Liston:Computer Scripts

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Python Script Conventions


   python [modifiers] <Arguments>. 









would cause a help menu to be printed to the screen.

Python Scripts

Script NameDiscriptionInput File FormatOutput File Format v2.0 A pipeline for combining the free aligner NUCmer and the free short read assembler YASRA so full alignments can be made with one command. Alignreads uses the following scripts from the Liston lab:,, and It must be possible for the python interpreter to find these scripts to run alignreads; this can be done saving copies of scripts in the Python26 folder, your bin folder, or modifying you .chsrc file to search where they are saved on your system. alignreads preserves almost all of the functionality and output of the 5 programs it uses, so there are many options (over 40). Because there are so many modifiers, the help menu reached by not providing arguments only has what are expected to be the options used most often; to get all of the options type 'python -H' or 'python --advanced-help'. Since there are many files associated with the alignment the output is a folder with numerous files organized into subfolders. can also start the pipeline from a folder produced by a previous run of or In that case, the output is saved in the input folder. A FASTA file containing reads, and A FASTA file containg a reference OR a folder from a previous run of alingreades or runyasra. A folder containing all of the ouput from every part of the pipeline organized in subfolders based on each programs' output. v1.2 Finds all possible combinations of elements (or group of elements) for every line of a tab-delimitated text file and output every combination, on its own line, to a .txt file. tab-delimitated .txt file tab-delimitated .txt file v1.0 Converts a file containing a list of annotations, as well as each of their respective start and stop indices, into a file containing a list of base indices, each followed by any annotations that apply at that specific base. Each line of the input file is expected to be whitespace-deliminated, however if your annotations have spaces in them, the script can be made to enforce tab-delimitation. The output file is always tab-delaminated. [Annotation text] [Start Index] [End Index] [Base Index] [Annotation1] [Annotation2] ... [AnnotationX] v1.2 Finds base differences between multiple aligned sequences in a single FASTA file and output a tab-deliminated txt file containing the base values for all the sequences at the index where the difference occurred. The script has many modifiers that change what is considered a difference. FASTA file containing two or more aligned sequences .txt file in the following format: [Base index] [Seq 1 value] [Seq 2 value] ... [Seq N value] v1.2 Performs and outputs various statistical tests for each contig in a GSS basepile output. it is assumed that the information for each contig is 1000 bases long. The following statistics are outputted in a tab-delimitated list for each contig by the script:
GSS Basepile output. 1000 bases per contig tab-deliminated list of the statistics for each contig v1.0 Creates a MUMmer-style output from a FASTA file of aligned sequences. The first line is always considered the reference and is not included in the output. The start index in terms of the reference, and in terms of the contig, as well as the length are recorded for each matching section of the contig. FASTA file containing a reference and its aligned contigs MUMmuer-like output v1.0 Removes all of the gaps (i.e. '-') that are common (i.e. at the same index) to all of the sequences in an aligned FASTA file. By default, the first sequence is considered the reference and is excluded from the analysis, but the number of sequences that are treated as such can be changed. FASTA file containing two or more aligned sequences. FASTA file same number of sequences as the input file but, with gaps removed v1.0 Runs the free short read aligner YASRA and orgainzes its output into a folder. A FASTA file containing reads, and a FASTA file containg a reference OR a folder from a previous run of alingreades or runyasra. A folder containing all of YASRA's output as well as links to the input data. v1.7 A script used in conjunction with the free aligners NUCmer and the free short read assembler YASRA. Creates a file with a similar to the format to that of the .qual file YASRA outputs, except each base can have multiple sets of quality values. Uses a .qual file containing the quality scores of multiple contigs and the output file of NUCmer to make a "consensus" .qual file, which contains the quality values in terms of the reference. Given the reference used with NUCmer to get the alignment, sumqual can output a fasta file containing all the sequence for which there is no quality data.
  • FASTA file containing the sequence of multiple contigs
  • NUCmer output file
  • Reference file used with Nucmer
similar to .qual input file, except each base can hold the information from more than one contig v2.3 Selectively extracts the sequence from a quality file and outputs it to a FASTA file. It is designed to be used in conjunction with and accepts its consensus-style output. Conflicting bases from a consensus-style output are condensed into IUPAC ambiguity codes or gaps are added to the reference to accomodate repeated or unmatched sequence. It has an option to mask all bases with a quality value of less than a user-specified threshold. Another threshold can be assigned for SNPs if a reference is given. quality file (.qual); accepts's output FASTA file
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