, Canada Cobius Lab: https://cobius.usherbrooke.ca/ for questions email us at Safa.Jammali@USherbrooke.ca

Requirements:

-Python2.7 -Python3 -argparse -glob -numpy -multiprocessing -functools -Bio -Ete3 -scipy -skbio -Muscle standalone -Blast+ standalone -Mafft standalone -TCoffee standalone -Splign standalone

Usage to compute the spliced alignments for the examples contained in directory examples/input

Command line for simulated gene families contained in examples/input/simulated/

./launchSimulated.sh

Results are written in directory examples/output/simulated.

Command line for real gene families contained in examples/input/real/97/

./launchReal.sh

Results are written in directory examples/output/real/97.

Usage to compute pairwise spliced alignments for any gene family

usage: src/main.py [-h] [-c CHOICESTRUCTURE] [-pm PAIRWISEMETHOD] [-s STEP]
               [-ce COMPAREEXON] [-sf SOURCEFILE] [-tf TARGETFILE]
               [-s2tf SOURCE2TARGETFILE] [-sef SOURCEEXONFILE]
               [-op OUTPUTPREFIX] [-of OUTPUTFORMAT] [-oa OUTPUTALIGNMENT]

-h, --help show help message and exit

-c CHOICESTRUCTURE, --choiceStructure CHOICESTRUCTURE Method used to infer splicing structure when a splicing structure file is not given: blast or splign

-pm PAIRWISEMETHOD, --pairwiseMethod PAIRWISEMETHOD Method used to compute pairwise spliced alignment: sfa or splign

-s STEP, --step STEP The method goes until Step 1, 2, or 3: 1, 2 or 3 (required)

-ce COMPAREEXON, --compareExon COMPAREEXON The method includes in Step2 a comparison of exons: Yes or No (required)

-sf SOURCEFILE, --sourceFile SOURCEFILE Source (CDS) file name (required)

-tf TARGETFILE, --targetFile TARGETFILE Target (gene) file name (required)

-s2tf SOURCE2TARGETFILE, --source2TargetFile SOURCE2TARGETFILE Association between source and target file name (required)

-sef SOURCEEXONFILE, --sourceExonFile SOURCEEXONFILE Source Exon (splicing structure) file name

-op OUTPUTPREFIX, --outputPrefix OUTPUTPREFIX Output prefix (required)

-of OUTPUTFORMAT, --outputFormat OUTPUTFORMAT Output format : list or aln (required)

-oa OUTPUTALIGNMENT, --outputAlignment OUTPUTALIGNMENT Output alignment : method used to compute pairwise block alignment: nm or fsepsa

Computing pairwise alignments:

Command line

python2.7 src/main.py -ce Yes -s 2  -sf path_to_cds_fasta_file -tf path_to_gene_fasta_file -s2tf path_to_mapping_cds_gene_file  -sef path_to_cds_exon_structure_file  -op output_path_prefix -of list

Example of command line

python3 src/main.py -ce Yes -s 2  -sf examples/input/simulated/small/_iteration_1_initialsource.fasta -tf examples/input/simulated/small/_iteration_1_target.fasta -s2tf examples/input/simulated/small/_iteration_1_initialsource2target.txt -sef examples/input/simulated/small/_iteration_1_initialsourceexonlist.txt -op examples/output/simulated/small/_iteration_1_ -of list

Results are written in directory examples/output/simulated/small with prefix _iteration_1_.

