Commands

clean_multi_ssake.sh

Run to remove intermediate files generated by multi_ssake.py from the current directory.

WARNING: Removes all files matching *.fasta and *paired.fa from the current directory!

compare_genomes.py

Finds differences between genomes based on the input multi-aligned fasta file

python: can't open file 'compare_genomes_test.py': [Errno 2] No such file or directory

fastq_to_fasta.py

Converts fastq files to fasta files

Traceback (most recent call last):
  File "fastq_to_fasta.py", line 12, in <module>
    from Bio.SeqIO.QualityIO import FastqGeneralIterator
ImportError: No module named Bio.SeqIO.QualityIO

find_contig_deletions.py

Find contigs in an assembly that have sections deleted and provide an option to insert the missing pieces

Traceback (most recent call last):
  File "fastq_to_fasta.py", line 12, in <module>
    from Bio.SeqIO.QualityIO import FastqGeneralIterator
ImportError: No module named Bio.SeqIO.QualityIO

gff2gtf_simple.py

Attempts to convert GFF files to GTF files.

Traceback (most recent call last):
  File "gff2gtf_simple.py", line 17, in <module>
    import pybedtools
ImportError: No module named pybedtools

maf_net.py

Stitch together alignment block from a MAF file, forming an alignment net.

Traceback (most recent call last):
  File "maf_net.py", line 5, in <module>
    import Bio.AlignIO
ImportError: No module named Bio.AlignIO

makePairedOutput2EQUALfiles_vamp.pl

See makePairedOutput2UNEQUALfiles_vamp.pl:

Usage: makePairedOutput2EQUALfiles_vamp.pl <fasta file 1> <fasta file 2> <library insert size>
       --- ** Both files must have the same number of records & arranged in the same order

makePairedOutput2UNEQUALfiles_vamp.pl

Modified versions of scripts provided by SSAKE. They are used to prepare two separate paired end fastq files for use by SSAKE. The modifications made were to accommodate new Illumina style sequence identifiers introduced with CASAVA 1.8.:

Usage: makePairedOutput2UNEQUALfiles_vamp.pl <fasta file 1> <fasta file 2> <library insert size>
       --- files could have different # of records & arranged in different order but template ids must match

multi_ssake.py

Run TQSFastq preprocessing and SSAKE using various combinations of parameters and combine the results.

Traceback (most recent call last):
  File "multi_ssake.py", line 11, in <module>
    import vamp.utils
ImportError: No module named vamp.utils

translate_cds.py

Takes GFF and Fasta input and translates spliced CDS regions from DNA to Amino Acid sequence, reporting errors.

Traceback (most recent call last):
  File "translate_cds.py", line 14, in <module>
    from Bio import SeqIO
ImportError: No module named Bio