Usage to compute multiple spliced alignments using SFAM_tcoffee for any gene family

usage: src_tcoffee/main.py [-h] [-idty IDENTITYTHRESHOLD] [-sf SOURCEFILE]
               [-tf TARGETFILE] [-s2tf SOURCE2TARGETFILE]
               [-sef SOURCEEXONFILE] [-palnf PAIRWISEALNFILE]
               [-psegf PAIRWISESEGMENTFILE] [-ba BLOCKALIGNMENT]
               [-op OUTPUTPREFIX] [-oa OUTPUTALIGNMENT] [-ce COMPAREEXON]
               [-msa MSAMETHOD]

-h, --help show help message and exit

-idty IDENTITYTHRESHOLD, --identityThreshold IDENTITYTHRESHOLD Identity threshold: real between 0.0 and 1.0 (default = 0.3)

-sf SOURCEFILE, --sourceFile SOURCEFILE Source file name (required)

-tf TARGETFILE, --targetFile TARGETFILE Target file name (required)

-s2tf SOURCE2TARGETFILE, --source2TargetFile SOURCE2TARGETFILE Source to target file name (required)

-sef SOURCEEXONFILE, --sourceExonFile SOURCEEXONFILE Source exon file name

-palnf PAIRWISEALNFILE, --pairwiseAlnFile PAIRWISEALNFILE Pairwise alignment file name (required)

-psegf PAIRWISESEGMENTFILE, --pairwiseSegmentFile PAIRWISESEGMENTFILE Pairwise segment file name (required)

-ba BLOCKALIGNMENT, --blockAlignment BLOCKALIGNMENT Method for block alignment

-op OUTPUTPREFIX, --outputPrefix OUTPUTPREFIX Output prefix (required)

-oa OUTPUTALIGNMENT, --outputAlignment OUTPUTALIGNMENT Method for final alignment

-ce COMPAREEXON, --compareExon COMPAREEXON The method includes a final step that compares exons of blocks for further merges: Yes or No

-msa MSAMETHOD, --msaMethod MSAMETHOD Multiple sequence aligner: muscle or mafft

Computing multiple alignment using SFAM_tcoffee_p:

Command line

python3 src_tcoffee/main.py -sf path_to_cds_fasta_file -tf path_to_gene_fasta_file -s2tf path_to_mapping_cds_gene_file  -sef path_to_cds_exon_structure_file -palnf output_path_prefix_result.txt -psegf output_path_prefix_segment.txt -op output_path_prefix -of list

Example of command line

python3 src_tcoffee/main.py -sf examples/input/simulated/small/_iteration_1_initialsource.fasta -tf examples/input/simulated/small/_iteration_1_target.fasta -s2tf examples/input/simulated/small/_iteration_1_initialsource2target.txt -sef examples/input/simulated/small/_iteration_1_initialsourceexonlist.txt -palnf examples/output/simulated/small/_iteration_1_result.txt -psegf examples/output/simulated/small/_iteration_1_segment.txt -op examples/output/simulated/small/_iteration_1_tcoffee_p_ -of list

Results are written in directory examples/output/simulated/small with prefix _iteration_1_tcoffee_p_.

Computing multiple alignment using SFAM_tcoffee_m:

Command line

python3 src_tcoffee/main.py -sf path_to_cds_fasta_file -tf path_to_gene_fasta_file -s2tf path_to_mapping_cds_gene_file  -sef path_to_cds_exon_structure_file -palnf output_path_prefix_result.txt -op output_path_prefix -of list

Example of command line

python3 src_tcoffee/main.py -sf examples/input/simulated/small/_iteration_1_initialsource.fasta -tf examples/input/simulated/small/_iteration_1_target.fasta -s2tf examples/input/simulated/small/_iteration_1_initialsource2target.txt -sef examples/input/simulated/small/_iteration_1_initialsourceexonlist.txt -palnf examples/output/simulated/small/_iteration_1_result.txt -op examples/output/simulated/small/_iteration_1_tcoffee_m_ -of list

Results are written in directory examples/output/simulated/small with prefix _iteration_1_tcoffee_m_.

Usage to compute multiple spliced alignments using SFAM_mblock for any gene family

usage: src_mblock/main.py [-h] [-idty IDENTITYTHRESHOLD]
               [-sf SOURCEFILE] [-tf TARGETFILE] [-s2tf SOURCE2TARGETFILE]
               [-sef SOURCEEXONFILE] [-palnf PAIRWISEALNFILE]
               [-op OUTPUTPREFIX] [-ce COMPAREEXON] [-msa MSAMETHOD]